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Selected Abbreviations Used in This Manual APPENDIX 1A

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Selected Abbreviations Used in This Manual APPENDIX 1A STANDARD NOMENCLATURE, DATA, APPENDIX 1 AND ABBREVIATIONS Selected Abbreviations Used in This Manual APPENDIX 1A A adenine; adenosine cAMP adenosine 3,5-cyclic- Ac acetyl monophosphate ACE acetoxyethoxy; acetoxyethyl CD circular dichroism ADA adenosine deaminase CDI 1,1-carbonyldiimidazole ADP adenosine 5-diphosphate cDNA complementary deoxyribonucleic ADTT 3-amino-1,2,4-dithiazoline- acid 5-thione CDP cytidine 5-diphosphate AEEA 2-aminoethoxy-2-ethoxy acetic CE capillary electrophoresis; cyanoethyl ex acid C p excess heat capacity AFM atomic force microscopy CHA α-cyano-4-hydroxycinnamic acid AMP adenosine 5-monophosphate Ci curie AMV-RT avian myoblastosis virus reverse CID collision-induced dissociation transcriptase CMCT 1-cyclohexyl-3-(2- ANA arabinonucleic acid morpholinoethyl)carbodiimide AP alkaline phosphatase metho-p-toluene sulfonate 3-APA 3-aminopicolinic acid CMP cytidine 5-monophosphate APS ammonium persulfate COSY correlation spectroscopy Ar aryl CPG controlled-pore glass ASY average stepwise yield CPI cyclopropapyrroloindole ATP adenosine 5-triphosphate CPK Corey-Pauling-Koltun (molecular ATPase adenosine triphosphatase models) ATT 6-aza-2-thiothymine cpm counts per minute AU absorbance units CPMB Current Protocols in Molecular AUFS absorbance units full scale Biology B base (nucleobase) CSA D-10-camphorsulfonic acid BAP bacterial alkaline phosphatase CSO (1S)-(+)(10-camphorsulfonyl)- BCIP 5-bromo-4-chloro-3-indolyl oxaziridine phosphate CSP calf spleen phosphodiesterase BDT 3H-1,2-benzodithiol- CTAB cetyltrimethylammonium 3-one-1,1-dioxide Ctmp 1-(2-chloro-4-methylphenyl)-4- BHOC benzhydryloxycarbonyl methoxypiperidin-4-yl BIT benzimidazolium triflate CTP cytidine 5-triphosphate BMPM 1,1-bis(4-methoxyphenyl)-1- dA deoxyadenosine pyrenylmethyl Dabcyl 4-[4-(dimethylamino)phenyl]- Bn benzyl azobenzoic acid bNA branched nucleic acid dADP deoxyadenosine diphosphate BOC tert-butyloxycarbonyl dAMP deoxyadenosine monophosphate BOMP 2-(benzotriazol-1-yloxy)- DAP diaminopurine 1,1-dimethyl-2-(pyrrolidin-1-yl)-1,3,2- DAST (diethylamino)sulfur trifluoride diazaphospholidinium dATP deoxyadenosine triphosphate hexafluorophosphate DBMB 2-(dibromomethyl)benzoyl BSA bovine serum albumin; DBPNC 2,6-dibromo-4-benzoquinone- bis(trimethylsilyl)acetamide N-chloroimine Bu butyl DBU 1,8-diazabicyclo[3.4.0]undecene- Bz benzoyl 7-ene C cytidine; cytosine dC deoxycytosine Abbreviations and Useful Data Current Protocols in Nucleic Acid Chemistry (2004) A.1A.1-A.1A.5 A.1A.1 Copyright C 2004 by John Wiley & Sons, Inc. Supplement 18 DCA dichloroacetic acid DSC differential scanning calorimetry; DCC 1,3-dicyclohexylcarbodiimide disuccinimidyl carbonate dCDP deoxycytosine diphosphate dsDNA double-stranded DNA DCHA dicyclohexylamine dT deoxythymidine DCI 4,5-dicyanoimidazole dTDP deoxythymidine diphosphate DCM dichloromethane DTE dithioerythritol dCMP deoxycytosine monophosphate dTMP deoxythymidine monophosphate dCTP deoxycytosine triphosphate DTMT 2-(isopropylthiomethoxymethyl)- DDQ 2,3-dichloro-5,6- benzoyl dicyano-1,4-benzoquinone DTr 