Index

A Aequorea victoria 182, 192 post-column aerosols, danger of contamination 770 derivatization 303–305 Abbe, Ernst 181, 187, 485, 493 affinity capillary electrophoresis pre-column absolute molecule mass 4 (ACE) 285–286 derivatization 305–308 absolute quantification (AQUA) of binding constant, determined by 285 reagents used for 310 modified peptides 660 changing mobility 286 sample preparation 302 absorption complexation of monovalent acidic hydrolysis 302 bands, of most biological molecules 139 protein–ligand complexes 285 alkaline hydrolysis 303 measurement 140–142 affinity chromatography 91, 268, 650 enzymatic hydrolysis 303 of photon 135 affinity purification mass spectrometry using mass spectrometry 309 spectroscopy 131 (AP-MS) 381, 1003 L-α-amino acid residues/termini 225 acetic acid 228 agarose concentrations amino acid sequence analysis acetonitrile 227 DNA fragments, coarse separation milestones in 319 N-acetyl-α-D-glucosamine of 692 problems 322 (αGlcNAc) 579 migration distance and fragment amino acids 323–324 acetylated proteins length 692 background 324 detection of 651 agarose gels, advantages of 260 initial yield 324 separation and enrichment 649 agglutination 72 modified amino acids 324 acetylation 224, 645–647 aggregation number 288 purity of chemicals 324 sites, in proteins 656 AK2-antibodies 102 sample to be sequenced 322–323 identification of 655 alanine 562 sensitivity of HPLC system 325 N-acetyl-β-D-glucosamine alanine-scanning method 870 state of the art 325 (βGlcNAc) 579 albumin 3, 995 6-aminoquinoyl-N-hydroxysuccinimidyl N-acetylgalactosamine 129 alcohol dehydrogenase (ADH) gene carbamate (ACQ) 307 achromatic objectives 183 promoter 382 ammonium sulfate 10 acid-base properties 5, 234 alkaline phosphatase (AP) 87, 741, 746, Amoeba dubia 785 acidic and basic acrylamide 753 AMPD anion 747 derivatives 261 alkylation 32 amyotrophic lateral sclerosis (ALS) acidic native electrophoresis 257 of cysteine residues 210 1059 acidic peptides 562 allele-specific hybridization probes 774 analogue sensitive kinase alleles (ASKAs) acidification 3 allergies 65 approach 1047, 1048 activation domain (AD) fusion allotype determinations 80 kinases 1050 proteins 385 all-trans conformation 48 analogue-sensitive kinases, inhibitors and activation energy 37, 38 amidation 110 cofactors 1049 acylation 109, 110 amino acid analysis 118, 207, 301, 313 analytical method, development adeno-associated viruses 913 biophysical properties of 887 of 234–235 adenosine triphosphate (ATP) binding identification of 316–317 analysis of fractionations 238 pocket 1050 liquid chromatography with optical column efficiency, optimization site 1048 detection systems 303 of 235

Bioanalytics: Analytical Methods and Concepts in Biochemistry and Molecular Biology, First Edition. Edited by Friedrich Lottspeich and Joachim Engels.  2018 Wiley-VCH Verlag GmbH & Co. KGaA. Published 2018 by Wiley-VCH Verlag GmbH & Co. KGaA. 1086 Index analytical method, development aptamers 869, 971 benzophenone of (continued ) high-affinity RNA/DNA- derivatives 123 fractionation 237–238 oligonucleotides 971–974 photolabels 127 retention factors, optimization selection of 971–973 benzoyl cyanide (BzCN) 865 of 235–236 Selex procedure 869 p-benzoyl-L-phenylalanine 123 scaling up to preparative uses of 973–974 bicinchoninic acid assay 27–28 chromatography 236–237 aqueous DNA solutions bifunctional reagents 121, 122 selectivity, optimization of 235 phenolic extraction of 666 binding tests 73, 85, 86, 99 analytical ultracentrifugation 409–410 Ardenne, Manfred von 486 binocular tubes 184 basics of centrifugation 411–412 arginine-rich motif (ARM) 859 biochemical pathways photoelectric scanner in 410 aromatic amino acid 225, 561 complex structures, representation principles of instrumentation 410 Arrhenius’ equation 44 of 1024 sedimentation velocity aryl azides 125 oxygen demand 425–426 experiments 412 aryl(trifluoromethyl)diazirines 126 bioinformatics analysis 219 experimental procedures 413–414 asparagine 579 biological functions, alteration of 97–98 N-acetyl-L-glutamate-kinase and signal Aspergillus orizae 862, 863, 896, 899 biologically relevant lipids, classification protein PII, interaction atomic force microscope (AFM) 486, of 614 between 414–415 519 biological starting materials, disruption physical principles 412–413 detection of ligand binding and methods 9 sedimentation–diffusion equilibrium function of 526 bioluminescence resonance energy experiments 415–416 determining protein complex assembly transfer (BRET) 408 anilinothiazolinone (ATZ) amino and function by 524 BioMed Central Bioinformatics 877 acid 316 functional states and interactions of biomimetic recognition elements 419 antibiotic resistance genes 914 individual proteins 526–527 biomimetic sensors 427 antibodies 63, 64, 1034 gap junctions 523 aptamers 428 allotype 65 imaging with 521 molecularly imprinted binding 87 interaction between tip and polymers 427–428 in conjunction with use of natural sample 521–522 biophysical methods 131 Fcγ-effector functions 104 mapping biological biopolymers 131 engineering 99–102, 101 macromolecules 522–524 biosensors 419, 428 Fc-receptor 65 preparation procedures 522 anti-interference principle 424 handling of 68–69 schematic representation of 520 concept of 420–421 microarrays 956 single molecules 524–526 construction/function 421–423 production 98 atomic orbitals (AOs) 134 coupled enzyme reactions in 424 properties of 64–65 attenuated total reflection (ATR) 166 enzymatic analyte cycles 424 IgA 64 automated projection spectroscopy enzyme electrodes IgD 65 (APSY) 463 generation 423–424 IgG 64, 65 autoradiogram 791 sequence/competition 424 IgM 64, 65 autoradiography 652 BIO system as reagents 64 avian myeloblastosis virus (AMV) 761 detection system 746 types of 98–99 avidin–biotin complex formation (ABC labeled nucleotides 742 antibody-directed cellular cytotoxicity system) 87 biotin (ADCC) 104 azido salicylic acid 125 biotinylation, reagents for 128 antigen–antibody-complexes biotinyl groups 129 in vitro, reversible separation of 65 B disadvantage of 746 antigen–antibody reaction 64, 71–72 labeled dNTPs structure 743 antigenic system 74 Bacillus amyloliquefaciens 683 biphasic column reactor, sequencers antigen interaction at combining Bacon, Roger 181 with 321–322 site 67–68 bacterial artificial chromosomes bis(1,10-ortho-phenanthroline)-copper (I) antigens 69–71 (BACs) 788, 934 complex (OP-Cu) 849 antisense oligonucleotides 959, 961, bacterial suspension 672 bispecific antibodies 100 963, 964 Bacto tryptone 671 bis(trimethylsilyl)trifluoroacetamide antisense probe band broadening 222, 223 (BSTFA) 621 in vitro synthesis of 899 barcode array 955 bisulfite methylation analysis 819, 821 ApA-wedge/B-junction models 832 base-catalyzed β-elimination 651 bisulfite PCR aperture diaphragm 183 base pairing, complementarity of 720 enzymes for restriction analysis 822 apochromatic objectives 183 Baumeister, Wolfgang 486 RASSF1A-promoter 822 apolipoprotein B 3 B-cell 99, 100 restriction analysis 820–822, 821 apoptosis 645 Beckman Optima 410 bisulfite-treated DNA 820 Index 1087

amplification and sequencing fluorescence detection 280 centimorgans (cM) 926, 929 of 819–820 mass spectrometry centrifugation 9, 11, 411 biuret assay 26 detection 280–281 basic principles 12 BLOSUM 62, 887 UV-detection 280 density gradient 14 mutation data matrix 888 engine, electroosmotic flow 278–279 CsCl solutions 14 blotting 22. see also electroblotting; historical overview 275–276 sucrose 14 nucleic acid blotting Joule heating 279 fractionation of separated bands 14 capillary blots 706 sample injection 277 rotors for 11 dot blotting unit 707 electrokinetic injection 277 techniques 12 membranes 705 hydrodynamic injection 277 differential 12–13 blue native polyacrylamide gel stacking 277 isopycnic 14 electrophoresis 259 schematic view 276 zonal 13–14 Bolton–Hunter reagent 109 setup 276–277 ceramides 641 bonding energy 37 capillary 276–277 cetyl(trimethyl)ammonium bromide Borries, Bodo von 486 instrumental setup 276 (CTAB) 258, 279, 670 “bottom up” protein analysis 314 voltage unit 276 chain termination method 789, 790 bovine serum albumin (BSA) 24, 54 capillary gel electrophoresis channel electron multiplier (CEM) 356 Bradford assay 28 (CGE) 290–291, 701, 711 chaotropic reagents 7 branched DNA (bDNA) 752 sifting media for 290 charged coupled device (CCD) amplification method 782 capillary isoelectric focusing cameras 144, 497, 544, 1059 Bravais lattices 535 (CIEF) 291–294 sensor 808 brilliant blue 251 focusing with chemical biology 1041 Broglie, Louis de 486 chemical mobilization 292–293 innovative chemical approaches to 5-bromo-4-chloro-indoxyl phosphate (BCIP) pressure/voltage mobilization 292 study biological NBT, coupled optical redox one-step focusing 292 phenomena 1041 reaction 748 capillary zone electrophoresis multidisciplinary approach 1042 5-bromo-UTP (BrU) (CZE) 281–285, 561, 1027 chemical crosslinking, reagents structures of 906 buffer additives 284–285 properties 866 bruton tyrosine kinase (BTK) 1049 capillary coating 284 chemical diversity 224 bufadienolide K-strophanthin 745 electrodispersion 282 chemical genetics 1046 buffer systems 255 ionic strength 283 protein–protein interaction stabilizer substance 43–44 optimization of separation 283 fusicoccin 1046 bump-and-hole method 1047 peak broadening 282 small organic molecules, for protein t-butyldimethylsilyl ether pH-value of buffer 283 function modulation 1042 (TBDMS) 710 temperature 283 ASKA technology 1050–1051 carbene forming reagents 126 bump-and-hole C carbodiimides 125 approach 1047–1050 carbohydrates 572 cyclic process 1042 Caenorhabditis elegans 942, 967, 1015, 5-carboxylcytosine (5caC) 817 forward and reverse 1046–1047 1052 carboxymethylaspartic acid 233 study of 1044–1046 caesium chloride (CsCl) carboxypeptidases 328 switching biological density gradient 703, 721 cleaved amino acids, detection 328 systems 1051–1052 solutions 14 polypeptides, degradation 327 chemical labeling reactions 734 caged compounds 111 specificity of 327 chemical nucleases, structure of 849 + Ca2 imaging 205 carotenoids 638 chemical protein 107 calcium phosphate 913 carrier ampholyte IEF chemical reactions, rate of 36–37 calibration curve 24, 25 advantages/disadvantages 261 chemical shifts 459 calorimetry 47 properties for ideal carrier chemiluminescence 652 Candida albicans 768 ampholyte 261 detection, of hydroperoxy lipids cap analysis of gene expression catalysts 37 621 (CAGE) 868 cationic detergent electrophoresis 258 substrates 745 capillary blots 706 cDNA libraries 385 chimeric antibodies 100 capillary columns 621 cell adhesion 64 chiral MEKC 289 capillary electrochromatography cell arrangements 1039 principle 290 (CEC) 288–289 cell disruption 7 chiral separations 289 capillary electrophoresis (CE) 244, 275, cell isolation 96 chloramphenicol acetyltransferase 281–295, 296, 299, 649, 650, 827 cell sensors 425 (CAT) 911, 914 basic principles 277 cellular immunology 95–97 N-chlorobenzenesulfonamide 33 detection methods 279–281 cellulose esters 16 chlorobutane 316 1088 Index

