Physical Data II. Theoretical Investigations

4.5.1 Introduction and definition of terms....Pages 1-4
4.5.2 Determination of superhelix density....Pages 5-7
4.5.3 Sedimentation properties of closed circular DNA....Pages 8-10
4.5.4 Gel electrophoresis of closed circular DNA....Pages 10-11
4.5.5 Energy parameters for closed circular DNA....Pages 12-14
4.5.6 Ligand binding to closed circular DNA....Pages 15-20
4.5.7 Helix-coil transitions....Pages 21-23
4.5.8 Local structural transitions....Pages 24-27
4.5.9 References for 4.5....Pages 28-30
4.6.1 Introduction....Pages 31-32
4.6.2 Techniques....Pages 32-36
4.6.3.1 Oligonucleotides....Pages 37-43
4.6.3.2 Natural RNA and polyribonucleotides....Pages 43-48
4.6.3.3 DNA restriction fragments....Pages 48-53
4.6.3.4 Plasmids and phages....Pages 53-55
4.6.3.5 RNA transcripts, RNA-DNA hybrids, single-stranded (ss) and double-stranded (ds) DNA....Pages 56-57
4.6.3.6 Pre-purification and recovery of nucleic acids....Pages 58-59
4.6.4 References for 4.6....Pages 59-60
4.7.1 Introduction....Pages 61-66
Ligands 1 - 22....Pages 66-75
Ligands 23 - 55....Pages 76-85
4.7.2.2.1 Absorption data....Pages 85-97
4.7.2.2.2 Thermal melting....Pages 98-113
4.7.2.2.3 Fluorescence....Pages 114-121
4.7.2.2.4 Circular dichroism....Pages 121-132
4.7.2.3 Nuclear magnetic resonance....Pages 133-138
Tables 8 - 19....Pages 139-143
Figs. 121 - 172....Pages 144-157
Table 20....Pages 158-169
Tables 21 - 30....Pages 170-173
Figs. 173 - 208....Pages 174-184
4.7.2.6 Thermodynamics, kinetics and theoretical computations....Pages 184-189
4.7.3 References for 4.7....Pages 190-193
4.8.1 Introduction....Pages 194-195
4.8.2 Sequences and homologies....Pages 196-202
4.8.3 Size and shape in solution....Pages 202-208
4.8.4 Calculation of secondary structures and their transitions....Pages 209-222
4.8.5 Thermodynamic experiments....Pages 222-231
4.8.6 Kinetic data of conformational transitions of viroids....Pages 232-237
4.8.7 Ligand binding....Pages 238-241
4.8.8 References for 4.8....Pages 241-243
4.9.1 Introduction....Pages 244-245
4.9.2 Thermodynamic formalism and experimental methods....Pages 245-249
4.9.3 Protein-nucleic acid binding parameters....Pages 250-261
4.9.4 References for 4.9....Pages 262-263
4.10.1 Introduction....Pages 264-265
4.10.2.1 Interactions in non-aqueous solvents....Pages 266-267
4.10.2.2 Interactions of monomer residues in aqueous solution....Pages 268-271
4.10.2.3 Interactions of peptides containing basic amino acids with nucleic acids....Pages 271-273
4.10.2.4 Interactions of amino acids and peptides of mixed sequence with polynucleotides....Pages 274-277
4.10.2.5 Enthalpy- and entropy-changes from calorimetric and van’t Hoff analysis....Pages 278-279
4.10.2.6 Kinetic (and equilibrium) parameters from relaxation measurements....Pages 280-281
4.10.2.7 Effects of amino acid and peptide ligands on the cooperative helix-coil transition of polynucleotides....Pages 281-286
4.10.2.8 Model complexes formed with polypeptides....Pages 287-290
4.10.2.9 Miscellaneous....Pages 291-292
4.10.3 References for 4.10....Pages 293-294
4.11.1 Introduction....Pages 295-297
4.11.2 Data....Pages 298-306
4.11.3 References for 4.11....Pages 307-307
4.12.1 Introduction....Pages 308-311
4.12.2 Predominant tautomeric species of nucleic acid components....Pages 311-312
4.12.3.1 Minor tautomeric species of neutral forms of purines, pyrimidines, some analogues and nucleosides....Pages 313-314
4.12.3.2 Prototropic tautomerism in the imidazole ring of common purines....Pages 315-315
4.12.3.3 Monocationic forms (protonation sites) of purines and pyrimidines....Pages 316-317
4.12.3.4 Protonation sites in the cationic forms of the purine and pyrimidine bases of nucleosides....Pages 317-317
4.12.3.5 Protonation sites of purines and pyrimidines involved in various types of base pairing in different systems....Pages 318-322
4.12.3.6 Monoanionic species of purines and purine nucleosides....Pages 323-324
4.12.3.7 Monoanions of 2,4-diketopyrimidines....Pages 325-325
4.12.3.9 Neutral forms of 2(4)-monooxopyrimidines....Pages 326-327
4.12.3.10 Reduced pyrimidines (metabolic intermediates) and their nucleosides....Pages 327-329
4.12.3.11 Barbituric acids and barbitals....Pages 330-331
4.12.3.12 Isocytosines....Pages 332-332
4.12.3.13 Isoguanine and isoguanosines....Pages 333-334
4.12.3.14 Promutagenic analogues of cytosine....Pages 335-337
4.12.3.15 Promutagenic analogues of adenosine....Pages 337-337
4.12.3.16 4-Aminopyrazolo (3,4-d)pyrimidine....Pages 338-340
4.12.3.17 Pyrazolo(4,3-d)pyrimidines and their nucleosides....Pages 340-343
4.12.4 References for 4.12....Pages 344-348
5.1.1 Introduction....Pages 349-349
5.1.2 Methods of calculation and representation....Pages 350-351
5.1.3 Results....Pages 351-356
Tables for 5.1....Pages 356-371
Figs. 1 - 23....Pages 372-384
Figs. 24 - 52....Pages 385-399
Figs. 53 - 72....Pages 400-412
5.1.4 References for 5.1....Pages 413-414
5.2.1 Introduction....Pages 415-415
5.2.3 Nonbonded interactions....Pages 416-419
5.2.4 Comparisons....Pages 419-421
5.2.5 Discussion....Pages 421-421
5.2.6.2 Van der Waals parameters of selected atom pairs in the nucleic acid chain....Pages 422-432
5.2.6.3 Partial atomic charges and interaction potentials....Pages 433-434
5.2.7 References for 5.2....Pages 434-435
5.3.1 Introduction....Pages 436-436
5.3.2 Molecular mechanics and dynamics theory....Pages 437-442
5.3.3.1 Molecular mechanics....Pages 443-449
5.3.3.2 Molecular dynamics....Pages 449-453
5.3.4 References for 5.3....Pages 453-454
5.4.1 Introduction....Pages 455-456
5.4.2 Methods....Pages 456-457
5.4.3 Models for A, B, C and D forms of DNA, with mononucleotide repeating units....Pages 457-458
5.4.4 Models for DNA with dinucleotide repeating units....Pages 459-459
Tables....Pages 460-474
Figures....Pages 475-485
5.4.6 References for 5.4....Pages 485-486