Spectroscopic And Kinetic Data. Physical Data I / Spektroskopische Und Kinetische Daten. Physikalische Daten I (landolt-börnstein: Numerical Data And ... In Science And Technology - New Series)

Group VII of the **Landolt-Börnstein New Series** is devoted to the physical properties of biological systems. It begins with volume VII/1 covering the nucleic acids which are of central importance in all processes in- volving gene expression. This field has become of practical consequence during the last decade through the development of genetic engineering. Because of the amount of the data available, volume VII/1 had to be divided into several subvolumes. The first two subvolumes, VII/1a and VII/1b, which appeared in 1988, deal with crystallographic and structural data which give a comprehensive information on the three-dimensional structure of the nucleic acids, their folding properties, their hydrogen bonding schemes, their metal binding capabilities, their hydration and their drug complexation. The present subvolume VII/1c covers the first part of spectroscopic, kinetic and physical data; the following subvolume VII/1d concludes this chapter and also deals with theoretical investigations. 3.1.2 Methods....Pages 1-2 3.1.3 Comments on the CD data....Pages 2-2 3.1.4.1 CD spectra for nucleic acid monomers....Pages 3-5 3.1.4.2 CD spectra for dinucleotides....Pages 5-9 3.1.4.3 CD spectra for homopolynucleotides....Pages 9-13 3.1.4.4 CD spectra for other synthetic polynucleotides....Pages 13-20 3.1.4.5 CD spectra for natural nucleic acids....Pages 21-23 3.1.5 References for 3.1....Pages 24-24 3.2.1.3 Data presentation....Pages 25-26 3.2.1.4 List of constituents of nucleotides....Pages 26-34 3.2.2.1 Melting temperatures of polydeoxyribonucleotide hetero-complexes....Pages 35-38 3.2.2.2 Melting temperatures of polyribonucleotide hetero-complexes....Pages 38-45 3.2.2.3 Melting temperatures of hybrid hetero-complexes....Pages 46-48 3.2.2.4 Melting temperatures of homo-complexes....Pages 49-52 3.2.2.5 pK values of homo-complexes....Pages 53-55 3.2.3 References for 3.2....Pages 56-59 3.3.2 The theory of the relation between vibrational frequencies and conformation....Pages 60-61 3.3.4 Characterization of experimentally induced changes in DNA conformation by Raman spectroscopy....Pages 61-64 3.3.5 The use of Raman spectroscopy to solve the conformational code of DNA....Pages 64-65 3.3.8 The characterization of the conformations of nucleic acids using infrared spectroscopy....Pages 65-66 3.3.9 Data on Raman spectroscopy of nucleic acids....Pages 66-71 Figures for 3.3....Pages 72-85 3.3.10 References for 3.3....Pages 86-87 3.4.2 Proton NMR spectroscopy of oligomers....Pages 88-90 3.4.3 Structure and conformations of oligomers....Pages 90-92 3.4.4 Organization of the oligonucleotide H-1 NMR tables....Pages 92-99 3.4.5.1 Coupling constants of RNA sequences....Pages 100-107 Tables 22 - 53....Pages 108-119 Tables 54 - 78....Pages 120-129 3.4.5.3 Coupling constants of DNA sequences and RNA-DNA hybrids....Pages 129-143 Tables 116 - 156....Pages 143-158 Tables 157 - 184....Pages 159-172 Tables 185 - 205....Pages 173-186 3.4.6 References for 3.4....Pages 186-190 3.5.1 Introduction....Pages 191-191 3.5.2 Data on H-1, C-13 and N-15 nuclei resonances in tRNAs....Pages 192-199 3.5.3 References for 3.5....Pages 200-200 3.6.2 Methods....Pages 201-202 3.6.3 Arrangement of data....Pages 202-203 3.6.4 List of symbols and abbreviations....Pages 203-203 3.6.5.1 Thermodynamic parameters for duplex formation by RNA oligonucleotides....Pages 204-207 3.6.5.2 Thermodynamic parameters for oligonucleotides with loops....Pages 208-209 3.6.5.4 Thermodynamic parameters for duplex formation by DNA oligonucleotides....Pages 210-210 3.6.5.5 Thermodynamic parameters for duplex formation by DNA oligonucleotides containing mismatches....Pages 211-212 3.6.5.6 