4-chloro-7-nitrobenz-2-oxa-1, distance between genes 925 complete MOTIFs 885 3-diazole 118 interaction analyses 828–829 complex 3D data sets, analysis of 514 chlorophyll–protein complexes 152 chymotrypsin 24, 207 combination of EM and x-ray cholesterol, lipophilic molecules 969 circular dichroism (CD) 178–180 data 514–515 chromatin epigenetic modifications cyclic peptides 567 flexible fitting 515 analysis 828 15mer peptides with typical α-helical hybrid approach 514 chromatin immunoprecipitation (ChIP) conformation 566 identifying protein complexes in assay 826, 850, 895 spectroscopy 564 cellular tomograms 515–516 chip analysis (ChIP chip) 939 circular polarized light 133 rigid body docking 515 ChIP-on-chip analysis 952 Clark, L.C. 429 segmenting tomograms and chromatin-immuno-precipitation clone-based mapping procedures 936 visualization 515 sequencing (ChipSeq) 813, 828 cloned gene, riboprobe creation 900 complex protein mixtures, quantification chromatin modifications 828 cloning systems 934, 935 of 24 chromatograms 220, 221 positional cloning 938 computer-aided analysis 413 chromatographically incompletely reference system 937 concentration 17 separated components cloud 875 condenser 184 ESI spectra 716 CLUSTAL alignment 892 conditional protein splicing 1054 chromatographic dimension, peak- clustered regulatory interspaced short confocal high-speed-spinning disk picking module 1008 palindromic repeats systems (Nipkow systems) 199 chromatographic material, binding to 17 (CRISPR) 974 confocal laser scanning microscopy chromatographic separation modes 220, CMC. see critical micellar concentration (cLSM), principle 198 224 (CMC) confocal spinning disk microscopy employed in peptide and protein CNBr cleavage 108 (Nipkow) 199 separation and 233 coefficients of variation (CVs) 1003 principle 199 high-performance affinity coherent light 184 trans conformation 48 chromatography (HP-AC) 233 co-immunoprecipitation contour-clamped homogenous electric high-performance aqueous normal (co-IP) 398–399 field (CHEF) method 698, 699 phase chromatography cold-shock proteins (CSPs) 860 contrast transfer function (HP-ANPC) 230 ColE1 multi-copy plasmids, of (CTF) 499–501, 501–503 high-performance hydrophilic enterobacteriaceae family 671 cooling curves 54 interaction chromatography collision energy (CE) 1005 cooling rates 49 (HP-HILIC) 229–230 collision induced dissociation Coomassie Brilliant Blue G250 28 high-performance hydrophobic (CID) 357–358, 999 Coomassie staining 252 interaction chromatography column efficiency 222, 234 spot analysis 985 (HP-HIC) 230–232 combinatorial molecular phenotypes Coons, Albert 182 high-performance ion exchange (CMPs) copper ion 151 chromatography motif 1063 Cotton effect 564 (HP-IEX) 232–233 with proteins 1061 coumarins 119 high-performance normal-phase combined bisulfite restriction analysis coupling liquid chromatography (LC) chromatography (CoBRA) 820 and mass spectrometry (MS), (HP-NPC) 228–229 comparative genomic hybridization advantage 375 high-performance reversed-phase (CGH) 747, 917, 921–924, 951 cover slip 184 chromatography chromosomal 922 CpG adjuvants 709 (HP-RPC) 227–228 exemplary demonstration 923 CpG dimer 948 high-performance size exclusion hybridization and data CpG island 688 chromatography 227 acquisition 923 CpG-methylation 817 for peptides and proteins 225–226 intermixture 921–922 critical micellar concentration chromatographic traces 1007 microarray 920, 922–924 (CMC) 18, 59, 288 chromophores in biological normalization 921 crosslinked protein 129 macromolecules probes 918 crosslinking factor 250, 251 electronic absorption properties competitive inhibitors 40–41 crossover-electrophoresis 78 of 154 competitive (RT) PCR 765, 766 cryo-electron microscopy 496, 497 chromoproteins 148 competitive radioimmunoassay cryo-electrontomography(CET) 486,517 chromosomal in situ suppression (RIA) 82, 83 cryopreservation 69 (CISS) 919 complementarity determining regions crystallization 3 chromosome (CDRs) 101 crystallographic R-factor 543 breakage sites, physical markers 927 complementary DNA (cDNA) 761, 843 crystallographic unit cell conformation capture technique complementary target sequences 758 and crystal packing 534 chromosomal interactions 829 complement fixation 94–95 crystallography 529 Index 1089 crystals, and x-ray diffraction 533–538 DNA sequencing, gel-supported principle 271 C-terminal sequence analysis 325 methods 792 saturation labeling 271 chemical degradation methods 325 proteins 7 different extraction methods 21 degradation of polypeptides with in situ hybridization 919 differential centrifugation 12–13 carboxypeptidases 327 Denny–Jaffe reagent 126 differential equation 36 detection of the cleaved amino deoxynucleotide triphosphates 759 differential interference contrast 186 acids 328 depletion 982 differential RNA-seq (dRNA-seq) 868 specificity of depurination reaction 710 differential scanning calorimeters carboxypeptidases 327 detection methods 189 (DSCs) 47, 48, 54 peptide quantities and quality of chemical staining 189 curve 50–53 chemical degradation 327 direct and indirect immunofluorescence design 49 Schlack–Kumpf labeling 190–191 instrument requirements 48–49 degradation 325–327 fluorescence labeling 189–190 diffraction phenomena and imaging 187 cw-EPR spectroscopy 468–469 for live cell imaging 191 Digitalis lanata 745 cyan fluorescent protein 406 fluorescence microscopy, fluorophores/ Digitalis purpurea 745 cyanoethyl adducts, formation 711 light sources 193–194 digoxigenin cycle sequencing 795 histological staining 189 detection system 745 cyclic peptides 224 incandescent lights 194 digoxigenin:anti-digoxigenin (DIG) cyclodextrins 289 labeling with quantum dots 192 hapten 753 cyclotron-movement 349 lasers 195 system 744 Cy-dyes 986 mercury vapor lamps (HBO structure of 744 cysteines 656 lamps) 195 4-(N,N-dihexadecyl) amino-7-nitrobenz- acetylated 655 mercury–xenon vapor lamps 195 2-oxa-1,3-diazole (NBD- residues, chemical modification of 210 physical chemistry of staining dihexadecylamine) 619 cystic fibrosis (CF) 767 (electro-adsorption) 189 dihydrorhodamine (DHR) 96 cytochromes 149–151 physical staining 189 2,5-dihydroxybenzoic acid (DHB) 1066 cytogenetic methods 917–924 types of light sources 194 N,N´-diisopropylcarbodiimide cytolytic T-cells in vitro labeling (DIC) 558 effector cells, activation of 105 with fluorescent fusion proteins dilution 15 recruitment of 105 (GFP and variants) 192–193 4,5-dimethoxy-2-nitrobenzyl cytomegalovirus (CMV) 772 with organic fluorophores 191, 192 chloroformate 111 DNA virus 965 xenon vapor lamps 195 dimethylformamide (DMF) 558 cytoplasmic RNA 677 detergents 19 dimethyl sulfate (DMS) 846 migration of 698 chromatographic support materials for modification 849 cytosine methylation 817 separation of 21–22 dimyristoyl-phosphatidylglycerol 60 cytosine, to uracil 819 ionic 20 dinitrophenol (DNP) 749 cytotoxicity 64 micelles, formation of 18 2,4-dinitrophenol (DNP) 742 nonionic 20 diode array photometer 142 D properties of 18 dioxetane chemiluminescence and removal 18 reaction 748 dabsyl chloride (DABS-Cl) 116, 307 removal of 20–22 diphenylthiourea (DPTU) 315, 316 dansyl derivatives, optical properties zwitterionic 20 diphosphatase 793 of 117 diafiltration 16 dipolar coupling 473 dark field microscopy 188 dialysis 15, 17 direct agglutination 72 data dependent acquisition (DDA) 1000 diamagnetic biomolecules 466 direct blotting electrophoresis peptide quantification 1002 diastereomers 710 (DBE) 741 data independent acquisition diatomic molecule, vibration properties disc electrophoresis 255–257 (DIA) 1000, 1008 of 163 discontinuous polyacrylamide gel data interpretation 369 diazopyruvoyl compounds 126 electrophoresis (disc data mining 1030–1031 dideoxy method 789 PAGE) 244 ´ ´ DAVID database 878 2 ,3 -di-deoxynucleotide 789 principle of 256 Dcm-methylation 817 dielectric coefficient 247 discovery proteomics 996 deamidation 224 diethyl pyrocarbonate (DEPC) 864 disruption method 9 decipher regulatory cis-elements 907 chemical formula/mechanism 676 disulfide bonds , cleavage of 209–210 van Deemter-Knox equation 222 difference gel electrophoresis dithioerythritol (DTE) 685 delta restrictions cloning 787 (DIGE) 252, 270–271, dithiothreitol (DTT) 126, 209, 269, 685 denaturation 986 DNA analysis 957 denaturing high-performance liquid internal standard 271 adenine methyltransferase 851 chromatography (dHPLC) 940 minimal labeling 270–271 associated protein modifications 828 1090 Index

DNA analysis (continued ) DNA-protein complex 837, 839, 867 chemical cleavage, according to backbone 801 chemical reagents Maxam/Gilbert binding motifs 835 diethyl pyrocarbonate (DEPC) cleavage reactions 801–804 binding proteins 828, 951 847 end labeling 800–801 calcium phosphate crystals 913 dimethyl sulfate (DMS) 846 A G-cleavage reaction 802 copying enzyme 846 halo-acetaldehydes 847 Maxam–Gilbert method 800 double helix 720 hydroxyl radical multiplex DNA footprint analysis 844 footprint 847–848 sequencing 804–805 scheme of 849 KMnO4/OsO4 846–847 RNA sequencing 805–806 fragments 721, 833 N-ethyl-N-nitrosourea (ENU) 847 solid phase process 804 helix parameters 832 gel analysis of 838 α-thionucleotide analogues hybridization 161, 948 interactions 857 804 hydrolysis method 827 DNA curvature 832–833 thymine- and cytosine-specific methylation analysis 827–828 DNA topology 833–834 fission reaction 803 length standards 693 double-helical structures 831–832 cycle sequencing with methylation specific restriction DNA-RNA hybrid 961 principle of 795 enzymes 823–825 DNase-I digest 845, 918 with thermostable DNA molecule 689 DNA sequencing 785 polymerases 795–796 non-viral introduction 912 automated capillary 799 denaturation/neutralization 792 oligonucleotides 730, 732, 736, 843, device 799 2´-deoxynucleotide 790 896, 953, 962 energy transfer dyes 797 deoxynucleotide analogues structure, in DNA chip technologies 429, 1035 fluorescent markings 796 dideoxy sequencing DNA complexity, cot value 721 gel-free methods 806 reactions 794 DNA Data Bank of Japan (DDBJ) 875 adaptations to library preparation/ dideoxy method 789 DNA:DNA hybrids 722 sequencing 810 2´,3´-di-deoxynucleotide 789 DNA–DNA interactions 1036 classic pyrosequencing 807 diphosphatase 793 DNA library 675 illumina sequencing 809–810 final denaturation 795 DNA methylation 818, 895, 949, 950 indexed libraries 811 labeling techniques/verification with methyl-binding proteins 826 mate-pair library creation 810–811 methods specific restriction enzymes 824 multiplex DNA sequencing 805 automated sample DNA methyltransferases (DNMTs) 817 paired-end-sequencing 810 preparation 798–800 DNA microarray technologies 939, 945, pyrosequencing, principle of 807 energy transfer dyes 797 953, 1036 454-technology (Roche) fluorescent labeling/online barcode identification 954–955 807–808 detection 797 beyond nucleic acids 956–957 microdrop PCR internal labeling, with labeled DNA analyses genomic sequencing/ deoxynucleotides 798 comparative genomic hybridization resequencing 812–813 isotopic labeling 796–797 (CGH) 951 semiconductor labeled terminators 798 genotyping 948 sequencing 811–812 online detection systems methylation studies 948–949 sequencing technologies, 798 protein–DNA applications 812 primer labeling 797–798 interactions 951–952 tag counting–RNASeq/ primer hybridization 792–793 sequencing 949–951 ChipSeq 813 strand synthesis DNA synthesis 952 target (exome) enrichment 811 and additives 794 on-chip protein next generation sequencing cofactors 794 expression 953–954 (NGS) 786 nucleotide analogs 794–795 RNA synthesis 953 principle of 799 pyrophosphorolysis 793 RNA analyses 946 single molecule sequencing 813 T7 DNA polymerase 791–792, splicing 947 nanopore sequencing 814 796 structure/functionality 947–948 native hemolysin pore, in dot blotting unit 707 transcriptome analysis 946–947 membrane 814 dot immunoassay 88 structural analyses 956 PacBio RS single molecule 814 double beam spectrometer 143 universal microarray single molecule real time double-stranded RNA-binding domain platform 955–956 (SMRT) 814 (dsRBD) 860 DNA-modifications, analysis of 818 DNA sequencing, gel-supported Down’s syndrome 719 DNA polymerase 207, 429, 798 methods 786 doxorubicin 104 advantage of 756 autoradiogram 791 doxycycline-inducible DNA-binding DNA polymorphisms 927 chain termination method, to unit 1051 DNA–protein binding partner 870 Sanger 790 Drosophila embryos 720, 729 Index 1091

Drosophila melanogaster 785, 942, imaging and information content double-stranded DNA, non- 947, 967, 1016, 1052 of 493–494 denaturing PAGE of 694 dry chemistry 420 mass determination 494 low melting agarose/sieving DryLab G/plus 236 Fourier transformation 499–501 agarose 694 dual-beam photometer 142 perspectives of 516–517 native polyacrylamide gels, Duchenne muscular dystrophy 767 with phase plate 495–496 abnormal migrational dye pixel size 498–499 behavior 694–695 energy transfer 797 resolution 492–493 oligonucleotide laser-induced emission 797 scanning electron purification 696–697 dynodes 356 microscopy 494–495 polyacrylamide gels 694 electron nuclear double resonance practical considerations 692–693 E (ENDOR) 477–478 protein–DNA complexes, non- experiments 477–478 denaturing gels 694 Eddy diffusion 222 electron paramagnetic resonance single-stranded DNA Edman degradation 116, 210, 313, 315, (EPR) 119 (SSCP) 695–696 564, 654 applications for 479 gel media for 250 amino acids, identification local pH values 480 pulsed-field gel electrophoresis of 316–317 mobility 480–481 (PFGE) 698–700 cleavage reaction of 316 quantification of spin sites and applications 699–700 length of amino acid sequence 319 binding constants 479–480 principle 698–699 phosphorylated and acetylated amino basics 467 RNA, gel electrophoresis 697 acids, localization of 654 comparison EPR/NMR 481–482 formaldehyde gels 697 quality of 317–319 cw-EPR spectroscopy 468 RNA standards 697–698 reactions of 315–316 electron spin and resonance two-dimensional gel electrophoresis repetitive yield 317–319 condition 467–468 (2D gel electrophoresis) 700 Edman, Pehr 313 electron spin nuclear spin of DNA 700–701 Edman sequencing 108 coupling 469–470 of RNA 700 EDTA-containing buffer 845 g-value 469 temperature gradient gel Egger, David 182 hyperfine anisotropy 470–472 electrophoresis (TGGE) 701 Einstein’s formula 412 significance 481 electrophoretic mobilities 253 Ekins, Roger 1034 spectroscopy of biological electrophoretic mobility shift analysis elastic scattering 171 systems 466 (EMSA) 836 