4-decyloxytrityl (C10Tr) DEAD diethyl azodicarboxylate DTT dithiothreitol DEC 1-(3-dimethylaminopropyl)-3- dTTP deoxythymidine triphosphate ethylcarbodiimide dUTP deoxyuridine triphosphate DEMA diethoxymethyl acetate DVB divinylbenzene DEPC diethylpyrocarbonate DX double cross-over dG deoxyguanosine EC Enzyme Commission DG distance geometry EDC 1-[3-(dimethylamino)propyl]-3- dGDP deoxyguanosine diphosphate ethylcarbodiimide dGMP deoxyguanosine monophosphate EDITH 3-ethoxy-1,2,4-dithiazoline-5-one dGTP deoxyguanosine triphosphate EDTA ethylenediaminetetraacetic acid DHB dihydroxybenzoic acid EI electron impact (mass spectrometry) DHPC dihexanoylphosphatidylcholine ENU ethylnitrosourea dI deoxyinosine ESI electrospray ionization (mass DIAD diisopropyl azodicarboxylate spectrometry) DIP 4,7-diphenyl-1,10-phenanthroline Et ethyl DIPEA or DIEA diisopropylethylamine FAB fast atom bombardment (mass DMAEDE 2-O-2-[2-(N,N- spectrometry) dimethylamino)ethyloxy]ethyl FAM 5-carboxyfluorescein DMAoE 2-O-[2-(N,N- FDA (United States) Food and Drug dimethylaminooxy)ethyl Administration DMAP 4-dimethylaminopyridine FFT fast Fourier transform DMBOC 3,5- dimethoxybenzoin- FLB formamide loading buffer oxycarbonyl Fm fluorenylmethyl DMEM Dulbecco’s minimal essential FMN flavin mononucleotide medium (or Dulbecco’s modified Eagle’s FMOC 9-fluorenylmethoxycarbonyl medium) For formyl Dmf dimethylaminomethylene FPLC fast protein liquid chromatography DMF dimethylformamide Fpmp 1-(2-fluorophenyl)- DMS dimethyl suberimidate; dimethyl 4-methoxypiperidin-4-yl sulfate FRET fluorescence resonance energy DMSO dimethylsulfoxide transfer DMPC dimyristoylphosphatidylcholine FTICR Fourier-transform ion-cyclotron DMTr 4,4-dimethoxytrityl resonance (mass spectrometry) DNA deoxyribonucleic acid G guanine; guanosine DNBSB 2-(2,4-dinitrophenylsulfenyl- GDP guanosine 5-diphosphate oxymethyl)benzoyl GMP guanosine 5-monophosphate dNDP deoxynucleoside diphosphate GTP guanosine 5-triphosphate dNMP deoxynucleoside monophosphate HATU O-(7-azabenzotriazol-1-yl)-1,1,3,3- DNP 2,4-dinitrophenyl tetramethyluronium hexafluorophosphate DNPEOC 2-(2,4-dinitrophenyl)- HBTU 2-(1H-benzotriazol-1-yl)-1,1,3,3- ethoxycarbonyl tetramethyluronium hexafluorophosphate dNTP deoxynucleoside triphosphate HEC hydroxyethylcellulose DODC 3,3-diethyloxadicarbocyanine HEG hexa(ethylene glycol) DPC diphenylcarbamoyl HEPES N-(2-hydroxyethyl)piperazine-N- Selected DPI 1,2-dihydro-3H-pyrrolo[3,2-e]indole- (2-ethanesulfonic acid) Abbreviations carboxylate HEPPSO N-(2-hydroxyethyl)piperazine- Used in This dpm disintegrations per minute N-(2-hydroxypropanesulfonic acid) Manual A.1A.2 Supplement 18 Current Protocols in Nucleic Acid Chemistry HMDS hexamethyldisilazane MeNPOC methylnitropiperonyloxy- HMFS N-[9-(hydroxymethyl)-2- carbonyl fluorenyl]succinamic acid Me-P methylphosphonate HMQC heteronuclear multiple quantum MES 2-(N-morpholino)ethanesulfonic acid coherence MICS methylisocarbostyril HNA hexitol nucleic acid MM molecular mechanical HOAt 7-aza-1-hydroxybenzotriazole MMI methylenemethylimino HOBt or HOBT 1-hydroxybenzotriazole MMTr 4-monomethoxytrityl 3-HPA 3-hydroxypicolinic acid MOPS 3-(N-morpholino)propane sulfonic HPLC high-performance liquid acid chromatography MOTr 4-methoxy-4-octyloxytrityl HPMC hydroxypropylmethylcellulose