Thermodynamic parameters for helix initiation and propagation in 1 M NaCl.....Pages 213-213 3.6.5.8 Free energy increments for internal G:U pairs in RNA oligonucleotides....Pages 214-214 3.6.5.9 Free energy parameters for RNA helix termini....Pages 215-215 3.6.5.10 Free energy increments for loops....Pages 216-216 3.6.5.11 Thermodynamic parameters for single mismatches in DNA oligonucleotides....Pages 217-217 3.6.5.12 Kinetic parameters for double helix formation by oligonucleotides....Pages 218-219 3.6.5.13 Kinetics of hairpin loop formation by oligomers....Pages 220-220 3.6.5.14 Kinetic parameters for binding between tRNA and oligonucleotides....Pages 221-221 3.6.5.15 Kinetics of tRNA associations through complementary anticodons....Pages 222-222 3.6.5.16 Kinetics of double helix formation for polynucleotides....Pages 223-223 3.6.5.17 Kinetic parameters for intramolecular conformational changes in RNA....Pages 224-224 3.6.5.18 Kinetic parameters for stacking in single strands....Pages 225-225 3.6.6 References for 3.6....Pages 226-227 4.1.1 Introduction....Pages 228-229 4.1.2 Bending and torsional rigidity of double helices....Pages 230-232 4.1.3 Energetics of the helix-coil transition....Pages 232-236 4.1.4 Energetics of the B-Z transition....Pages 236-238 4.1.5 References for 4.1....Pages 239-240 4.2.1 Introduction....Pages 241-243 4.2.2.1 Conformational transitions in helical polynucleotides....Pages 243-246 4.2.2.2 Property diagrams of all double helical polynucleotides....Pages 246-250 4.2.2.3 Energetics of helix/helix transitions....Pages 250-253 4.2.2.4 Thermodynamics of RNA single-strand unfolding....Pages 253-253 4.2.2.5 Molecular forces that stabilize DNA sequences....Pages 254-254 4.2.3 References for 4.2....Pages 255-256 4.3.1 Introduction....Pages 257-258 4.3.2.1 Ultracentrifugation, partial volumes and interaction parameters....Pages 258-260 4.3.2.2 Total intensity light scattering....Pages 260-260 4.3.2.3 Small angle X-ray and neutron scattering....Pages 261-261 4.3.2.4 Viscometry....Pages 262-263 4.3.3 The persistent chain....Pages 263-264 4.3.4.2 Hydration of DNA....Pages 265-267 4.3.4.3 Molecular parameters of aqueous solutions of linear X-DNA (X = Na, Cs, Li, Rb)....Pages 268-269 4.3.4.4 Calculated neutron scattering length increments for linear CsDNA....Pages 270-270 4.3.4.5 Molecular parameters of linear ColE 1 DNA....Pages 271-271 4.3.4.6 Physical chemical properties of ColE 1-plasmid DNA in solution....Pages 272-272 4.3.4.8 Persistence length and excluded volume parameters for high molar mass linear T7 DNA....Pages 273-273 4.3.5 References for 4.3....Pages 274-276 4.4.1 Introduction....Pages 277-281 4.4.2.1.1 Association constants....Pages 282-288 4.4.2.1.2 Binding characteristics....Pages 288-295 Metal ions Li(I) - Cs(I)....Pages 296-307 Metal ions Cs(I) - U(IV)....Pages 308-320 4.4.2.2.2 Transition between right- and left-handed helix....Pages 320-333 4.4.2.2.3 Other conformational changes: secondary (except right-left handed), tertiary, quaternary structures....Pages 334-340 4.4.2.2.4 Hydrodynamic property changes....Pages 341-344 4.4.3.1.1 Types of metal ion binding sites in tRNAs....Pages 345-345 Metal ions Mg(II) - Cu(II) in tRNS....Pages 346-354 Metal ions Zn(II) - Cs(I) in tRNS....Pages 355-362 RNS other than tRNS....Pages 362-363 4.4.3.1.3 Association constants for metal ion-tRNA interactions....Pages 364-367 4.4.3.2.1 Effects on secondary structure....Pages 368-375 4.4.3.2.2 Effects on tertiary structures....Pages 376-389 4.4.3.2.3 Thermal melting effects - tRNAs....Pages 390-393 Order of reactivity....Pages 394-394 Degradation rate: Mg(II) - La(III)....Pages 395-404 Degradation rate: Ce(III) - Bi(III)....Pages 405-410 4.4.5 Data on metal ion catalyzed degradation of DNAs and polydeoxynucleotides....Pages 411-425 Figures for 4.4....Pages 426-433 4.4.6 References for 4.4....Pages 434-445