electric field vector 134 electron spin echo envelope modulation electrophoretic separation electric ion traps 348–349 (ESEEM) 475–476 techniques 243 electroblotting 272 problems 475 historical review 244 blot membranes 273 three-pulse spectrum 476 media 243 blot systems 272 electron spin–electron spin separation principle 243 semidry blotting 272–273 coupling 472–473 theoretical fundamentals 245–248 tank blotting 272 anisotropic component 473 electrospray ionization (ESI) 335, 998, transfer buffers 273 electron spin nuclear spin coupling 1064 electrochemical luminescence (hyperfine coupling) 469–470 charged residue model 337 markers 742 cw-X-band EPR spectrum of TPA in interfaces, types of 281 electrodiffusion 78 liquid solution 470 ion emission model (IEM) 337 electroelution from gels 263–264 Fermi contact interaction 469 ionization, principle of 335–338 electroendosmosis 247, 248 electron tomography of individual macroscopic/microscopic 336 electrokinetic injections 277–278 objects 512–514 mass spectra, properties of 339–341 electromagnetic radiation 132, 133 electron transfer dissociation (ETD) 999 mass spectrometry 220, 234 electromagnetic waves 132, 134 fragmentation sources 992 MS/MS instruments 377 electron crystallography 486 electropherogram 296 MS spectrum, of metabolically electronic DNA biochips 428–429 electrophoresis 243, 690–691 labeled 1015 electronic transition 133 capillary gel electrophoresis sample preparation 341 electron microscope, imaging (CGE) 701–702 schematic structure and variants of process 183, 485, 492, 498 DNA fingerprinting 696 electrospray sources 339 analytical electron DNA, gel electrophoresis of source and interface 338–339 microscopy 494–495 agarose gels 691 spectra 715 electron beam with object, interactions circular DNA, separation of 692 chromatographically incompletely of 493–495 denaturing agarose gels 693–694 separated components electron energy loss double-stranded DNA 716 spectroscopy 494 fragments 691–692 components detection 716 1092 Index electrospray ionization mass spectrometry Epstein-Barr virus (EBV) 785, 913 Fe 1-(p-bromoacetamidobenzyl)- (ESI-MS) 228, 711 Er-YAG-laser 331 ethylenediaminetetraacetic acid electrospray mass spectrometry erythropoietin (EPO) 581 (Fe-BABE) hydrophobic transmembrane peptide amino acid sequence with 588 structure of 850 fragment 565 GluC peptides, theoretical/ Ferguson plot 253 purified 16mer peptide amide 565 experimental masses of 589, 590 field inversion gel electrophoresis electrostatic attraction 60 RP-HPLC/ESI-MS, total ion (FIGE) 698 electrostatic interactions 60 current 588 filamentous phages 676 ellipticity 179 schematic representation 582 finger-printing methods 787 Ellman’s reagent 112 Escherichia coli 385, 683, 785, 933, Fischer, Emil 573 EMBL Nucleotide Sequence 934, 953, 978 five-stranded β-sheet 460 Database 786 cell 856 flame ionization detectors (FID) 620 emulsion-PCR reaction (emPCR) 807 cytosine 825 florescence resonance energy transfer ENCODE project 882, 883, 939 DNApolymerase holoenzyme 736 (FRET) 851 endoplasmic reticulum 129, 579 DNApolymerase I 736 flow cell 266 endoprotease AspN 985 promoter sequences 883 flow velocities 222 endoprotease LysC 985 ethidium bromide 253 9-fluorenylmethoxycarbonyl (FMOC) endoproteinases 328 chemical structure of 702 chloride 306–307 endothermic processes 48 geometric properties of circular fluorescamine 304 endothermic transition 48, 49 DNA 703 fluorescein 119, 797 energy levels, transitions between 137 ethyl acetate 316 fluorescein:anti-fluorescein (FLUGS) energy transfer group systems 797 ethylcyanoglyoxylate-2-oxime system 742, 746 enthalpy 35, 49, 59, 147 (Oxyma) 558 fluorescein cadaverine 119 Entrez database system 878 ethyl trifluorothioacetate 110 fluorescein isothiocyanate (FITC) 116, entropy 35, 36, 147 eukaryotic cells 1059 enzymatic activity 44 cytoplasmic RNA 697 fluorescein-tagged enzymatic digestion 313 eukaryotic DNA 721 phosphoramidites 851 enzymatic DNA synthesis 952 eukaryotic mRNA species 678 fluorescence 652 enzymatic labeling 735 European Bioinformatics Institute action spectroscopy 157 of DNA 736 (EBI) 875 coded beads 1034 nick translation 736 European Molecular Biology laboratory detection methods 653 PCR amplification 736 Open Software Suite (EMBOSS) detector 220 random priming 736 analysis package 881 DNA chips 429 reactions 735 PEPSTATS routine 882 energy transfer 117 reverse transcription 736 sequence analysis, on web 881–882 labeling 116, 119 of RNA 736–737 E-value 890 with dansyl chloride 118 terminal transferase reaction 736 evaporative light scattering detectors with fluorescamine 118 enzymatic methods 651 (ELSD) 620 with phthaldialdehyde in as catalysts 37–38 exon sequencing 940 thiols 118 enzyme-catalyzed DNA exonuclease III (Exo III) 845 methods 651 polymerization 794 exothermic heat 54 microscope 486 (see also enzyme-controlled reactions, rate of 38 expressed protein ligation (EPL) 1052, fluorescence microscopic enzyme diaphorase (DP) 753 1053 analysis, special) enzyme immunoassays (EIA) 91–93 expressed sequence-tagged (EST) 776 principles of 188 Biacore technique 93–94 extracted ion chromatogram (EIC) 713, fluorescence correlation spectroscopy enzyme-linked immunosorbent assay 717 (FCS) 160, 202–203, 856, 1042 (ELISA) 745, 1033 measurement 856 signal amplification 751 F fluorescence energy resonance transfer enzyme–substrate complex 39 (FRET) 749 enzyme–substrate interactions 1038 Fab fragment 745 fluorescence in situ hybridization enzyme sulfurylase catalyzes 807 Faraday cup 357 (FISH) 729 epidermal growth factor 119 schematic design and operating fluorescence labeling, with fluorescein epidermal growth factor receptor principle 357 isothiocyanate (FITC) 118 (EGFR) 1041 far-Western blot 399–400 fluorescence lifetime imaging microscopy epifluorescence microscope 188 FASTA format 879, 880 (FLIM) 160, 204–205, 406 epigenetic modifications, analysis Fayyad, U. 1029 fluorescence loss in photobleaching of 817 Fc-engineering 101 (FLIP) 202 DNA replication 817 Fenton reaction fluorescence microscopic analysis, epitope mappingz 70 hydroxyl radicals 847 special 186, 188, 197–198, 1064 Index 1093

confocal high-speed-spinning disk emission and action spectra 156–157 formic acid 560, 561 systems (Nipkow systems) 199 frequent mistakes in 161–163 5-formylcytosine (5fC) 817 light microscopic super resolution fluorescence of Förster distance 852 below Abbe limit 200–201 complexes 162–163 Förster resonance energy transfer live cell imaging 199–200 FRET overdone 162 (FRET) 108, 160–161, measurement of movement of GFP overdone 162 203–204 molecules 202 incomplete/wrong labeling with comparison between PELDOR Ca2+ imaging 205 fluorophores 161 and 479 fluorescence correlation quantum dots overdone 162 components 749 spectroscopy (FCS) 202–203 shading and inner filter effect I 162 efficiency (E) 406 fluorescence lifetime imaging shading and inner filter effect II 162 principle 728 (FLIM) 204–205 principles 154–156 rate 161 fluorescence loss in photobleaching fluorescence staining 252 Fourier analysis 500 (FLIP) 202 fluorescence studies using intrinsic and Fourier, Joseph 499 fluorescence recovery after extrinsic probes 157–158 Fourier transformation 350, 351, photobleaching (FRAP) 202 fluorescence techniques 131 499–501, 500, 501 fluorescent-speckle microscopy fluorescent activated cell sorter (FACS) mass spectrometer 219 (FSM) 203 apparatus 96 fragmentation techniques 296, 357 Förster resonance energy transfer fluorescent antibodies 116 collision induced dissociation (FRET) 203–204 fluorescent detection 744 (CID) 357–358 Raster image correlation fluorescent DNA hybridization 917 generation of free radicals (ECD, spectroscopy (RICS) 203 absorption vs. emission-spectra 920 HECD, ETD) 360–362 spectral unmixing 204 DNA probes 918 photon-induced dissociation (PID, multiphoton fluorescence fluorescent hybridization signals, IRMPD) 360 microscopy 198–199 evaluation of 920 prompt and metastable decay (ISD, NSOM/SNOM (near-field scanning labeling strategy 917–918 PSD) 358–360 optical microscopy) 202 DNA probes 918–919 Franck–Condon principle 137, 154 PALM (photoactivated localization nick translation 919 Fraunhofer scattering 142 microscopy) 201 PCR labeling 919 free amino acids, analysis of 303 (S)SIM ((saturated) structured random priming 919 free electron laser (FEL) 529, 550 illumination microscopy) 201 signals, absorption vs. emission- free energy 35 stimulated emission depletion spectra 920 free flow electrophoresis 266–267 (STED) 201 in situ hybridization 919 principle 266 stochastic optical reconstruction denaturation 919 free working distance 183 microscopy (STORM) 201 hybridization 919 frozen-hydrated specimens, imaging total internal reflection fluorescence pre-annealing 919 procedure for 496–497 microscopy (TIRFM) 202 stringency 919 fundamentally different network fluorescence quenching 119 fluorescent in situ hybridization architectures 1030 fluorescence recovery after (FISH) 742, 917, 936, 940 fusion proteins 182 photobleaching (FRAP) 108, of genomic DNA 920–921 160, 202 interphase-FISH/fiber-FISH 921 G fluorescence resonance energy transfer metaphase 921 (FRET) 381, 402–403, 852–853 multicolor 920–921 galactocerebrosides 641 bioluminescence resonance energy fluorescent labeling 918 Galilei, Galileo 181 ´ transfer (BRET) 408 2 -deoxynucleotides GAL4 system 869 fluorescent probes for 406–407 (fluorescein-15-dATP) 798 DNA-binding domain 868 FRET based on fluorescence lifetime terminators 798 yeast Gal4 protein 381 measurements 406 fluorescent-speckle microscopy g anisotropy 470–472 FRET estimation based on sensitized (FSM) 203 gas chromatography (GC) 1027 acceptor emission 404–405 1-fluoro-2,4-dinitrobenzene 313 gas-phase fragmentation FRET estimation using acceptor fluorophores 119, 193, 194, 950 approaches 992 photobleaching 405–406 4-methylumbelliferone (4-MU) 915 gas phase sequencer 321 genetically encoded FRET pairs— 5-fluorouridine (FU) gauche-conformers 48 caveats and challenges 407–408 structures of 906 gel chromatography 16 instrumentation for intensity-based in vivo labeling of nascent RNA 907 gel electrophoresis 248, 806, 839, 982, FRET measurements 404 foam formation 617 984 key physical principles 403 FokI 683 gel retardation, background 836–838 methods of measurements 403–406 advantage of 828 nucleic acids 841 fluorescence spectroscopy 154 Folin–Ciocalteau phenol reagent 26 proteins separated 984 1094 Index gel electrophoresis (continued ) genome-level regulatory glycopeptides, mass spectrometric two-dimensional information 882 analysis on basis of 588–590 principle and practical genome sequencing 610 glycoproteins 251, 258, 571, 572, 579, application 700 genome-wide association studies 611 gel filtration methods 21, 666, 667, 708 (GWAS) 940 intact, analysis on basis of 582 gel-free sequencing methods 806 genome-wide gene inhibition analysis, electrophoretic analyses 582–584 gel phase 48 schematic representation 955 monosaccharide components 585 gel retardation 837, 839, 840 genomic loci 906 neutral monosaccharide gel-supported DNA sequencing genomic region, integrated map 941 components 585–587 methods 789 genotyping 948, 950 sialic acid 587 GenBank flat-file formatted to phenotype, organizational using lectins 584–585 database 880 structure 1025 purification 572 gene defects 719 Gibbs free energy 241 glycoproteome research, special challenge generation of free radicals (ECD, HECD, Gibbs–Helmholtz equation 61 of 610 ETD) 360–362 Giemsa staining 941 glycosidic bond 572, 574–578 genetic defects, detection of 773–776 G-less cassettes, for in vitro anomeric configuration 575, 576 allele-specific PCR 775 transcription 909 exo-anomeric effect 577–578 denaturing gradient gel electrophoresis β-globin gene 765 linkage direction 577 (DGGE) 776 glucose disaccharides 572 glycosylation 224, 329, 571, 579 length variation mutations 773–774 glucose enzyme electrodes 428–429 O-glycosylation 579 oligonucleotide-ligation assay (OLA) D-glucose, stereochemistry of 573 glycosyltransferases 579, 610 technique 775 glutamate dehydrogenase 42 glyoxal gels 697 restriction fragment length glutathione S-transferase (GST) good laboratory practice (GLP) polymorphisms 774 analyzing interactions in vitro, conditions 611 reverse dot blot 774 GST-pulldown 397–398 good manufacturing practice (GMP) 611 sequencing 774 protein 398 G-protein coupled receptors 107 single-strand conformational N-glycans guide RNA (gRNA) 974 polymorphism (SSCP) 775–776 chemical shift 604 Gquery interface 878 genetic engineering 571 composition analysis 600 gradient elution 227, 236 genetic mapping 925 core structures 581 green fluorescent protein disease genes 932 coupling constants 605–606 (GFP) 158–159, 182, 406, 911, genetic markers 927 exoglycosidase digestion 602–604 915, 1043 human genome 931–932, 942 1H