Landolt-Brnstein Group VII
: Biophysics
Volume 1 
Nucleic Acids Subvolume C
Spectroscopic and Kinetic Data. Physical Data I

3
Spectroscopic and kinetic data 1 
3.1

Electronic circular dichroism (CD) spectroscopy of nucleic acids (W.C. JOHNSON) 1 
3.1.1

Introduction 1 
3.1.2

Methods 1 
3.1.3

Comments on the CD data 2 
3.1.4

Data 3 
3.1.4.1

CD spectra for nucleic acid monomers 3 
3.1.4.2

CD spectra for dinucleotides 5 
3.1.4.3

CD spectra for homopolynucleotides 9 
3.1.4.4

CD spectra for other synthetic polynucleotides 13 
3.1.4.5

CD spectra for natural nucleic acids 21 
3.1.5

References for 3.1 24 
3.2

Melting temperatures of polynucleotide complexes (W. GUSCHLBAUER) 25 
3.2.1

Introduction 25 
3.2.2

Data 35 
3.2.2.1

Melting temperatures of polydeoxyribonucleotide hetero-complexes 35 
3.2.2.2

Melting temperatures of polyribonucleotide hetero-complexes 38 
3.2.2.3

Melting temperatures of hybrid hetero-complexes 46 
3.2.2.4

Melting temperatures of homo-complexes 49 
3.2.2.5

pK values of homo-complexes 53 
3.2.3

References for 3.2 56 
3.3

The classical Raman, resonance Raman, and infrared spectroscopy of nucleic acids 60 
3.3.1

Introduction 60 
3.3.2

The theory of the relation between vibrational frequencies and conformation 60 
3.3.3

Theory of Raman intensity and Raman hypochromism 61 
3.3.4

Characterization of experimentally induced changes in DNA conformation by Raman 61 
3.3.5

The use of Raman spectroscopy to solve the conformational code of DNA 64 
3.3.6

The resonance Raman effect in nucleic acids 65 
3.3.7

Low frequency Raman modes and dynamics of DNA 65 
3.3.8

The characterization of the conformations of nucleic acids using infrared spectroscopy 65 
3.3.9

Data on Raman spectroscopy of nucleic acids 66 
3.3.10

References for 3.3 86 
(W.L.
 PETICOLAS)
spectroscopy 

NMR data on oligonucleotides (C. ALTONA) 88

General remarks 88

Proton NMR spectroscopy of oligomers 88

Structure and conformations of oligomers 90

Organization of the oligonucleotide H-1 NMR tables 92

Data 100

Coupling constants of RNA sequences 100

Chemical shifts of RNA sequences 108

Coupling constants of DNA sequences and RNA-DNA hybrids 129

Chemical shifts of DNA sequences and RNA-DNA hybrids 143

References for 3.4 186

Survey of chemical shift values in tRNA (C.W. HILBERS, J.A.L.I. WALTERS) 191

Introduction 191

Data on H-1, C-13 and N-15 nuclei resonances in tRNAs 192

References for 3.5 200

Thermodynamics and kinetics of base-pairing 201

(D.H.
 TURNER, N. SUGIMOTO, S.M. FREIER)Introduction 201

Methods 201

Arrangement of data 202

List of symbols and abbreviations 203

Data 204

Thermodynamic parameters for duplex formation by RNA oligonucleotides 204

Thermodynamic parameters for oligonucleotides with loops 208

Thermodynamic parameters for coil-helix transition in single stranded RNA 210

Thermodynamic parameters for duplex formation by DNA oligonucleotides 210

Thermodynamic parameters for duplex formation by DNA oligonucleotides containing 211

mismatches
Thermodynamic parameters for helix initiation and propagation in 1 M NaCl. 213

