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LIST OF PARTICIPANTS TO THE NATO ADVANCED STUDY INSTITUTE ON" BIOPOLYMERS STRUCTURE AND DYNAMICS" - INTERNATIONAL SCHOOL OF PURE AND APPLIED BIOSTRUCURE 22 JUNE - 4 JULY 1986

F. ABOUL-ELA w. BURKART 315 Hildebrand Hall Biologie & Umwelt, Abt. 81/SU Dept. Chemistry Swiss Federal Inst Reactor Res University of California EIR BERKELEY, CA 94704 USA CH-5303 WURENLINGEN, Switzerland

P. ANDER F. CARATOZZOLO Seton Hall University DIBE Department of Chemistry Viale Francesco Causa, 13 SOUTH ORANGE, New Jersey 07079 USA 16145 GENOVA, Italy

H. BAGCI G. CHIRICO Dept. Medical Biology and Genetics Dipartimento di Fisica Medical Faculty Sezione Stati Aggregati University of Akdeniz Via Ce loria, 16 ANTALYA, Turkey 20133 MILANO Italy

R.L. BALDWIN M. DAUNE Department of Biochemistry IBMC - CNRS Stanford University Medical Center 15, rue Descartes STANFORD, CA 94305 USA 07004 STRASBOURG, France

J. BENBASAT G. DEMlREL Univ. British Columbia Dept. Chemistry Dept. Microbiology Middle East Technical University Vancouver B.L. ANKARA, Turkey CANADA V6TIW5

C. BENHAM A. DIASPRO University of Kentucky Chair of Biophysics Mathematics Dept. University of Genova College of Arts and Sciences Viale Benedetto XV, 2 Patterson Office Tower 16132 GENOVA, Italy LEXINGTON, Kentucky 40506-0027, USA

M. BERTOLOTTO M. DONADONI OMODEO Cattedra di Biofisica Via Degan, 98 Universita' di Genova Roma, Italy Viale Benedetto XV, 2 16132 GENOVA , Italy

D. ERIE M. GRATTAROLA The State University of New Jersey DIBE RUTGERS Viale Causa, 13 Department of Chemistry 16145 GENOVA, Italy New Brunswick P.O. Box 939 PISCATAWAY, New Jersey 08854 USA 260

A. ELGSAETER F. HAUGEN Division of Biophysics Institute of Biotechnology Univ. of Trondheim Unit/NTH N-7034 TRONDHEIM-NTN, Norway N 7034 TRONDHEIM-NTH, Norway

A. FEIS C.W. HILBERS Laboratorio di Spettroscopia Laboratory of Biophysical Molecolare Chemistry Dipartimento di Chimica Katholieke Universiteit Via Gino Capponi, 9 Toernooiveld 50121 FIRENZE, Italy 6225 ED NIJMEGEN, The Netherlan c. FRONTALI R. JOHNSTON Istituto Superiore di Sanita' Dept. Experimental Pathology Viale Regina Margherita 299 Life Sciences Division 00198 GENOVA, Italy Los Alamos National Laboratory P.O. Box 1663 Mail Stop GUZSK CALIK LOS ALAMOS, New Mexico, USA Chemical Eng. dept. Ankara Univ. K. KNUDSEN ANKARA, Turkey Division of Biophysics Univ. of Trondheim P. GERMANO N-7034 TRONDHEIM-NTH, Norway Cattedra di Biofisica Universita' di Genova M. LE BRET 16100 GENOVA, Italy Institute Gustave-Roussy Physiochimie Macromomoleculaire G. GIANNETTI rue Camille Desmoulins Dipartimento di Ingegneria, 9480 VILLEJUIF, France Biofisica ed Elettronica Via F. Causa 13 D.M.J. LILLEY 16145 GENOVA, Italy Department of Biochemistry University of Dundee G. LULECI DUNDEE DD1 4HN, UK Department of Medical BioI. and Genetics C. NICOLINI I Medical Faculty Cattedra di Biofisica University of Akdeniz Facolta' di Medicina ANTALYA, Turkey Unive rsita' di Genova 16100 GENOVA, Italy M. MACCARONE Via San Sisto, 87 B. OZDEN 67100 L'AQUILA, Italy Dept. Biology Middle East Technical University G.S. MANNING ANKARA, Turkey Department of Chemistry Rutgers University S. PAOLETTI P.O. Box 939 Dipartimento Biochimica e Biof. PISCATAWAY, NJ 08854, USA Univ. di Trieste 34127 TREISTE, Italy A.M. MARTINS Laboratorio Nacional de Engenharia I. PEPE e Tecnologia Industrial Universita' di Genova Estrada das Palmeiras Dipartimento di Fisica Queluz de Baixo Via Dodecaneso 33 2745 QUELUZ, Portugal 16146 GENOVA, Italy 261