NMR spectroscopy 604 variants 193 integration of 940–942 1H NMR spectrum 607 g-value 469 linkage analysis 929 individual, analysis of 581–610 χ2 test 929–930 isolation of individual H for plausibility 930–931 N-glycans 599–600 microsatellites 927 linkage with peptide backbone 579 Hahn, Erwin 475 physical mapping mass spectrometry 604 Halobacterium salinarium 149, 523 cloning systems 934, 935, 936 methylation analysis 600–602 HapMap Project 932 genes, identification/isolation nuclear Overhauser effect hapten of 937–939 (NOE) 607–608 antibodies 99 hereditary disease 940 pentasaccharide Man3-GlcNAc2 dNTP 733 high-throughput 580 structure of 743 sequencing 936–937 pool, release and isolation H-bond donors 832 recombinant clones 934–935 of 590–599 heat capacity 49 restriction of whole spatial interaction of sugar heating rates 49 genomes 932–934 residues 609–610 heavy metals 25 STS mapping 935 structural reporter groups 606 height equivalent to one theoretical plate transcription maps, of human structure 580 (HETP) 222 genome 939–940 types of 580 HEK293T cells 913 recombination 925–927 O-glycans structure 580–581 helical B-DNA, structure of 832 restriction fragment length glycerophospholipids (GP) 614 helical DNA conformations 832 polymorphisms (RFLPs) 927 glycine-glycine removal 994 helix-loop-helix proteins (HLHs) 835 single nucleotide polymorphisms glyco-analytical studies 582 helix-turn-helix structures (HTHs) 835 (SNPs)/single nucleotide variants glycolipids (GL) 614 hemagglutination 72, 73 (SNVs) 927–929 glycolysis 1024 Henderson–Hasselbalch equation 44 genetic predisposition 932 glycome 610–611 hepatitis B surface antigen genome 610–611 goals 610 (HbsAg) 1035 Index 1095 hepatitis B virus (HBV) 772 first dimension, IEF in IPG hybridization methods hepatitis C-virus (HCV) 752, 764, 772, strips 269–270 heterogeneous systems for qualitative 967 workflow 267 analysis 723 heptafluorobutyric acid 228 prefractionation 268 heterogeneous systems for quantitative Herpes simplex 514 affinity chromatography 268 analysis 723–724 heterogeneous amplification fractionation according to homogeneous systems for quantitative systems 724 charge 269 analysis 725 heteronuclear NMR-spectroscopy 219 subcellular components 268 FRET system 728 hexaminidase 129 proteins, detection and identification intercalation assay 728–729 higher-energy collisional dissociation of 270 molecular beacon system 728 (HCD) 990, 999 sample preparation 268 in situ systems 729 high field/high-frequency EPR second dimension, SDS TaqMan/5´ nuclease spectrometer 471–472 polyacrylamide Gel methods 725–728 high-performance anion exchange electrophoresis 270 hybridoma technique 99 chromatography (HP-AEX) 232 high-throughput technology hydrogen bonds 169, 177 high-performance aqueous normal phase (hSHAPE) 866 hydrolysis methods, DNA molecule 844 chromatography high voltage transmission electron DNA polymerases, exonuclease (HP-ANPC) 230 microscopes (HVTEMs) 493 activity of 845 high performance cation exchange HiSeq 810 DNase I 844–845 chromatography (HP-CEX) 232 histologic stains 190 exonuclease III (Exo III) 845 high-performance gel permeation histone acetyl transferases (HATs) λ exonuclease 845 chromatography (HP-GPC) 227 enzymes 647 hydrolytic cleavage 313 high-performance hydrophilic interaction internal lysine residues 646 hydrophilic contaminants 15 chromatography (HP-HILIC) histone deacetylases (HDACs) 646–647 hydrophilic peptide 316 229–230 enzymes 647 hydrophilic proteins 20 high-performance hydrophobic histone H4 proteoforms 997 hydrophobic molecules 59 interaction chromatography Hoechst 33258 669 hydrophobic peptides 562 (HP-HIC) 230–232 Hofmeister series 10 1-hydroxybenzotriazole (HOBt) 558 effect of salt cations 231 homing endonucleases genes hydroxyethyl cellulose (HEC) 701 protein–hydrophobic surface (HEGs) 683 hydroxyl radical reactions 847, 848 interactions, enhanced by 232 homogenization 7 5-hydroxymethylcytosine (5hmC) 817 protein separations, selectivity of Hoogsteen base pairing 961 hydroxypropylmethyl cellulose 230 Hooke, Robert 181, 485 (HPMC) 701 salts used in mobile phase 231 horizontal electrophoresis system 249 N-hydroxysuccinimide (NHS) 125, 270 high-performance ion exchange house-keeping gene 764 N-hydroxysuccinimidyl-4-azidosalicylic chromatography (HP-IEX) HPLC buffer 713 acid 125 232–233 HPLC chromatography 715 hypercholesterolemia 767 high performance liquid chromatography HP-RPC purification 234 hyperfine anisotropy 472 (HPLC) 219, 220, 827, 1027 hubs 1030 hyperfine sublevel correlation experiment chromatogram of peptide Human Genome Project (HGP) 719, (HYSCORE) 476–477 mixture 564 785 pulse sequence 476 column, operating ranges 237 human immunodeficiency virus splitting scheme 476 narrow bore 643 (HIV) 772 theoretical HYSCORE spectrum 477 separation of peptides by 561 HIV-Rev protein 869 hypochromism 139 high-performance normal-phase provirus genomes 765 hysteresis effects 54 chromatography trans-activator response element (HP-NPC) 228–229 (TAR) 869 I high-performance reversed-phase humanized antibody 100 chromatography human proteins identification, detection, and structure (HP-RPC) 227–228 monoisotopic masses 989 elucidation 368 high-performance size exclusion human X chromosome identification 368–369 chromatography (HP-SEC) 227 physical and genetic map 931 structure elucidation 369–375 high-resolution two-dimensional Huntington gene locus 773 verification 369 electrophoresis 267–268 Huntington’s disease (HD) 773 IgG antibody 828 difference gel electrophoresis trinucleotide (CAG-) expansion 773 IgG immunoglobulins (DIGE) 270–271 HybProbes 725, 728 antigen interaction at combining internal standard 271 HybProbes 728 site 67–68 minimal labeling 270–271 hybrid antibodies 100 functional structure 66 saturation labeling 271 hybrid instruments 351 schematic structure and function 66 1096 Index

Illumina sequencing systems 809, 810 principles 163–164 isoelectric focusing (IEF) 244, 259–260 exome enrichment 812 proteins, infrared spectra of 168–171 carrier ampholytes 261 Ilyobacter tartaricus 523 technical aspects 165–168 cathodal drift 261 image analysis 498 inhibitors 40 electrode solutions 261 image cycler microscopy (ICM) 1058, competitive 40–41 immobilized pH gradients 261–262 1060 non-competitive 41 preparation of 262–263 antibody based 1057 RNA (RNAi) molecules 953 measuring pH gradient 260 image isomerism, D-glucose/ in situ hybridization (ISH) 917 pH gradients, kinds of 260 L-glucose 576 in situ protein expression 954 principle 260 imaging cycler robots 1059–1063 insoluble proteins 6 separation media 260 multi-pipetting unit, a fluorescence instrumentation 319–322 separator IEF 261 microscope, and CCD intact nuclei, isolation of 906 titration curve analysis 263 camera 1059 Intelligent Systems in Molecular Biology isopycnic centrifugation 14 imidazole 33 Conference (ISMB) 877 isoschizomer EcoRII I-BstNI 825 iminodiacetic acid 233 interactomics–systematic protein–protein isoschizomers 824 immobilization 23, 88 interactions isotachophoresis (ITP) 293–295 immobilized metal-chelate affinity DNA to protein order of electrolytes and 294 chromatography (IMAC) microarrays 1035–1036 isothermal titration calorimeters 233, 649 protein microarrays 1033–1034 (ITCs) 48, 54, 58, 61 on a membrane 17 antibody–antigen curve 55, 59, 60 pH gradients 244 interaction 1037–1038 scheme 55 reagents, analysis using 419 application of 1037–1039 isothiocyanate, reaction with 111 immune agglutination 73 enzyme–substrate interaction 1038 isotope-coded affinity tag 650 immune binding 84–88 ligand–receptor interaction 1038 isotope coded protein label immune conjugates 104–105 reverse phase (ICPL) 1018–1019 immune defense 63–64 microarrays 1038–1039 ICPLQuant 1019 immune fixation 80 sensitivity through reagents 1018 immunoagglutination 72, 73 miniaturization–ambient analyte isotopically labeled linker (ICAT) 660 application 72–73 assay 1034–1035 reagent 1016, 1017 direct agglutination 72 interference 184 technique 1017 immunochemical detection 651, 652 contrast microscopy 188–189 isotopic distributions 989 immunocompromised AIDS interfering substances 24 isotopomer envelope 989 patients 965 International HapMap Project 927 isotopomers 987 immunocytochemistry 90 interspersed repetitive sequences immunodetection 88 (IRSs) 918 J immunodiffusion 75, 78 hybridization with singular probes 918 one-dimensional simple intrinsically disordered proteins (IDP) 464 Jablonski diagram 137–140 immunodiffusion of in vivo proteolysis 207 JASPAR database 884, 885 Oudin 75–76 iodinations 33 Joule heating 279 two-dimensional immunodiffusion of iodoacetamides 119, 125 Ouchterlony 77–80 ion chromatograms 1008 K immunoelectrophoresis 79 ion detectors 355 immunofluorescence labeling 191, 196 ion exchange chromatography (IEX) 240 karyograms 917 direct and indirect 190 ionic detergents 20 drawbacks of 917 immunoglobulins 995 ionic retardation 21 Kepler, Johannes 181 VL variable domain 892 ionic strength 43, 60 Ketenes 126 immunohistochemistry 90 ionization methods 329, 330 K-homology domain (KH) 859 immunopharmaceuticals, strategies for ion mobility spectrometry (IMS) 378 RNA-binding motif 860 production 103 ion pairing reagent 236 Kjeldahl method 25 immunoprecipitating systems 73–75, ion pair reversed-phase HPLC 712 Klebsiella pneumoniae 768 98, 649 separation 714 Klenow fragment 788, 791 immunosensors 426–427 ion-trap mass spectrometer 219 of DNA polymerase I 843 immunotherapeutics 64 isobaric tags for relative and absolute Knoll, Max 486 industrial-scale sequence quantitation (iTRAQ) 1020 Koch, Robert 182, 485 production 875 enzymatically cleaved proteome Köhler, August 485 inelastic scattering 171 states 1020 Köhler illumination optimization 184 informative markers 927 isobaric reagents 1020 Krebs cycle 1024 infrared spectroscopy (IR) 163, 1026 isocratic elution, optimization of 236 Kyoto Encyclopedia of Genes and molecular vibrations 164–165 isocyanate 316 Genomes (KEGG) 1024 Index 1097

L whole lipid extracts 626–627 differential 1H ÍÌR spectroscopic biological functions 613 analysis 1027 labeled oligonucleotides 729 combining analytical systems 623 living systems, hierarchical representation label probes coupling of gas chromatography and of complexity 1025 radioisotopes, characteristics of 739 mass spectrometry (GC/ loading capacity 228 RNA probes, synthesis of 731 MS) 625–626 locked nucleic acids (LNAs) 732 LabExpert 236 coupling of HPLC and mass probes 733 laboratory information management spectrometry (LC/MS) 625 locus control regions (LCRs) 895 system (LIMS) 800 coupling of HPLC and UV/Vis Lowry assay 26–27 lactate oxidase (LOD) score 931 spectroscopy 623–624 LTYYTPEYETK 1015 Lambert–Beer law 25, 140–142, 253 tandem mass spectrometry luciferase enzymes 748 Lamm’s differential equation 412, 415 (MS/MS) 626 luciferin bioluminescence reaction 748 Larmor frequencies 474, 475 extraction 615 luminescence 744 laser, for fluorescence excitation 280 hormones and intracellular signaling Luria-Broth 671 laser microprobe mass analysis molecules 633–638 lymphocytes 65 (LAMMA) 1064 liquid phase extraction 616 resistant to HIV 967 N-Lauryl-sarcosine 678 membranes 4 lysate 672 law of mass action 36, 416 methods for analysis 618 LysC digest 1019 lectin-affinity chromatography 611 chromatographic lysine residues 108 Leeuwenhoek, Antoni van 181 methods 618–622 lysis 105 Leucine zipper proteins 835 1H, 13C, and 31PNMR Leu2 gene 382 spectroscopy 623 M ligase chain reaction (LCR) 751, 779–780 immunoassays 622–623 LightCycler® 728, 756 mass spectrometry 622 macromolecular crowding 515 profiles 729 UV/Vis spectroscopy 623 MAFFT 891 light emitting diodes (LEDs) 143, 144, modified proteins, magnetic bead isolation 679 157 analysis 1052–1053 magnetic force microscope (MFM) 519 light field diaphragm 184–185 perspectives 642–643 forces between AFM tip and object 520 light field microscopy 187 solid phase extraction 616–617 principle 520 light induced co-clustering structure and classification 613–615 magnetic ion trap 349–355 (LINC) 408–409 vitamins 638–640 magnification light microscopic technologies 183 lipofection 913 of lens 185 light scattering 144 lipoproteins 251 total, of a microscope 186 consequence for absorption liposomes 48, 50 major histocompatibility complex measurement 141 liquid chromatography (LC) 144, 220, (MHC) 63 linear combinations of atomic orbitals 995, 998 maleimides 119 (LCAO) 134 liquid chromatography tandem mass Malpighi, Marcello 181 linear dichroism (LD) 177 spectrometry (LC-MS/MS) 999 mammalian cells, in vivo analysis 571 IR spectroscopy 178 analysis 713 DNA transfer 912 linear discriminant analysis bottom-up workflow 999 chemical-based transfection 913 (LDA) 1008 high-throughput analysis 996 electroporation 913 linear gradient gel, casting of 255 instruments 376–377 lipofection 913 