MOX 9-(p-anisyl)xanthen-9-yl HQDA hydroquinone-O,O-diacetic acid MPC N-methylpyrrolecarboxamide HRMS high-resolution mass spectrometry MPLC medium-pressure liquid HSDIS hydroxystyryldiisopropylsilyl chromatography HSDMS hydroxystyryldimethylsilyl mRNA messenger ribonucleic acid HSQC heteronuclear single quantum MS mass spectrometry coherence MSNT 1-(mesitylene-2-sulfonyl)-3-nitro- HZ hydrazine 1,2,4-triazole I inosine MTHP 4-methoxytetrahydropyran-4-yl i-Bu isobutyl; isobutyryl MTMB 2-(methylthiomethoxymethyl) ICS isocarbostyril butyryl IEC ion-exchange chromatography MTMT 2-(methylthiomethoxymethyl) IMT imidazolium triflate benzoyl i-Pr isopropyl MTPI methyltriphenoxyphosphonium IR infrared iodide IRAA internal reference amino acid MWCO molecular weight cutoff ITC isothermal titration calorimetry NAB nucleic acid builder (computer IUB International Union of Biochemistry program) IUPAC International Union of Pure and NAIM nucleotide analog interference Applied Chemistry mapping JOE 6-carboxy-4,5-dichloro-2,7- NAIS nucleotide analog interference dimethoxyfluorescein suppression LCAA long-chain alkylamine NBOM 2-nitrobenzyloxymethyl LNA locked nucleic acid NBT 5-nitrobenzimidazolium triflate; LSIMS liquid secondary-ion mass nitroblue tetrazolium spectrometry n-Bu n-butyl L-TOF linear time-of-flight (mass NDB Nucleic Acid Database spectrometry) NDP nucleoside diphosphate MALDI matrix-assisted laser NDPK nucleoside diphosphate kinase desorption/ionization (mass spectrometry) NHS N-hydroxysuccinimide MAST [bis(2-methoxyethyl)amino]sulfur NMI N-methylimidazole trifluoride NMM N-methylmesoporphyrin MB minor groove binder NMP nucleoside monophosphate; MB-ODN minor groove binder– N-methylpyrrolidinone oligodeoxyribonucleotide conjugate NMR nuclear magnetic resonance MBHA p-methylbenzhydrylamine NOE nuclear Overhauser effect MC Monte Carlo NOESY nuclear Overhauser effect mCPBA meta-chloroperoxybenzoic acid spectroscopy (also 3-chloroperoxybenzoic acid) N-P phosphoramidate MD molecular dynamics NP1 nuclease P1 MDMP 1,5-dimethoxylcarbonyl-3- NPE 2-(4-nitrophenyl)ethyl methoxypentan-3-yl NPEOC 2-(4-nitrophenyl)ethoxycarbonyl Me methyl NPOC nitrophenyloxycarbonyl Abbreviations and Useful Data A.1A.3 Current Protocols in Nucleic Acid Chemistry Supplement 18 NPPOC 2-(2-nitrophenyl) PyAOP 7-aza-benzotriazol-1-yl- propoxycarbonyl oxytripyrrolidinophosphonium NRC Nuclear Regulatory Commission hexafluorophosphate nt nucleotide PyBOP 1H-benzotriazol-1-yl- NTP nucleoside triphosphate oxytripyrrolidinophosphonium ODN oligodeoxyribonucleotide hexafluorophosphate PA picolinic acid QM quantum mechanics or quantum Pacorpac phenoxyacetyl mechanical PACE phosphonoacetate QNAIM quantitative nucleotide analog PAGE polyacrylamide gel electrophoresis interference mapping PAL peptide amide linker (resin) R, R... alkyl groups PAM 4-hydroxymethylphenylamido- Rf retention factor (TLC) methyl (resin) RFP radiofrequency plasma PAPOC p-phenylazophenyloxycarbonyl RFLP restriction fragment length PAPS 3-phosphoadenosine- polymorphism 5-phosphosulfate rMD restrained molecular dynamics PASS product-anchored sequential RMSD root mean squared deviation synthesis RNA ribonucleic acid PBS phosphate-buffered saline RNAi
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