K. MARX L. PIANTONI Department of Chemistry Via Madre Cabrini 9 University of Lowell 20122 MILANO, Italy LOWELL, MA 01854, USA E. PISKIN L. Mc INTOSH Hacettepe University University of Oregon Chemical Eng. Dept. Inst. P.K. 716 Kiz Hay EUGENE, OR 97403-1229 ANKARA, Turkey USA

N. MERT D. PORSCHKE Vice Dean Max-Planck-Institute School of Veterinary fur Biophysikalische Chemie 100. Yil University 34, GOTTIGEN,FRG VAN, Turkey

J • D. PUGLISI I. TINOCO Department of Chemistry Department of Chemistry 321 Hildebrand Hall University of California University of California BERKELEY, CA 94720 USA BERKELEY, California 94720 USA I. TOBIAS M. ROCCO The State University of New Jersey Jersey Laboratorio di Mutagenesi Department of Chemistry Istituto Nazionale Ricerca Cancro P.O. Box 939 Via Ie Benedetto XV, 19 PISCATAWAY New Jersey 08854, USA 16132 GENOVA, Italy

M. SANDVOLD M. TORTONESE Division of Biophysics P.zza G. Verdi, 1/1 Univ. of Trondheim 16121 GENOVA N-7034 TRONDHEIM-NTH, Norway Italy

W. SCHREIL Institute of Zooology G. VARANI Univ. Heidelberg Unive rsita' degli Studi di Milano HEIDELBERG, FRG Dipartimento di Fisica Via Celoria 16 D. SCHUMMER 20133 MILANO, Italy Laboratoire de Biochimie Universite' Catholique de Louvain P. PEDERIVA 1, Place Louis Pasteur Universita' di Trento 1348 LOUVAIN-LA NEUVE, Belgium Facolta' di Matematica Via Dosso Dossi S. TAKACI 38110 TRENTO, Italy Ankara University Fen F. Dept. of Chemical Eng. 06100 ANKARA, Turkey