linear polarized light 132 oligonucleotides 709 non-chemical methods 913 linear polyacrylamide 701 mass spectrometric transient/stable expression 913 linear-solvent-strength theory 236 investigation 712–714 viral transduction 913 Lineweaver–Burk plot 40, 41 phosphorothioate oligonucleotide, gene-regulatory cis-elements 911 linkage analysis 929 IP-RP-HPLC-MS investigation promoters 911–912 linoleic acid 621 of 714–717 promoter activity 911 lipidation 224 principles of 709–711 marker chromosome 920 lipidome analysis 640–642, 641 purity investigation/ mass analyzer 329, 341–343 advantages of ESI-MS based 641 characterization 711–712 time-of-flight analyzers biological sample, experimental liquid handling system 798 (TOF) 343–345 strategy for mass spectrometric liquid-ordered state 48 mass determination 362 analysis 641 liquid phase sequenator 320 calculation of mass 362 lipids 48, 613 Listeria monocytogenes 700 calibration 365 analysis of selected lipid classes 626 live cell imaging 199–200 derivation of mass 366 fatty acids 627–628 liver alcohol dehydrogenase determination of number of nonpolar neutral lipids 628–629 (LADH) 174 charges 365–366 polar ester lipids 630–633 liver tissue influence of isotopy 362–365 1098 Index mass determination (continued ) mass spectra, characteristics of 332 methidiumpropyl-EDTA-Fe problems 366–367 mass spectrometry (MALDI-MS) (MPE-Fe) 849 signal processing and analysis 366 330–331, 345, 643 methionine 563 massively parallel sequencing in biochemical analytics, typical methoxyamine hydrochloride 621 (MPS) 785, 786, 806 matrix substances for 331 methylated-CpG island recovery assay mass spectrometry (MS) 108, 219, 220, protein analysis 333 (MIRA) 825 315, 329, 394, 711, 982, 1064 sample preparation 332–335 methylated DNA immune-precipitation accurate MALDI mass spectrometry matrix solution 296 (MeDIP) 826 imaging 1068–1069 mouse spinal cord 1070 methylation analysis achievable spatial peptide mass fingerprint (PMF) 1015 with bisulfite method 819 resolution 1065–1067 proof-of-principle 1064 by DNA hydrolysis/nearest amino acid analysis using 309 sample preparation 334 neighbor-assays 827–828 aTRAQ-LC-MS-MS 309 time of flight (MALDI-TOF) by methylcytosine-binding CE-MS 309 analysis 840 proteins 825–826 direct infusion MS-MS 309 mass spectrum, chemically by methylcytosine-specific GC-MS 309 acetylated histone H4 653 antibodies 826–827 HILIC-MS 309 spectrometry 867 principle of 820 ion pair-LC-MS-MS 309 spectrum, monoclonal methylation specific PCR analysis 397 antibody 333 (MSP) 822–823 analytical microprobes 1064 spectrum, peptide angiotensin principle of 822 basic principles 1001 II 333 RASSF1A-promoter 823 coarse screening, by MS Maxam-Gilbert method methylation specific restriction enzymes, imaging 1068 DNA sequence reaction 897 DNA analysis 823–825 components of 330 reaction 846 methyl binding domain (MBD) 825 glioblastoma tissue section, MALDI sequencing reaction 847 5-methylcytosine 817 images 1068 Maxam–Gilbert method 789, 800, 804, methylcytosine-binding proteins, identification/characterization 820 methylation analysis 825–826 of 1069–1070 MaxQuant 1019 methylcytosine-specific antibodies, lateral resolution/analytical limit of Mbp1 protein 878 methylation analysis 826–827 detection 1067 mean proteins 24 N,N´-methylenebisacrylamide 250 mass spectrometric pixel meiosis, recombination/crossing MethyLight method 823 images 1064–1065 over 926 4-methylumbelliferyl-β-D- mouse spinal cord, SMALDI MS/MS melting 47 galactopyranoside image of 1070 membrane-bound DNA probe 906 (4-MUG) 915 mouse urinary bladder tissue section, membrane lipids 58 micellar electrokinetic chromatography SMALDI images 1069 membrane proteins 6, 82 (MEKC) 286–288 peptide within, standard MALDI membrane–water interface 119 capacity factor 286 preparation 1065 2-mercaptoethanol 209, 685 electrophoretic mobility 286 phosphorylated/acetylated proteins, β-mercaptoethanol 126 principle 287 detection of 653 Merrifield, Bruce 555 time window 287 position information messenger RNA 128 micelle building agents 288 microanalytical image 1065 metabolic fingerprinting 1023 Michael addition 651 visual coding 1066 metabolic labeling 660, 1015, 1016 Michaelis–Menten equation 39–41 protozoa during mating, SIMS images metabolic profiling 1023 Michaelis–Menten theory 38–39 of 1068 metabolite target analysis 1023 microarray analyses 945 quantification 378–379 metabolomics 1023, 1024 microarray suitability sequencing of peptides, principle analytic techniques, coupling DNA vs. proteins 1036 of 371 with separation technologies 1028 microbial sensors 425–426 SIMS/ME-SIMS/cluster SIMS application 1032 microcalorimetry 47 imaging 1067 general strategies and microchannel plate 356–357 SMALDI mass spectrometry imaging techniques 1027 microchip electrophoresis (MCE) dried-droplet preparation 1067 knowledge mining 1029–1030 297 techniques 866 profiling 1027–1028 miniaturization 298 toponome mapping, by ICM 1064 and systems biology 1025–1026 separation of amino acid derivatives by mate-pair sequencing 811 technological platforms 1026–1027 chip-MEKC 298 Mathieu equations 346, 347, 349 metabonomics 1023 microelectromechanical systems matrix-assisted laser desorption ionization metalloproteins 151 (MEMSs) 680 (MALDI) 329, 1064, 1068 metarhodopsin I (MI) 149 micro RNAs (miRNAs) 856, 959, instrument 345 metarhodopsin II (MII) 149 970–971 Index 1099 microsatellites 927. see also multidimensional HPLC 238 nick translation 736 polymorphic sequence tagged design of scheme 240–241 ninhydrin 304 sites fractionation of complex peptide and reagent 25 microscopic stages 184 protein mixtures by 239 nitrilotriacetic acid 233 microscopy techniques, biological purification of peptides and proteins nitro-blue tetrazolium salt (NBT) structures and suitable 485 by 238–239 coupled optical redox reaction 748 microspots sensitivity 1035 strategies for 239–240 nitrocellulose 652 micro-total analysis systems multiphoton fluorescence membranes 706 (μ TAS) 297 microscopy 198–199 nitrogen laser 331 Mie scattering 142 multiple anomalous dispersion o-nitrophenol (ONP) 915 migration behavior, of superhelical 693 (MAD) 540–541 o-nitrophenyl-β-D-galactopyranoside MIRArecombinantGST-tagged MBD2b multiple cloning site (MCS) 911 (ONPG) 915 protein 825 multiple isomorphous replacement p-nitrophenyl diazopyruvate 126, 127 miRNA-122, liver-specific 971 (MIR) 538–540 nitroxides 480 mixed mode HILIC/cation-exchange multiplicity 135 protonated/unprotonated, chromatography (HILIC/ MUSCLE tool 891 structure 480 CEX) 229 Mus musculus 942 N6-methyladenine 817 MMLV RTase 761 mutated proteins 120 N-nitroso-alkylating reagent 865 mobile phase 221, 222, 618 Mycobacterium tuberculosis 1009, NOESY spectra 459 salts used for HP-HIC 231 1011 Nomarski, Georges 182 modern LC-ESI-MS systems 376 Mycoplasma genitalium 938 non-coding RNAs (ncRNAs) 856 modern microscopic techniques 485 m/z values 345, 351, 354 non-competitive inhibitors 41 modulation transfer function (MTF) 497 non-crystallographic symmetry molar mass 4 N (NCS) 540 molar ratio 58 nonionic detergents 20 molar transition enthalpy 51 N-acetyl-L-glutamate-kinase triton X-100 673 molecular orbitals (MOs) 134 (NAGK) 414 nonlinear anisotropic diffusion 513 molecular probes Naja naja oxiana 863 nonpolar gas chromatographic caging gives temporal and spatial nano-crystals 529 columns 621 control 1051 nano-HPLC flow rates 375 nonpolar ligands 227 molecular replacement (MR) 541–542 nano-RP-HPLC 650 non-protein nitrogen 25 molecular vibrations 164–165 National Center for Biotechnology non-radioactive detection systems 742 molecules binding, to membranes 58 Information (NCBI) 875 non-radioactive labeling 739 insertion and peripheral BLAST (Basic Local Alignment Search bioluminescence 748–749 binding 58–61 Tool) 890 biotin system 745–746 molecules, energy levels of 135–137 yeast Mbp1 protein 889 chemiluminescence 747–748 molecules properties 134–135 native chemical ligation (NCL) 1052 digoxigenin system 744–745 monochromatic light 141 native proteins 207 dinitrophenol system 746 monochromator 143, 144 natural killer cells 104 direct detection systems 740–742 monoclonal antibodies 99 natural light 132 electrochemiluminescence 748 optimized, constructs with effector nearest neighbor-analysis 827 fluorescein:anti-fluorescein (FLUGS) functions for therapeutic nearest neighbor-assays, methylation system 746 application 102–105 analysis 827–828 fluorescence detection 749 monoisotopic mass 987 near-field scanning optical microscopy FRET detection 749 monolithic polymer 288 (NSOM) 202 indirect detection systems 742–747 monomer–dimer equilibrium 413 Neisseria gonorrhoeae 723 luminescence detection 747 monomeric proteins 413 Neisseria meningitidis 723 optical detection 747 monosaccharide nephelometry 84 signal-generating reporter group 740 building blocks 574 Nernst function 151 in situ detection 749 sequence 572 nested PCR 766–767 non-radioactive modifications 733 3-N-morpholino-1-propane sulfonic acid one tube 767 non-radioactive reporter groups 741 (MOPS) 697 neutral fragment masses 991 non-small cell lung cancer (NSCLC) 1041 mouse embryonal fibroblasts neutral loss scan 352 N-terminal sequence analysis 315 (MEFs) 914 new antibody techniques 99–102 nuclear magnetic resonance mRNA stability 978 next generation sequencing (NGS) 108, (NMR) 1026 MS-based proteomics 997 785 spectroscopy 107, 120, 314, MSn-spectra of peptide, measured with application areas 786 433–434, 486, 530 ESI ion trap 374 N-hydroxysuccinimide-activated Bloch equations 436–437 multichannel spectrometers 144 haptens 737 limitations 433 1100 Index nuclear magnetic resonance (NMR) photochemical labeling genomic DNA 669 (continued ) reactions 737 additional steps 670 nuclear spin and energy positions 733–735 cell membranes/protein degradation, quantization 434–435 mixture 700, 721 lysis of 669 populations and equilibrium photoactive substances for detection enzymes/lysis reagents 669 magnetization 436 of 737 phenolic extraction/subsequent pulsed Fourier transformation probes for 729 ethanol precipitation 670 spectroscopy 437–438 DNA probes 730–731 precipitation 670 relaxation 437 LNA probes 732–733 lab-on-a-chip (LOC) system 680 speeding-up 463 PNA probes 732 low molecular weight DNA theory 434–438 RNA probes 731–732 anion exchange nuclear-run-on assays 905 restriction analysis 681 chromatography 673 nuclear-run-on transcription 906 historical overview 682 bacterial culture 671 5´ nuclease reaction format principle of 681–682 density gradient (TaqMan) 726 restriction enzymes centrifugation 673–674 coupled amplification/detection 727 biological function 682 lysis of bacteria 671–673 homogeneous detection systems 727 classification of 682–683 plasmid from bacteria 670–671 nucleic acid blotting 704 isoschizomeres 685 magnetic particles 679–680 colony/plaque recognition sequences 683–685 optical density (OD) 668 hybridization 707–708 type II 683 phenolic purification 665–666 dot/slot-blotting 707 staining (see staining methods) photometric determination 668 membrane, choice of 704–705 stringency, specificity 722–723 plasmid DNA by CsCl density gradient Northern blotting 706–707 in vitro restriction/applications centrifugation 674 Southern blotting 705–706 complete restriction 685 precipitation with ethanol 667–668 nucleic acids 705 genetic fingerprint 689 protein containing amplification systems 750 genomic DNA, restriction analysis contaminations 665 signal amplification 752–753 of 686–688 RNA isolation 676 target amplification 751–752 incomplete/partial restriction 686 poly(A) 678–679 blotting (see nucleic acid blotting) methylated bases, detection of 688 sensitive quantification method 669 detection systems 738 multiple restriction enzymes, single-stranded DNA 676 by hybridization 722 combination of 686 double-stranded DNA 676 non-radioactive systems 739–749 partial restriction 686 M13 phage DNA 676 radioactive systems 738–739 restriction fragment length small RNA, isolation of 679 staining methods 738 polymorphisms Tris-HCl or TE (Tris-HCl/ electrophoresis (see electrophoresis) (RFLP) 688–690 EDTA) 665 fragments isolation, purification 729 restriction mapping 686, 687, 688 viral DNA, phage DNA 674–675 using electroelution 708–709 nucleic acid sequence-based amplification Nucleic Acids Research (NAR) 877 using gel filtration/reversed phase 708 (NASBA) 751, 755, 778 nucleophiles 125 using glass beads 708 nucleic acids, isolation/purification of nucleotide sequence 876 in gel matrix 691 alkaline lysis, principle of 672 management, in laboratory 881 hybridization 719 ampicillin-containing media 670 nucleotide triphosphate 951 basic principles of 720 carrier 668 numeric aperture (NA) 186, 187 heterogeneous systems for cetyltrimethylammonium bromide qualitative analysis 723 (CTAB ) 670 O heterogeneous systems for CsCl density gradient 673 quantitative analysis 723–724 cytoplasmic RNA object characteristics 501–502, 504 homogeneous systems 725, 729 cultivated cells 677 n-octyl-β-D-thioglucopyranoside intercalation assay 728–729 tissue/cultivated cells 677–678 (OSPG) 673 molecular beacon system 728 determination of octylglucoside 59, 60 practice of 721–722 concentration 668–669 off-gel isoelectric focusing, principle in situ assays 729 DNA yield after anion exchange of 266 specificity 722–723 purification 673 Ogston sieving effect 691 ´ TaqMan/5 nuclease amplification double-single-stranded DNA Ohm’s law 293 detection 725–728 absorption curves of 668 oil-immersion objective 187 isolation of fragments (see nucleic acid with ethanol 667 okadaic acid 1045 fragments, isolation of) eukaryotic low molecular weight oligodeoxyribonucleotide, comparison labeling methods 733 DNA 674 of 963 chemical labeling 737–738 eukaryotic viral DNA 675 oligonucleotides 738, 793, 960 enzymatic labeling 735–737 gel filtration 666–667 antisense 960, 963 Index 1101