Bimolecular helix initiation for RNA and DNA 214

Free energy increments for internal G:U pairs in RNA oligonucleotides 214

Free energy parameters for RNA helix termini 215

Free energy increments for loops 216

Thermodynamic parameters for single mismatches in DNA oligonucleotides 217

Kinetic parameters for double helix formation by oligonucleotides 218

Kinetics of hairpin loop formation by oligomers 220

Kinetic parameters for binding between tRNA and oligonucleotides 221

Kinetics of tRNA associations through complementary anticodons 222

Kinetics of double helix formation for polynucleotides 223

Kinetic parameters for intramolecular conformational changes in RNA 224

Kinetic parameters for stacking in single strands 225

References for 3.6 226



4 
Physical data for nucleic acids and their constituents	228

4.1 
Energetics of DNA and RNA double helices (M.D. FRANK-KAMENETSKII)	228

4.1.1 
Introduction	228

4.1.2 
Bending and torsional rigidity of double helices	230

4.1.3 
Energetics of the helix-coil transition	232

4.1.4 
Energetics of the B-Z transition	236

4.1.5 
References for 4.1	239

4.2 
Calorimetric studies on DNAs and RNAs (H.H. KLUMP)	241

4.2.1 
Introduction	241

4.2.2 
Data	243

4.2.2.1 
Conformational transitions in helical polynucleotides	243

4.2.2.2 
Property diagrams of all double helical polynucleotides	246

4.2.2.3 
Energetics of helix/helix transitions	250

4.2.2.4 
Thermodynamics of RNA single-strand unfolding	253

4.2.2.5 
Molecular forces that stabilize DNA sequences	254

4.2.2.6	
Concluding remarks 255

4.2.3	
References for 4.2 255

4.3	
Solution properties of DNA: sedimentation, scattering of light, X-rays and neutrons, 257

and viscometry (H. EISENBERG)

4.3.1	
Introduction 257

4.3.2	
Methods 258

4.3.2.1	
Ultracentrifugation, partial volumes and interaction parameters 258

4.3.2.2	
Total intensity light scattering 260

4.3.2.3	
Small angle X-ray and neutron scattering 261

4.3.2.4	
Viscometry 262

4.3.2.5	
Quasielastic light scattering 263

4.3.3	
The persistent chain 263

4.3.4	
Data on solution properties 265

4.3.4.1	
Partial volumes and interaction parameters in multicomponent systems 265

4.3.4.2	
Hydration of DNA 265

4.3.4.3	
Molecular parameters of aqueous solutions of linear X-DNA (X = Na, Cs, Li, Rb) 268

4.3.4.4	
Calculated neutron scattering length increments for linear CsDNA 270

4.3.4.5	
Molecular parameters of linear ColE 1 DNA 271

4.3.4.6	
Physical chemical properties of ColE 1-plasmid DNA in solution 272

4.3.4.7	
Molecular size and sedimentation coefficient for PM 2 Hae III uniformly sized NaDNA 273

fragments

4.3.4.8	
Persistence length and excluded volume parameters for high molar mass linear T7 273

DNA

4.3.4.9	
Temperature dependence of DNA apparent volumes 274

4.3.5	
References for 4.3 274




Title Page, Contributors, Preface 3.4 
3.4.1 
3.4.2 
3.4.3 
3.4.4 
3.4.5 
3.4.5.1 
3.4.5.2 
3.4.5.3 
3.4.5.4 
3.4.6 
3.5 
3.5.1 
3.5.2 
3.5.3 
3.6 
3.6.1 
3.6.2 
3.6.3 
3.6.4 
3.6.5 
3.6.5.1 
3.6.5.2 
3.6.5.3 
3.6.5.4 
3.6.5.5 
3.6.5.6 
3.6.5.7 
3.6.5.8 
3.6.5.9 
3.6.5.10 
3.6.5.11 
3.6.5.12 
3.6.5.13 
3.6.5.14 
3.6.5.15 
3.6.5.16 
3.6.5.17 
3.6.5.18 
3.6.6 
4.4 
4.4.1 
4.4.2 
4.4.2.1 
4.4.2.1.1 
4.4.2.1.2 
4.4.2.2 
4.4.2.2.1 
4.4.2.2.2 
4.4.2.2.3 
4.4.2.2.4 
4.4.3 
4.4.3.1 
4.4.3.1.1 
4.4.3.1.2 
4.4.3.1.3 
4.4.3.2 
4.4.3.2.1 
4.4.3.2.2 
4.4.3.2.3 
4.4.4 
4.4.5 
4.4.6 
Interaction of DNA and RNA with metal ions 277

(J.J.
 BUTZOW, G.L. EICHHORN, Y.A. SHIN)Introduction 277

Data on interaction of metal ions with DNA, synthetic polydeoxynucleotides and 282
synthetic polyribonucleotides
quaternary structures

Binding of metal ions 282

Association constants 282

Binding characteristics 288

Effects of metal ion binding on conformation of DNA 296

Helix coil transition (melting temperature) 296

Transition between right- and left-handed helix 320

Other conformational changes: secondary (except right-left handed), tertiary, 334

Hydrodynamic property changes 341

Data on interaction of metal ions with RNA 345

Binding of metal ions 345

Types of metal ion binding sites in tRNAs 345

Details of metal ion binding sites in RNAs 346

Association constants for metal ion-tRNA interactions 364

Effects of metal ion binding on conformation of RNA 368

Effects on secondary structure 368

Effects on tertiary structures 376

Thermal melting effects - tRNAs 390

Data on metal ion catalyzed degradation of RNAs and polyribonucleotides 394

Data on metal ion catalyzed degradation of DNAs and polydeoxynucleotides 411

References for 4.4 434


