Landolt-Brnstein Group VII: Biophysics 
Volume 1 Nucleic Acids 
Subvolume D Physical Data II. Theoretical Investigations 
Title Page, Contributors, Preface  
4  Physical data for nucleic acids and their constituents  1  
4.1  Energetics of DNA and RNA double helices (See Vol. 1C)  
4.2  Calorimetric studies on DNAs and RNAs (See Vol. 1C)  
4.3  Solution properties of DNA: sedimentation, scattering of light, X-rays and  
neutrons, and viscometry (See Vol. 1C)  
4.4  Interaction of DNA and RNA with metal ions (See Vol. 1C)  
4.5  Physical data of supercoiled DNA (W.R. BAUER)  1  
4.5.1  Introduction and definition of terms  1  
4.5.2  Determination of superhelix density  5  
4.5.3  Sedimentation properties of closed circular DNA  8  
4.5.4  Gel electrophoresis of closed circular DNA  10  
4.5.5  Energy parameters for closed circular DNA  12  
4.5.6  Ligand binding to closed circular DNA  15  
4.5.7  Helix-coil transitions  21  
4.5.8  Local structural transitions  24  
4.5.9  References for 4.5  28  
4.6  HPLC of oligonucleotides and natural nucleic acids (D. RIESNER)  31  
4.6.1  Introduction  31  
4.6.2  Techniques  32  
4.6.3  Applications  37  
4.6.3.1  Oligonucleotides  37  
4.6.3.2  Natural RNA and polyribonucleotides  43  
4.6.3.3  DNA restriction fragments  48  
4.6.3.4  Plasmids and phages  53  
4.6.3.5  RNA transcripts, RNA-DNA hybrids, single-stranded (ss) and double-stranded (ds)  56  
DNA  
4.6.3.6  Pre-purification and recovery of nucleic acids  58  
4.6.4  References for 4.6  59  
4.7  Physical data of DNA- and RNA interactions with drugs, dyes and other small  61  
organic compounds (CHR. ZIMMER, U. WHNERT)  
4.7.1  Introduction  61  
4.7.2  Data  66  
4.7.2.1  Chemical structures of ligands  66  
4.7.2.2  Spectral data  85  
4.7.2.2.1  Absorption data  85  

4.7.2.2.2 
4.7.2.2.3 
4.7.2.2.4 
4.7.2.3 
4.7.2.4 
4.7.2.5 
4.7.2.6 
4.7.3 
4.8 
4.8.1 
4.8.2 
4.8.3 
4.8.4 
4.8.5 
4.8.6 
4.8.7 
4.8.8 
4.9 
4.9.1 
4.9.2 
4.9.3 
4.9.4 
4.10 
4.10.1 
4.10.2 
4.10.2.1 
4.10.2.2 
4.10.2.3 
4.10.2.4 
4.10.2.5 
4.10.2.6 
4.10.2.7 
4.10.2.8 
4.10.2.9 
4.10.3 
4.11 
4.11.1 
4.11.2 
4.11.3 
Thermal melting
Fluorescence
Circular dichroism
Nuclear magnetic resonance

98 
114 
121 
133 

Hydrodynamic data (viscosity, helix unwinding, buoyant density) 139

Binding parameters 158

Thermodynamics, kinetics and theoretical computations 184

References for 4.7 190

Viroids and viroid-like RNAs (D. RIESNER, G. STEGER) 194

Introduction 194

Sequences and homologies 196

Size and shape in solution 202

Calculation of secondary structures and their transitions 209

Thermodynamic experiments 222

Kinetic data of conformational transitions of viroids 232

Ligand binding 238

References for 4.8 241

Thermodynamic data for protein-nucleic acid interactions 244

(S.C.
 KOWALCZYKOWSKI)Introduction 244

Thermodynamic formalism and experimental methods 245

Protein-nucleic acid binding parameters 250

References for 4.9 262

Model systems for the characterization of protein-nucleic acid interactions 264

(D.
 PORSCHKE)Introduction 264

Data 266

Interactions in non-aqueous solvents 266

Interactions of monomer residues in aqueous solution 268

Interactions of peptides containing basic amino acids with nucleic acids 271

Interactions of amino acids and peptides of mixed sequence with polynucleotides 274