cell culture/animal models 964 optical rotation dispersion (ORD) 178 ionization 999 human β-globin pre-mRNA 961 optical spectroscopic techniques 131, 132 mass measurement/ intermolecular triple helix 962 physical principles 132 fragmentation 999 mechanisms 960–961 optical tweezers 856 peptide separation 998 RNase H 960–961 orbital ion trap 349–350, 350–351 proteolysis using trypsin 998 RNA splicing, changes 961 Orbitrap 350 bottom-up proteomic strategies 1000 as therapeutics 964–965 linear ion trap with 354–355 DDA, principle of 1000 translation inhibition 961 organic radicals 466 DIA, principle of 1001 aptamers, high-affinity RNA/DNA- organic solvents 10 SRM, principle of 1000–1001 oligonucleotides 971–974 ortho-phthaldialdehyde (OPA) 305, 306 data dependent analysis (DDA) arrays 731 oscillating dipole moment 172 challenge 1003 CGE electropherogram of 702 Ouchterlony immunodiffusion principle/intended use 1002 fingerprinting 936 technique 78 strength/weaknesses 1002 gapmer 964 typical applications 1003 high-affinity 973 P extensions 1012 interferon response 967 MSE 1013 intermolecular triple helix 962 PacBio RS single molecule real time DNA MSX 1013 mechanism and location 960 sequencing 814 parallel reaction monitoring micro-RNA pathway 970 paired-end-sequences, alignment of 811 (PRM) 1012 nucleotides modifications 962 paired-end tag sequencing 829 precursor acquisition independent oligosaccharide binding fold (OB pair-end sequencing 810 from ion count fold) 860 Pancreatic DNase I 827 (PAcIFIC) 1012–1013 positions for nucleotides paraffin slices 197 peptide quantification 1001–1002 modifications 962 parallel reaction monitoring proteome, complexity of 1000 probes 918 (PRM) 1012 selected reaction monitoring disadvantage of 722 paramagnetic centers 467 (SRM) 1003 ribose, by fluorine paramagnetic dipole interaction 119 analysis software 1007–1009 ´ 2 position 973 parfocal distance 185 clinical studies 1010 RNA interference, mechanism of 968 partition coefficient 59, 60 data analysis 1007 SELEX-strategy, for RNA aptamers passive immunoagglutination 72 eukaryotic model isolation 972 Pauli principle 135 organisms 1009–1010 short hairpin RNA (shRNA) PCR. see also bisulfite PCR identification 1005–1006 vector expression 969 peak capacity 241 method 1004–1005 susceptibility to nucleases 962–964 peak dispersion 223 microbial 1009 synthesis 709, 710, 952 peak distance 221 principle of 1003–1004 phosphoramidites 737 peak variances 223 quantification 1006–1007 triplex forming oligonucleotides peak widths 221 strength/weaknesses 1009 (TFOs) 961–962 pentose phosphate pathway 1024 typical applications 1009 uses 959 pepsin 207 SWATH-MS oligosaccharides 572 peptide. see also peptide based principle/intended use 1010–1011 omics 1023, 1024 quantitative proteome analysis strength/weaknesses 1011 one-dimensional diffusion 76 analysis 329 typical applications 1011–1012 one-dimensional NMR antibodies 99 peptide libraries, analytics of 567–569 spectroscopy 437–438 bonds 23, 30, 224 approach to identifying 568 chemical shift 439 hydrolysis of 302 characterization 569 1D experiment 438 detection of 651 divide–couple–combine method 567 line width 442 ESI-MS spectrum 373 Edman degradation 567 scalar coupling 439–442 fragmentation 562 peptide nucleic acid (PNA) 730 spectral parameters 438–439 general structure 313 oligomers 732 online detection systems 798 monoisotopic masses 989 peptide synthesis 555–560 online sample concentration 295–296 separation and enrichment 649 common side products and side one buffer stacking system 295 sequences 313 reactions during 560 two buffer stacking system 295–296 Peptide Atlas projects 1008 approach 568 open reading frames (ORFs) 789 Peptide Atlas SRM Experimental Library characterization by ESI mass o-phosphoserine (OPS) 233 (PASSEL) 1004 spectrometry 569 o-phthaldialdehyde (OPA) 118 peptide based quantitative proteome divide–couple–combine optical enzymatic detection systems 747 analysis 998 method 567 optical multichannel analyzers bottom-up proteomics 998 Edman degradation 567 (OMAs) 144 data analysis/interpretation 999 Fmoc- or Boc-strategy 557 1102 Index peptide synthesis (continued ) photoaffinity labeling 121, 123 structure 250 and identification 555 photobleaching 199 vs. agarose 694 important reaction mechanisms photodetectors 133 polycystic kidneys 767 in 558 photolabeling peptides, with polydimethylsiloxane (PDMS) 277 principles 555 benzophenone 127 polyethersulfone 16 structure and abbreviation of selected photolysis 125, 126 poly(ethylene glycol) (PEG) 675 agents used in 557 caged probe 1051 poly(ethylene oxide) (PEO) 701 synthesis on solid support 556 photometric measurement 142, polyketides (PK) 614 peptide synthesizer 559 143–144 poly-L-lysine 180 peptidome frequent errors in 143 polymerase chain reaction (PCR) 721, analysis of 1029 main sources of error in 142 725, 751, 755, 918, 935, 950 collagenases 1029 principle of 132–133 alternative amplification peptidomics 1023, 1028–1029 with circular polarized light 133 procedures 777 peroxidase–anti-peroxidase (PAP) with linear polarized light 132 nucleic acid sequence-based complex 87 photon emission 915 amplification (NASBA) 777 Petran, Mojmir 182 photon energies 133 transcription-mediated amplification PFGE gels 699 photon-induced dissociation (PID, (TMA) 777 Pfu DNA polymerases 759 IRMPD) 360 Alu PCR 770 phagocytosis 64, 105 photoreceptors 133 amplification 819 phase contrast condenser 185 phototoxicity 200 avian myeloblastosis virus (AMV) phase contrast microscopy 187 Phred quality 808 RTase 761 phase contrast objective 185 pH sensors 429 enzymes 761 phase diagram of aqueous protein pH values 561 Moloney murine leukemia virus solution 532 phycoerythrins 741 RTase 761 phase transitions 53, 54 physical-chemical systems 35 primers 762 phenol/chloroform/isoamyl alcohol pico-Newtons (pN) 855 procedure 762 (PCIA) 665 piezoelectric quartz crystals (PQC) 429 RNA (RT-PCR) 761 phenolic extraction 666 pigment–protein complexes 140, 152 in single reaction tubes 762 phenotypic/biochemical markers 931 pI value 561 Tth DNA polymerase 762 phenylalanine 225 pixel protein profiling (PPP) 1062, 1063 in two reaction tubes 762 phenyl isothiocyanate (PITC) 306, 654 plan achromatic objectives 185 applications 772 phenylthiocarbamoyl (PTC)- plan apochromatic objectives 185 genetic defects, detection peptide 315 planar/bead-based arrays 1034 of 773–776 phosphatase/deacetylase-treated planar invitrogen microarray 1038 human genome project 776–777 sample 652 planar protein microarray 1033 infectious diseases, detection phosphatidylcholines 50, 641 plasma proteins 981 of 772–773 phosphatidylethanolamines 641 dynamic range 981 branched DNA amplification (bDNA) phosphodiester bonds 856 plasma proteome analyses 981 method 782 phospholipases 615 plasmid vector 788 contamination problems 770 phospholipid dimyristoyl- ColE1 origin 671 avoiding 770–771 phosphatidylcholine 59 copy numbers 671 decontamination 771–772 phosphomethylene-L-phenylalanine plasminogen 995 digital PCR 769 (Pmp) 1054 plate number 222, 223, 235 DNA amplification 758, 763 phosphopeptides 650 point spread function (psf) 185 additives 763 phosphoric acid (H3PO4) 650 polarimeter 178 buffer 759 phosphorothioates, disadvantages polarity 224, 225 cycles 758–759 of 962 polarization 132 enzyme 759 phosphorylated proteins 650 microscopy 188 hot start PCR 763 analysis of 1054 plane 178 magnesium ions 763 detection of 651 polarized light 132 nucleotides 759 separation and enrichment 649 linear dichroism 175–178 primers 759–760 phosphorylation 224, 329, 369, 561, methods using 175 probe preparation 758 645–646, 979 polyacrylamide gel electrophoresis RNA amplification 763 phosphoserine 648 (PAGE) 711, 901 template 763 phosphotyrosine-containing proteins, polyacrylamide gels 244, 694, 704 templates 760 generic detection of 652 advantages of 260 for DNA brand marking 794 photoactivatable groups 127 separation of DOP PCR 770 photoactivated localization microscopy oligonucleotides 696 helicase-dependent amplification (PALM) 201, 486 range 695 (HDA) 777–779 Index 1103

instruments 756–757 amino acids, localization/ protein aggregation 49 inverse PCR 769 identification 653–654 protein based quantitative proteome ligase chain reaction (LCR) 779–780 analysis, based on 648 analysis 982 master mixes 759 future perspective 661 intact protein mass spectrometry, mutagenesis techniques 870 quantitative analysis of 659–660 concepts 987–997 optimization of reaction 763 potential energy 35 closing remarks/perspective 996–997 polymerization of DNA 756 power of combinatorial molecular data analysis 991–995 possibilities of 755–756 discrimination (PCMD) 1061, high-throughput top-down PRINS PCR 770 1063 proteomics 995 prospects of 782 33P phosphates 733 mass spectrometry, to measure intact Qβ amplification 780–781 precipitation 3, 9, 17, 64 proteins 990–991 quantitative PCR 763 of nucleic acids 10–11 top-down proteomics competitive (RT) 765–766 using organic solvents 10 using intact protein mass external standard 764–765 using trichloroacetic acid 10 spectrometry 987 internal standardization 765 precursor acquisition independent from using isotope labels 986–987 RACE PCR 769 ion count (PAcIFIC) 1012 two-dimensional differential gel repair chain reaction (RCR) 780 precursor ion analyzes 352 electrophoresis (2DDIGE) 986 RT and Taq DNA polymerase 762 prenols (PR) 614 two-dimensional-gel-based schematic of 757 preparative immunoprecipitation 81–82 proteomics 982 special techniques 766 preparative techniques 263 peptide fragments, analysis asymmetric PCR 767 electroelution from gels 263–264 of 985–986 cycle sequencing 768 isoelectric focusing 265 proteins, imaging/ degenerate primers, use of 767 between isoelectric membranes, quantification 983–985 homogeneous detection principle of 265 proteins separation 982–983 procedures 768–769 preparative IEF between isoelectric sample preparation 982 multiplex PCR 767–768 membranes 265–266 protein co-compartmentalization nested PCR 766–767 preparative zone electrophoresis 264 machine 1058 quantitative amplification preparative zone electrophoresis 264 protein complexes 530 procedures 769 pressure perturbation calorimetry protein crosslinking 121 in situ PCR 769 (PPC) 61 protein crystallization using the hanging in vitro mutagenesis 768 primers 819 drop method 532 strand displacement amplification extension assay, principle of 902 Protein Data Bank (PDB) 543 (SDA) 777 oligo(dT) primers 760 protein degradation 978 temperature/time profile of 758 for RT-PCR 762 protein determination 23 typical course 764 secondary structures of 760 method for 24 vectorette PCR 769 types of 759 staining methods for 26 polymerization 251 principal component analysis protein–DNA interactions 951 poly(methyl methacrylate) (PCA) 506–508, 1031 protein dynamics, determination (PMMA) 277, 680 approach of 506 of 463–464 polymorphic markers 927, 931 factorial map 508 protein equivalent of a genome 977 polymorphic sequence tagged sites independent structures 507 protein expression 978 927 mathematical procedure 507 protein folding/misfolding 464 Polyoma/SV40 nucleic acids 675 motivation for 508 protein fragmentation 990, 992, 993 polypeptide 147 of prealigned projections of the protein protein functional groups, chemical poly(vinylidene fluoride) (PVDF) 16, complex 508 modification of 108–116 652 real EM data 508 acylation 109–110 membrane 984 real EM images, number of amidination 110 membranes 273 pixels 507 arginine residues 113 polyvinylpyrrolidone (PVP) 14, 701 representation of two-pixel images in caged compounds 111 pore size 251, 255 coordinate systems 507 cysteine residues 112 porosity 288 sensitivity of 508 glutamate and aspartate gradient gels 254–255 product ion analysis 352 residues 112–113 positional