T.TANAKA Department of Physics -MIT CAMBRIDGE MA 02139, USA 263 Index

A anti 109 bending energies 184 300 A fiber 204 bending fluctuations in DNA 158 A form 2, 108 bending of DNA 73 A-DNA 5 binding 14 A-A 100 birefringent 33 A-A mismatches 105 bisulphite 116 AAF binding to DNA 15 blood serum 64 about a transverse axis 6 Boltzmann distribution 22 about the axis 6 bound state 192 acridine rings 10 breathing 12, 13, 23, 158 acrylamide gel 241, 246 breathing reaction 183 acrylamyde 244 bromoacetaldehyde 116 acrylate copolymer gels 241 bulged bases 104 activation enthalpy 21 C-N bond I active 219 c-o bonds 3 activity coefficients 225, 227 C-type kinetics 130 adenine amino proton 86 C.T. DNA 197 adenine syn 109 C2' endo 2 alginates 221, 222 C3' endo 2 aminofluorene derivatives 13 C4'-C5' bond 2 amplitude 57, 60 carcinogen 14 antibiotics 19 carrageenan 222 (A-T)n sequences 126 CD parameters of DNA's 10 autocorrelation 75 cells 207, 209, 213 automated analysis 209 chemical structures 189, 222 chloresteric phase ISS B DNA 197 206 B form 2 chromatin-DNA 204 B-DNA 1 chromosomal evolution 163 B-DNA 5,194 CIDS 210, 212 B-form 105, 108 circular dichroism 10, 31, 32, 36, 39, 211 100 B nucleofilament 204 circular intensity differential scattering 210 B-type 86 circumferentially wrapped toruses 151 B-type double helix 81 ColE 1 cruciform 119 B-Z-cruciform 126 [Co(NH3)6]3 + 70 B-Z-cruciform equilibrium 123 collective diffusion of polymer network 250 B. subtilis 63 complex polarizability 52 backward scattering angles 63 condensation-decondensation transition 139 bacterial polysaccharides 223 conductivities 226 bacteriophage 161 conformation 101,225 bacteriophage lambda 151 conformational transition 226, 228 Bal31 nuclease 116 copolymer gel 248 base misincorporation 108 core DNA 50 base-base mismatch 98, 105 correlation time 10 beat frequency 57, 58 COSY 81 bending 177 counter-ion 10, 244 bending amplitudes 73 counter-ions 244 264 counterion condensed DNA 154 dye-nucleic acids interaction 18 coupled oscillator model 44, 50 dynamic fluctuations 192 coupled oscillator model of an oligonucleitide 39 dynamic structural 193 covalent bindings II, 23 crankshaft 23 E.coli. chromosomes 1649 critical behavior 252 EB-DNA complexes 7 cross relaxation rate 102 ecoli 63 crosslink 231 EcoRI endonuclease 179 cruciform extrusion 129 EcoRI site II9 cruciform formation 114 elastic instability 169 cruciform kinetics 128 electric dichroism 72 cruciform structures 112, 115 electric dipole moment 39 cyclic AMP 69 electric field 247 electro-optical 66 d[ljATCCTA(T)4TAGGAT[2j 82, 86 electronic paramagnetic resonance 9 dA-dT 153 energy minimization 88 l:>. H 230 enthalpy 206 deoxypolynucleotides 10 entropy 70 deuterium exchange 20 enzymatic cleavage 151 l:>. GO 97 EPR 9 l:>. HO 97 error frequencies 95 l:>. So 97 Escherichia coli 113 diamines 19 EthDi 194 dichroism decay 74 EthDi bound to nucleic acids 197 diethyl pyrocarbonate 116, II9 EthDi-DNA complex 191 diffusion coefficient 6 ethedium bromide 6 digestion 218 ethidium bromide 189,216 DNA 0 29 153 ethidium bromide between base pairs 17 DNA 10, 49, 70, 86, 177, 192,208 ethidium-acridine dimer 189 DNA bending 66, 175 eulerian buckling 171 DNA condensation 70 evolution 164 DNA flexibility 137 exchangeable protons 83 DNA fragments 73 experimental 211 DNA hairpin 78, 86 extrahelical cytosine 105 DNA polymerases 95, 108 extrusion mechanism 128 DNA structure 161 DNA supercoiling 112 fibrosome 206, 216 DNA synthesis 215 first-order decay of base-pairing 2 DNA toroids 72 Flory-Huggins 242 DNA torus cleavage model 142 flow birefringence 54 DNA 'cristallization' 162 fluorescence 191, 196 DNAase 152, 219 fluorescence polarisation anisotropy 5 DNAse digestion 209 formaldehyde 11 DNAase II 152 Fourier analysis 75 DNAse I 217 Fourier transform 78 2D Noe 86 FPA 7 2D NOESSY 106 free energy 95 2D NOESY experiment 103 free energy of binding 95 duplex winding angle 183 free energy of DNA supercoiling 113 dye binding 10 free energy of supercoilng 122 265 freeze-etch electron microscopy 142 intranuclear DNA 216 freeze-etch replica 145 ion competition 138 ionic gels 231, 242, 245 01 209,213,216,217 ionic polysaccharide 122, 221 O.A mismatch 109 ionic selectivity 227 (O-C)n sequences 126 ions 1 gel 240, 244 isopropylacrylamide polymer 247 gel volume on salts 246 gel-sol 238 J-couplings 83, 86 gelation 231 K+ 227 gels 221, 237, 242,244,247,252 k-carrageenans 221,227,230 activation 216 kinetic 14 genes 217 kinetics of gel swelling 252 glyoxal 116 kink 3 00213,216 kink angle 178, 181, 186 guanine amino proton 86 kink sites 179 kink-contraction 175 H-D exchange 196, 197 kinking 175, 177 H1216 kinking enthalpy 184 hairpin 78, 86, 88 kinking of DNA 169 hamiltonian 39 heat capacity 207 labeling patterns 215 helices and torsional angles 5 A-DNA 75 hepatocytes 213, 214 A2n NA 71 heteroduplex 92, 93 lambda 153 hexadecanucleotide 81, 86 lambda DNA torus 161 HMO 216 leptospira 64 IH NMR 84 leptospira bacteria 65 IHNMR NOESY 87 ligands 70 Hooke's law 178 light and neutron scattering 250 Hooke's law bending constant 171 light scattering 58 3H-thymidine pulse 215 limit values of the linear dichroism 68 human red blood cells 64 linear 49 hybridisation 121 linear polarizations 56 hydrated torus 152 linearly polarized light 33 hydrogen axchane kinetics 194 Lk 112 hydrogen bonding 78 local motions 252 hydrogen exchange 179 loopfolding 78 hydrogen-deuterium exchange 189, 191 hydrolysis 14 magnesium 246 hydropgen exchange kinetics 200 matrix formalism 58 hydroxystilbamidine 24 melting 84, 182, 209 methylene bridging 148 imidazole 194 Michaelis constant 95 imino proton 84, 106 microcalorimetry 206 initiation 216 micrococcal nuclease 116, 140, 217 instrument 56 mismatches 100 intercalated molecules 16 mixing entropy 243 intercalation 16 MKE open base 179 intercalation site 18 molar elipticity 35 266 mononucleosomes 50 phase diagram 139 movements of B-DNA 22 phase properties 239 Mueller scattering matrix 59 phase transition 242, 246 multiple dipole 210, 215 phosphate sugar backbone 196 mutagenesis 92 plasmid 113 mutant duplex 93 plRbke8 128 polarization 56 NA + counterions 227 polarization of a photon 37 networks 231 poleyectrolyte 226 NMR 78,101 poly (A).poly(U) 197 NMR meassurements 252 poly (dA).poly(dn 197 NMR NOESY 82 poly (dA-dT) 197 NOE 78, 81, 84 poly (dG-dC) 197 NOESY 81,86 poly (dG-msdC) 197 NOESY spectrum 80, 81 polyamine-DNA condensation 148 non intercalating molecules 19 polyamines 148 non-exchangeable protons 83 polyelectrolytes 224 non-Watson-Crick base-base mismatches I polymer network 237, 238 nuclear magnetic resonance 102 polymer-network concentration 242 nuclear Overhauser effect (NOE) 102 polymorphism 137 nuclear DNA 215 polynucleosomal superhelix 213 nuclease 218 polynucleosomes 215 nuclei 207 polynucleotides 1 nucleic acid-drug complexes 188 polysaccharides 221, 226, 231-233 nucleic acids 78, 92 polystryrene microspheres 61 nucleosomal DNA 207 porphyrins 195 nucleosome 179 potential energy 22, 39 nucleotide misincorporation 94 premelting 10 null-DNA 169, 170, 173, 180, 181 proflavine between base pairs 17 proofreading 93, 95 oligonucleotide 78 proton resonances 80 optical activity 32, 36 'II" to 'II" transition 50 optical rotation 227 purine 79 osmium tetroxide 116 pyrimidine 79 osmotic pressure 242 Overhauser effects 83 quantum mechanical origin 36 quaternary 204 pahse transition 247 quinternary structure 206 pCollR315 128 pectins 221, 222 Raman or microwave spectroscopy 22 'II" electrons 53 RBC 64 permanent dipole 67 reaction kinetics 11 persistence length 172, 175 refractive indices 33, 34, 214 persistence length >. 187 relaxation time 6, 197 pH and salt ions 245 repair 93, 108 pH dependence 244 replication 216 phage heads 76 reversible condensation 138 phase 57, 242 rotation time constants 69, 94 phase contrast 213 rotational brownian movements 7 phase contrast optical microscopy 214 rotational diffusion coefficient D2 6 267