Enthalpy- and entropy-changes from calorimetric and van't Hoff analysis 278

Kinetic (and equilibrium) parameters from relaxation measurements 280

Effects of amino acid and peptide ligands on the cooperative helix-coil transition of 281

polynucleotides
Model complexes formed with polypeptides 287

Miscellaneous 291

References for 4.10 293

Dipole moments and related data (K.L. WIERZCHOWSKI) 295

Introduction 295

Data 298

References for 4.11 307


5.3 
The flexibility and dynamics of DNA (P.A. KOLLMAN) 436

5.3.1 
Introduction 436

5.3.2 
Molecular mechanics and dynamics theory 437

5.3.3 
Applications of molecular mechanics and dynamics 443

5.3.3.1 
Molecular mechanics 443

5.3.3.2 
Molecular dynamics 449

5.3.4 
References for 5.3 453

5.4 
New theoretical models for DNA structure (M. BANSAL, V. SASISEKHARAN) 455

5.4.1 
Introduction 455

5.4.2 
Methods 456

5.4.3 
Models for A, B, C and D forms of DNA, with mononucleotide repeating units 457

5.4.4 
Models for DNA with dinucleotide repeating units 459

5.4.5 
Data 460

5.4.6 
References for 5.4 485



4.12  Tautomerism of purines and pyrimidines, their nucleosides and various analogues  308  
(D. SHUGAR, A. PSODA)  
4.12.1  Introduction  308  
4.12.2  Predominant tautomeric species of nucleic acid components  311  
4.12.3  Data on tautomerism  313  
4.12.3.1  Minor tautomeric species of neutral forms of purines, pyrimidines, some  313  
analogues and nucleosides  
4.12.3.2  Prototropic tautomerism in the imidazole ring of common purines  315  
4.12.3.3  Monocationic forms (protonation sites) of purines and pyrimidines  316  
4.12.3.4  Protonation sites in the cationic forms of the purine and pyrimidine bases of  317  
nucleosides  
4.12.3.5  Protonation sites of purines and pyrimidines involved in various types of base  318  
pairing in different systems  
4.12.3.6  Monoanionic species of purines and purine nucleosides  323  
4.12.3.7  Monoanions of 2,4-diketopyrimidines  325  
4.12.3.8  Monoanions of thiouracils  326  
4.12.3.9  Neutral forms of 2(4)-monooxopyrimidines  326  
4.12.3.10  Reduced pyrimidines (metabolic intermediates) and their nucleosides  327  
4.12.3.11  Barbituric acids and barbitals  330  
4.12.3.12  Isocytosines  332  
4.12.3.13  Isoguanine and isoguanosines  333  
4.12.3.14  Promutagenic analogues of cytosine  335  
4.12.3.15  Promutagenic analogues of adenosine  337  
4.12.3.16  4-Aminopyrazolo (3,4-d)pyrimidine  338  

4.12.3.17  Pyrazolo(4,3-d)pyrimidines and their nucleosides  340  
4.12.4  References for 4.12  344  
5  Theoretical investigations  349  
5.1  Electrostatic potentials fields and accessibilities (B. PULLMAN, R. LAVERY)  349  
5.1.1  Introduction  349  
5.1.2  Methods of calculation and representation  350  
5.1.3  Results  351  
5.1.4  References for 5.1  413  
5.2  Classical energy calculations of DNA, RNA and their constituents  415  
(W.K. OLSON, A.R. SRINIVASAN)  
5.2.1  Introduction  415  
5.2.2  Internal variables  416  
5.2.3  Nonbonded interactions  416  
5.2.4  Comparisons  419  
5.2.5  Discussion  421  
5.2.6  Data  422  
5.2.6.1  Torsional barrier heights  422  
5.2.6.2  Van der Waals parameters of selected atom pairs in the nucleic acid chain  422  
5.2.6.3  Partial atomic charges and interaction potentials  433  
5.2.7  References for 5.2  434  