candidate gene approach 939 prompt and metastable decay histidine residues 116–117 positional cloning 938 (ISD, PSD) 358–360 lysine residues 108 position-specific scoring matrix spectrum of angiotensin 372 methionine residues 114–115 (PSSM) 883 Prosite Motif PS00029 882 reaction with isothiocyanate 111 post-translational modification prosthetic groups 23 reductive alkylation 110–111 (PTM) 314, 315, 369, 645, 647, protease 588 tryptophan residues 114 648, 659, 998 protease inhibitors 8 tyrosine residues 113–114 1104 Index protein functions protein-protein interactions (PPIs) 381, proteolytic enzymes 207–208 biologically active molecules for 555, 1046 cleavage modulation 1044 protein purification 23, 219, 315 on membranes 208 switching off 1044 goal of 5 in SDS-polyacrylamide protein glycosylation 572, 579 proteins gels 208–209 analysis of 581 chemical modification 107 in solution 208 protein imaging 1068 complexity and individuality of 23 strategy 208 protein interactions 1036 complex structures, three-dimensional proteome analysis 108, 610–611, 977 protein–ligand interactions 299 reconstruction of 509 based diagnostics 956 protein localization 6 denaturation of 209 coverage 1012 protein mass spectrometry 987 alkylation of cysteine residues 210 general aspects 977 protein microarray applications, cleavage of disulfide bonds 209 protein based quantitative analysis (see schematic representation 1037 cysteine residues, chemical protein based quantitative protein microarrays 1037 modification of 210 proteome analysis) protein–nucleic acid complexes disulfide bonds and ProteomeXchange 1010 by gel electrophoretic methods 836 alkylation 209–210 proteomic databases 611 molecular beacons 853 2D gel 984 sample preparation 980–982 protein–nucleic acids interactions 831 immunogenicity of 70 SDS gel electrophoresis 977 dissociation constants, determination localization of 1033 starting conditions/project of 839–840 peptides, separation methods of 4 planning 979–980 DNA footprint analysis 841 properties of 3 prozone effect 72 chemical nucleases 849–850 size 3 protospacer adjacent motif (PAM) 974 chemical reagents for splicing, conditional 1054–1055 PTEN knockout 1010 modification 846–848 staining 983 pulsed electron double resonance genome-wide 850–851 ProteinScape 1019 (PELDOR) 478 hydrolysis methods 844–845 protein structure, determination 457, pulsed EPR experiments 473 interference conditions 848–849 462 basics 474 labeling 843 high molecular weight systems and electron nuclear double resonance primer extension reaction 843–844 membrane protein (ENDOR) 477–478 DNA–protein complex dynamics, structure and dynamics of 465–466 electron spin echo envelope modulation analysis of 840–841 in-cell NMR spectroscopy 466 (ESEEM) 475–476 filter binding 836 intrinsically disordered hyperfine sublevel correlation experiment gel electrophoresis, background to proteins 464–465 (HYSCORE) 476–477 retardation 836–838 NMR spectroscopy 462–463 pulsed electron double resonance genetic methods NOE signal intensity and respective (PELDOR) 478 aptamers/Selex procedure 869 proton distance, relationship relaxation 474 directed mutations, within binding between 457 spin echoes 474–475 domains 870 protein dynamics, pulsed-field gel electrophoresis tri-hybrid method 868–869 determination 463–464 (PFGE) 698, 934 physical analysis methods protein folding and misfolding 464 pulsed laser beam 1064 fluorescence correlation protein–ligand complexes pulsed liquid sequencer 321 spectroscopy (FCS) 856 thermodynamics and kinetics pure protein solutions 24 fluorescence methods 851 of 464 purification techniques 4, 6 fluorescence resonance energy residual dipolar couplings Pwo DNA polymerases 759 transfer (FRET) 852–853 (RDCs) 458 pyridoxal-5´-phosphate 111 fluorophores procedures 851–852 secondary structure, determination pyrimidines, 5,6-double bonds of 846 labeling procedures 851–852 of 458–461 pyrophosphorolysis 793 molecular beacons 853 structure calculation, constraints pyrosequencing 807, 820 optical tweezers 855 for 457–458 scanning force microscopy tertiary structure, calculation Q – – (SFM) 854 855 of 461 462 quadrupole analyzer 345–348 surface plasmon resonance distance geometry method 461 quadrupole-TOF (Q-TOF) 354 – (SPR) 853 854 root-mean-square deviation analyzers 377 – RNA interactions (see RNA protein (RMSD) 462 quantitative determination, by staining interactions) simulated annealing 461 tests 25–26 proteinogenic amino acids 876 protein toponome, concept quantitative immunoprecipitation 73 fi – protein pro les of 1058 1059 quantitative structure–retention fi disease speci c 100-dimensional protein transfer 88 relationships (QSRRs) 241 discovery 1062 proteoforms 981 quantitative trait loci (QTLs) 940 Index 1105 quantum dots relative centrifugal force (RCF) 12 ribosomal RNA 904 as fluorescence labels 159–160 relative molecular mass 4 ribosomes 530 labeling with 192 relative resolution map (RRM) 236 transfer-RNA (tRNA) molecules 947 quasi-isothermal conditions 48 Renilla luciferase 749 ribozymes 479, 959, 965, 967 reporter gene assay 1047 catalytic cycle of 966 R reporter gene vector discovery/classification 965–966 cis-acting sequences structure of 966 RabGDP-dissociation inhibitor principle of mapping 912 use of 966–967 (RabGDI) 1053 resolution 185 RNA Rab-GTPase Ypt1 1052 capacity 342 aptamers, SELEX-strategy 972 radioactive detection methods 652 optimization 224 characteristic structural elements 858 radioactive labeling 31–33, 109, 733 power of isoelectric focusing 260 DNA, helical grooves between 857 of DNA sequencing 797 range, different methods for 529 mimic fragments 765 exchange positions 735 resonance assignment 452 molecules radioactive methods 651 heteronuclear 3D spectra, analysis gel electrophoresis, two- radioactive nucleic acids of 454 dimensional 701 direct autoradiography 739 selective amino acid labeling 454 splicing, analyzing 947 fluid emulsions sequential assignment RNA-binding motifs, for cytological/cytogenetic in situ of homonuclear spectra 452–453 characteristic 859–860 applications 739 from triple-resonance RNA-binding proteins 859 fluorography 739 spectra 454–457 RNA-dependent DNA polymerases 761 indirect autoradiography, with resonance methods 134 RNA-DNA hybrid molecules 896, 901 intensifier screens 739 resonance Raman RNA/DNA sequences pre-exposed X-ray film, for direct spectroscopy 173–174 cloning/PCR amplification 788 autoradiography/ restricted access materials (RAMs) 238 electrophoresis 788 fluorography 739 sorbents materials 229 error correction/sequence data radioimmunoassays (RIA) 31, 82–83 restriction analysis, methylation sensitive analysis 789 radioisotopes 739 enzymes/insensitive nucleic acid, isolation/purification radiolabeling 32 isoschizomers 824 of 788 Raman spectroscopy 171, 1026 restriction enzymes 682 purification 788 principles 171–172 cleavage 685 reconstitution 788–789 Raman experiments 172–173 restriction fragment length RNA electrophoresis 697 Raster image correlation spectroscopy polymorphisms (RFLPs) 681, RNA-induced silencing complex (RICS) 203 927, 928 (RISC) 967 Rayleigh–Gans–Debye scattering 141 retention 228 RNA interference (RNAi) 959, Rayleigh scattering 142 factor 221, 223, 235 967–971, 968, 969 Rd1-SP-adapter ligation 812 times 220, 221 basics of 967–968 Reactome 1024 volume 221 mediated by expression reagents for introducing reveal bacteria 671 vectors 968–969 fluorophores 117 reversed-phase chromatography uses of 969–970 real-time RT-PCR (RT-qPCR) 904, 905 (RPC) 16–17, 240 RNA isolation 679 quantification of gene expression 904 reversed-phase HPLC 21 RNAi-triggered cellular processes 968 REases 683 reverse immunoagglutination 72 RNAi-triggered knockdown 955 type-II restriction enzymes 684 reverse phase protein microarrays 1038 RNA-modifying reagents recombinant antibody 100 reverse transcriptases (RTases) 761, reagents for 864 recombinant DNA technologies 120 896, 901 structural formula 864 recombinant glycoproteins 571 RNA-dependent DNA polymerase 901 RNA polymerases 899, 905, 908 recombinant proteins 7 Rev protein 859 analysis of binding 855 recombinant retroviruses 395 rhodamine-tagged RNApolymerases transcribe 908 recombinaseA(recA-), strains deficient phosphoramidites 851 RNA-protein complexes 866 of 671 Rhodobacter capsulatus 157 analysis of 860 recombination fraction 929 rhodopsins 149, 176 chemical modification 863–866 red-green-blue (RGB) images 1065 ribonuclease-protection assay chemical crosslinking 866–867 reductive alkylation 110–111 (RPA) 898–901, 900 CMCT (1-Cyclohexyl-3-(2- RefSeq 890 ribonucleases (RNases) 959 morpholinoethyl)carbodiimide regular expression functions 882 ribonucleoprotein (RNP) 856 metho-p-toluolsulfonate) regularly arrayed macromolecular domain 859 864–865 complexes, three-dimensional ribose by fluorine customary RNases 862–863 ´ reconstruction 511–512 2 position of 973 diethyl pyrocarbonate (DEPC) 864 1106 Index

RNA-protein complexes (continued ) green fluorescent protein isolated cells 195–196 dimethyl sulfate (DMS) 864 (GFP) 915 paraffin samples 196 ENU (ethylnitrosourea) 865 luciferase assay 915 proteome analysis 22 Fe-BABE transcripts from transfected tissue biopsies 196 (Fe 1-(p-bromoacetamidobenzyl) cells 915 Sanger method 785, 786, 805 ethylenediaminetetraacetic reverse transcription polymerase chain Sanger’s reagent 313 acid) 865 reaction (RT-PCR) 904–905 scanning calorimetry 47 hydroxyl radicals 865 ribonuclease-protection assay scanning cysteine accessibility method in-line probing 865 (RPA) 898–901 (SCAM) 120 kethoxal (α-keto-β-ethoxy- in vitro transcription, in cell-free scanning electron microscope butyraldehyde) 863–864 extracts 907 (SEM) 486 labeling methods 861–862 additional techniques to scanning force microscopy limited enzymatic hydrolyses 861 analyze 911 (SFM) 854–855 nuclease S1 863 G-less cassette 908–909 scanning ion conductance microscope photoreactive nucleotides, run-off transcription (SICM) 519 incorporation of 867 assays 909–910 scanning microprobe MALDI primer extension analysis 862 template DNA/detection 908 (SMALDI) 1065, 1068 RNase CL3 863 transcription assay 907–908 mouse spinal cord 1070 RNase CVE 863 transcription-competent cell extracts/ mouse urinary bladder tissue RNase T1 862 protein fractions, generation section 1069 RNase T2 863 of 908 scanning near-field infrared microscopy RNase U2 862 in vivo analysis (SNIM) 486 selective 2´-hydroxyl acylation nascent RNA labeling with 5- scanning near-field optical microscopy analyzed by primer extension fluoro-uridine (FUrd) 906–907 (SNOM) 486, 519 (SHAPE) analysis nuclear-run-on assay 905–906 scanning probe microscopies 865–866 ROBETTA server 893 (SPM) 486 transcription start sites (TSS), robot-assisted microdispension scanning tunneling microscope genome-wide identification system 610 (STM) 486 of 867–868 robotic system 50 scattering artefacts, correction for 142 RNA-protein interactions 857 rocket immunoelectrophoresis 80–81 scFv-Antibodies 100 dynamics of 857–859 Rohrer, Heinrich 486 Schiff base 111, 149 functional diversity 856–857 root-mean-square deviation Schlack–Kumpf degradation 326 secondary structure parameters/unusual (RMSD) 462 Schleiden, Matthias J. 182 base pairs 857 Rosetta program 893 Schwann, Theodor 182 RNA–protein recognition rotors, for centrifugation 11 secondary electron multiplier (SEV) tri-hybrid system for the in vivo Rous sarcoma virus (RSV) 960 356 characterization of 868 Royal Society of London 181 channel electron multiplier 356 RNA quantification, by Northern RP-LC-ESI-MS proteolytic digest of constructions with discrete blot 903 protein 377 dynodes 356 RNA-RNA hybrid molecules 899 RT-PCR techniques 904 microchannel plates 356 RNase H activity 777, 961 schematic portrayal 761 secondary ion mass spectrometry RNase inhibitors 676 run-off transcription reaction 910 (SIMS) 1064 RNAse protection assays 761 Ruska, Ernst 486 ion imaging mode 1064 RNASeq 813, 946 secretory proteins 886 RNases, specificities of 860, 861 S sedimentation coefficient 12, 412 RNA transcripts sedimentation–diffusion dot- and slot-blot analysis 903–904 Saccharomyces cerevisiae 785, 938, equilibrium 415 Northern blot 902–903 942, 947, 1009, 1037 selected or multiple reaction monitoring nuclease S1 analysis 896, 897 salts removal 15 (S/MRM) 1000 quantitative 896 sample concentration 295 mass spectrometer 1004 reaction principle 896 sample preparation 195, 249, 332–335 quantification 1002 ´ ´ ´ RNA 5 /3 ends 897–898 creation of paraffin slices 197 selective 2 -hydroxyl acylation overview 895–896 embedding 196–197 analyzed by primer extension primer extension assay 901–902 fixation 196 (SHAPE) reporter gene expression 914 frozen slices 197 reagents 866 β-galactosidase (β-Gal) creation of frozen slices (rapid selectivity 221, 239 915 slices) 197 selenium 25 chloramphenicol acetyltransferase embedding 197 Selex procedure 869 (CAT) assay 914 sealing 197 separated proteins zones 251 Index 1107