S phase 216 T4 DNA to ruses 154 S-type kinetics 130 T4 endonuclease 116 S-type sugar conformation 86 T7153 SI nuclease 116 T7 deletion mutants 159 scaffold 205 T-T 100 scattered intensity 58 T-T mismatches 105 Schreier and Baldwin model 189 temperature 241 set-up 212 temperature coefficient 183 shrinking 252 tertiary structure 31, 44, 50 sites of high enthalpy 8 tertiary structure of the mononucleosome 53 sites of structural irregularity 179 tetraalkylammonium salts 10 small electric field 246 theoretical cms 211 small groove 19 thermal profile of nuclei 209 spd-¢-174 140, 145 thermodynamics of misincorporating a spd-calf thymus DNA 139 nucleotide 96 spd-DNA torus 161 thermoreversible gels 231 spermidine 151 thin rod 171 spermine 70 thymi dines 88 spermine bindings 72 time constant T 22 spin diffusion 87 time constants 73 spin-labeled probe 9 topoisomer 122 standard free energies 98 toroidal 70 stereo drawing 23 toroidal DNA 137 stiffness 70 toroids 70 stopped-flow mixing 191 torsional angles I, 2 strep 63 torsional movement 22 stretching 16 torus formation 157 stretching of the double helix 16 torus ring thickness 145 structural model 23 torus shape 173 succinoglycan 221, 223, 230 torus structure 140 sugar conformation 83 toruses 142, 155 sugar moiety 86 train of two optical elements 50 sugar puckering 5 transconformation 24 supercoiled 49 transition free energy 95 supercoiled DNA 1I2, 1I4 transition moments 47, 49 supercoiled pCollR315 1I9 tRNA 197 superhelical folding 215 tRNA 3 superhelical turns 216 twist 122 superhelix 48 twist angle 8, 10 superhelix densities 125 superhelix density 1I3, 125 unpaired loop lIS supernucleosomes 204 unwinding 16 swelling 245 swelling 240 V. fluvialis 63 viscosity 232, 233 T-T pair 85, 90 volume-phase transition 239, 247 TI 81 volume transition 246 T281 winding angie 3 T4153 wormlike chain 177 268 writhing number 16 xanthan 221, 223, 230 yeast tRNAPhe 197

Z DNA 197 Z poly (dO-dC) 195 Z-DNA 125, 194 Z-DNA 5 Zeeman laser scattering (ZLS) 57 ZLS 56 ZLS instrument 56 ZLS phase 58, 60 ZLS theory 57