detection and quantification 251–252 simplified coordinate system software tools 984 imaging 252–253 visualization of experimental solid phase sequencer 320 separation efficiency 4 data 1031 soluble macromolecules 529 sequence composition 882 single beam photometer 142 somatic cells 925 sequence data analysis 875 single crystals, of amylase C 533 spatial frequency 499 abstraction for biomolecules 876 single ion monitoring (SIM) scan spectral absorption coefficients 25 and bioinformatics 875–876 mode 348 spectral unmixing 204 homology based methods single isomorphous replacement spectroscopic methods 28–29 basic local alignment search tool (SIR) 538–540 fluorescence method 31 (BLAST) 890 single molecule spectroscopy 174–175 measurements in UV range 29–30 identity 887–888 single nucleotide polymorphisms protein determination 29 optimal sequence (SNPs) 927, 940 spectral range 134 alignment 888–890 identification of 948 spectroscopy. see atomic force PSI-BLAST algorithm 890–891 microarray-based 948 microscope (AFM) similarity 887–888 polymerase extension reaction 949 sphingolipids (SP) 614 threshold 891 SNV analysis 940 sphingomyelins 641 internet databases/services 877 single nucleotide variants (SNVs) 927, spin label 119 data contents/file format 879–880 940 reagents for 120 nucleotide sequence management, in single particle splice acceptor (SA) 938 laboratory 881 analysis 516 splice donor (SD) sites 938 sequence retrieval, from public three-dimensional splitting scheme, for unpaired databases 878–879 reconstruction 509–511 electron 469 multiple alignment/consensus single reaction monitoring (SRM) spot patterns, phosphorylation status of sequences 891–892 and MRM-analysis 352–353 proteins 652 procedures 893 SRMAtlas project 1008 (S)SIM ((saturated) structured structure prediction 892–893 SRMCollider 1005, 1009 illumination microscopy) 201 sequence logo 883, 886 single-strand conformational stable isotope labeling 1014 sequence patterns 882–886 polymorphism (SSCP) 695, by amino acids in cell culture coding regions, identification 775–776 (SILAC) 1015 of 885–886 single-stranded binding (SSB) 742 bottom-up proteomics protein localization 886 single-stranded DNA(ssDNA) 775 isobaric labeling 1020–1021 transcription factor binding single-stranded RNA probes 731 non-isobaric labeling 1019 sites 884–885 singlet oxygen generator (SOG) 409 18O labeling 1019 sequence tagged sites (STSs) 776, 927 singlet oxygen sensitizer 409 reagents 1019–1020 physical markers 927 singlet oxygen triplet energy transfer peptide standards 1006 screening 936 (STET) 409 in quantitative proteomics 1013 serial femtosecond crystallography size exclusion chromatography top-down proteomics 1013 (SFX) 550 (SEC) 240 chemical stable isotope serum amyloid A (SAA) 96 Skyline software 1008 labeling 1016 short hairpin (SH) slot-blotting 707 isotope-coded affinity tag method groups modification 112 small angle X-ray scattering (ICAT) 1016–1018 with p-chloromercury benzoate, (SAXS) 529, 543–544 isotope coded protein label analysis 112 data analysis 547 (ICPL) 1018–1019 short-hairpin RNA (shRNA) 953, 968 de novo structure metabolic labeling 1014–1015 vector expression 969 determination 547–548 stable isotope labeling by amino shotgun method 786 method developments 549 acids in cell culture sickle cell anemia 688 machine setup 544–545 (SILAC) 1015–1016 signal amplification 751 theory 545–547 staining methods branch structures 752 SMART server domain 884 characteristics 983 coupled signal cascades 753 snake venom phosphodiesterase 827 fluorescent dyes 702 cyclic ADH 753 sodium bisulfite catalyzes 819 DNA geometry, influence 703 enzyme catalysis 752–753 sodium dodecyl sulfate (SDS) ethidium bromide (3,8-diamino-5- signal-to-noise ratio 144, 504–506 electrophoresis, for low molecular ethyl-6-phenylphenanthridinium averaging single particles 505–506 weight peptides 258 bromide) 702–703 correlation averaging 504–505 PAGE, analytical fluorescent dyes 703–704 filter approaches for crystal data 504 ultracentrifugation 409 silver staining 704 filtering in Fourier space 504 polyacrylamide gel standard free energy 61 silica coated magnetic beads 679 electrophoresis 257–258 Staphylococcus aureus 768 silver staining 251, 252, 704 sodium saline concentration (SSC) 723 stationary phase 221, 222, 618 1108 Index stereoisomers 572 limitations of 397 thermosensors 49 sterols (ST) 614 mass spectrometric analysis 397 thermostable DNA polymerases 795 stimulated emission depletion purification 395–397 thin-layer chromatography (TLC) 561, (STED) 201 retroviral transduction 395 618, 696, 911, 914 microscopy 486 tagging and purification of protein thiols 126 stochastic optical reconstruction complexes 394 three-dimensional electron microscopy (STORM) 201 tandem mass spectrometry microscopy 508 Stokes radius 254 phosphorylated and acetylated amino three-dimensional NMR strand displacement amplification acids, localization of 654–659 spectroscopy 449 (SDA) 779 tandem-TOF (TOF-TOF) 353–354 HCCH-TOCSY and HCCH-COSY Streptomyces avidinii 746 Taq DNA polymerases 730, 736, 758, 759 experiments 449–450 strong cation exchange (SCX) TaqMan® 756, 759 HNCA experiment 451–452 chromatography 649, 650 PCR 765 NOESY-HSQC and TOCSY-HSQC structural proteins 254 probes 725, 905 experiments 449 substance libraries, source of 1045 target amplification 751 nomenclature of triple-resonance N-succinimidyl-3 [4-hydroxyphenyl] elongation 751 experiments 451 propionate 109 transcription 751 triple-resonance D-sugars series 572 in vivo amplification 751 experiments 450–451 composition starting from targeted proteomics 1004 threonine 648 D-glyceraldehyde 572 target protein, temporal control 1051 thymine/cytosine-specific fission L-sugars series 574 TATA binding protein (TBP) 835 reaction 803 sulfonyl chloride 116 TAT protein 481 thyroid stimulating hormone (TSH) 1035 sulfuric acid 25 t-butyl trifluoroacetate 559 time-of-flight analysis 345 surface plasmon fluorescence T-cells 96 time-resolved fluorescence (TRF) 749 spectroscopy (SPFS) 402 T-Coffee 892 time-resolved spectroscopy 144–147 surface plasmon resonance T7 DNA polymerase-catalyzed TiO2 coated magnetic particles 649 (SPR) 853–854 sequencing reaction 791, 792 titer 73 Biacore technique T-effector cells (TE) 105 titration curve 60 measurement of antibody binding to temperature gradient gel electrophoresis analysis 263 antigen using 94 (TGGE) 701, 840, 841 TMHMM 886 measuring device, principle of 854 terminator exonuclease (TEX) 868 TOPCONS 886 spectroscopy 400–402 test strips 420 toponome surface tension 227, 231 test system set-up 41–42 cell/tissue, molecular networks Svedberg equation 412, 415 controls 45 of 1058 Svedberg, Theodor 244 detection system 42 defined 1057 Svensson–Rilbe’s concept of “natural” pH value 43 imaging cycler microscopy (ICM) pH gradients 244 physiological function, analysis of 42 antibody based 1057 SWATHAtlas 1010 selecting buffer substance map, structural representation 1058 SWATH-MS 1011 and ionic strength 43–44 reading technology, fundament SYBR Green 728, 905 selecting substrates 42 of 1059–1063 synthetic peptides substrate concentration 44 theory, schematic illustration 1060 characterization/identity of 562–564 temperature 44 toponomics analysis 1057 peptide nucleic acids (PNAs) 732 time dependence 43 biological systems 1057 purity of 561–562 TET enzymes 817 co-compartmentalization and structure, characterization tetrabutylammonium bromide topological association of 564–567 (TBAB) 711 rules 1058 systematic evolution of ligands by Tetrahymena thermophila 965, 1068 total internal reflection fluorescence exponential enrichment N,N,N´,N´-tetramethylethylenediamine microscopy (TIRFM) 160, 202 (SELEX) 972, 973 (TEMED) 292 total ion current (TIC) systems biology, hypotheses/knowledge tetramethylrhodamine (TAMRA) 749 chromatogram 713 circular system 1030 tetramethylrhodamine T7 phage DNA polymerases 845 454-system workflow 808 isothiocyanate 116 T4-polynucleotide kinase (PNK) 901 tet-repressor (TetR) 1051 phosphorylates 809 T therapeutic glycoproteins 571 transcriptional profiling analysis 946 thermal degradation 25 transcription factors 5 tandem affinity purification thermal denaturation 61 transcription-mediated amplification (TAP) 394–395, 395–397 DNA species 720 (TMA) 751, 755 advantages 395 thermal shift assay 531 transcription start site (TSS) 907, 909 limitations 397 thermograms 49, 51 transfer-RNA (tRNA) molecules 947 Index 1109 transglutaminase 119 homonuclear 2D NMR experiments V translocation 920 of proteins 446 transmission electron microscope HSQC – heteronuclear single quantum Van-Deemter-Knox plots 222, 223 (TEM) 487–488 coherence 447–449 van’t Hoff equation 61 approaches to preparation 488 NOESY spectrum 445–446 van’t Hoff transition enthalpy 52 labeling of proteins 492 TOCSY spectrum 445 V-genes 101 metal coating by two-hybrid system 381 vibrational modes 169 evaporation 491–492 AD fusion proteins and cDNA of peptide bond 169 native samples in ice 488–490 libraries 385–386 vibration cell mills 8 negative staining 490 bacterial two-hybrid system (BACTH virtual image 185 beam path 487 or B2H) 389, 391 viscosity 247 images of vitrified lipid vesicles 498 bait proteins, used in Y2H screen 385 vitamin A 638 instrumentation 487–488 biochemical and functional analysis of vitamin D 638–639 object holder, grids, and plunger for interactions 393 vitamin E 640 biological cryosamples 488 biological relevance 394 vitamin H 746 phase contrast 495 computational analysis of interaction vitamin K 640 resolution 492–493 data 394 von Helmholtz, Hermann 493 transmitted fluorescence independent verification 393 microscope 188 localization 394 W transposon-mediated DNA protein domains and motifs 394 sequencing 788 carrying out Y2H screen 386–391 Watson–Crick base pairing 832, 857, 1,4,7-triazacyclononane 233 construction of bait and prey 861, 862, 962, 971 tributylphosphine 209 proteins 382–385 Watson–Crick hydrogen bonding 961 trichloroacetic acid (TCA) 10 elements of 382 wavelength 538 precipitations 738 modifications 392 interference of light 187 triethylamine (TEA) 711 and extensions of wavenumbers 133 triethylammonium acetate (TEAA) 711 technology 391–393 wave-particle dualism 133 trifluoroacetates 561 principle of 381–382 WebMOTIF 884 trifluoroacetic acid (TFA) 228, 333, two-state model, curves 52 Web server based modeling 893 558, 560 tyrosine 33, 225, 648 Western blot analysis 88, 89, 252, trifluoromethyl 652 diazirinobenzoyllysine 129 U autoradiograph-based after 1-trifluoromethyl-1- 2D-PAGE 652 phenyldiazirine 126 ubiquitin whole protein molecules 1038 trigonometric operation 501 monoisotopic and average m/z Wiki pathways 1024 triple-quadrupole (triple-quad) 351–352 values 990 Wilkins, Marc 977 triplex forming oligonucleotides proteoforms, theoretical trypsin Wolff-rearrangement 126 (TFOs) 961 cleavage sites 994 tripropylamine (TPA) 742 top-down mass spectrum 988 X tris acetate (TAE) 692 ultrafiltration 16, 17 tris borate (TBE) 692 ultrahigh pressure liquid chromatography X-chromosome 951 tris-buffers 863 (UHPLC) 302 inactivation 817 tris-(carboxy methyl)ethylene-diamine 233 ultraviolet (UV) 133 Xenopus laevis 466 Triticum aestivum 785 HPLC chromatogram 717 XML/JSON 879 Trp1 gene 382 spectroscopy 220, 224 Xq28, candidate genes 932 trypsin 588, 985, 1019 UV-diode array detection x-ray crystallography 107, 120, 131, tryptophan 225, 303 (UV-DAD) 224 314, 486, 529, 530, 567 Tth DNA polymerases 759 VIS/NIR spectroscopy 146 crystallization 531–538 tumor tissue, differential methylation chlorophylls 152–153 model building and structure levels 826 chromoproteins 147–147 refinement 542–543 T values 258 cytochromes 149–151 phase problem 538–542 twin supercoiled domain model 834 metalloproteins 151–152 x-ray diffraction two-dimensional NMR principles 146–147 basics of 536 spectroscopy 443 rhodopsins 148–149 image of crystal 537 COSY spectrum 445 uniaxial orientation samples 177 x-ray free electron LASER (XFEL) 549 2D experiment, general scheme UniProt 879 detection and analysis 550 – of 443 445 unmethylated bases, chemical machine setup and theory 549–550 heteronuclear NMR modifications 818 principle 549 – experiments 446 447 Ustilago sphaerogena 862 samples 550 1110 Index

Y Z zone band broadening 223 zone electrophoresis 253–254, yeast artificial chromosome (YAC) Z-DNA sequences 956 278 libraries 935 Zeeman splitting 468 zwitterionic detergents yeast Mbp1 transcription factors 879 Zernike, Frits 182, 485 20 Y2H interactions 399 zero mode waveguide (ZMW) 814 zwitterionic/non-ionic detergents Y2H screen 386–391 zinc-finger proteins 835 982 Y2H system 381 zirconium oxide 649 zymogens 207 limits 390 zonal centrifugation 13–14 activation 208