Multiple Aspects of DNA and RNA: From Biophysics to Bioinformatics

Previous sessions......Page 7
Lecturers......Page 10
Organizers......Page 11
Participants......Page 12
Preface......Page 16
Contents......Page 18
DNA structure, dynamics and recognition......Page 26
Introduction to the DNA double helix......Page 30
Biophysical studies of DNA - structure and stability......Page 41
DNA dynamics......Page 46
Deformations of the double helix......Page 50
DNA recognition......Page 58
Introduction to non-Watson–Crick base pairs and RNA folding......Page 66
Definitions......Page 70
The annotation of non-Watson-Crick base pairs and of RNA motifs......Page 77
RNA-RNA recognition motifs......Page 81
Roles of RNA motifs in RNA-protein recognition......Page 86
References......Page 94
Regulation of transcription by RNA polymerase II......Page 98
Introduction......Page 102
DNA regulatory elements......Page 104
Basal/general transcription factors......Page 106
Sequence-specific DNA-binding factors......Page 108
Chromatin and transcription......Page 110
Conclusions and speculations......Page 112
References......Page 114
Basic concepts of statistical physics of polymers......Page 116
Fundamentals of physical viewpoint in polymer science......Page 120
Rotational-isomeric flexibility mechanism......Page 121
Types of polymer molecules......Page 123
Physical states of polymer materials......Page 125
Polymer solutions......Page 126
Size of ideal freely-jointed chain. Entangled coil......Page 127
Size of ideal chain with fixed valency angle......Page 129
Kuhn segment length of a polymer chain......Page 130
Persistent length of a polymer chain......Page 131
Stiff and flexible chains......Page 132
Gaussian distribution for the end-to-end vector for ideal chain......Page 133
The property of high elasticity......Page 134
Elasticity of a single ideal chain......Page 136
Elasticity of a polymer network (rubber)......Page 138
Main properties of entangled polymer fluids......Page 141
Viscosity of fluids......Page 142
The property of viscoelasticity......Page 143
Theory of reptations......Page 144
The method of gel-electrophoresis in application to DNA molecules......Page 147
Gel permeation chromatography......Page 149
References......Page 150
The physics of DNA electrophoresis......Page 152
Importance of DNA sorting in biology and how physics can help......Page 156
Physical description of DNA......Page 158
Electrophoretic force......Page 159
DNA sequencing: gel electrophoresis of single-stranded DNA......Page 160
Reptative dynamics......Page 161
Biased reptation......Page 162
Repton model......Page 165
Strategies for DNA sequencing......Page 166
Complex dynamics in constant fields......Page 167
Pulsed-field gel electrophoresis: separation of restriction fragments......Page 169
Difficulty of separating very large molecules......Page 172
Obstacle courses on microchips......Page 173
Collision of a DNA molecule with an obstacle......Page 174
Efficient pulsed-field fractionation in silicon arrays......Page 175
Continuous separation in asymmetric pulsed fields......Page 177
Asymmetric sieves for sorting DNA......Page 179
Rapid continuous separation in a divided laminar flow......Page 181
References......Page 183
Single-molecule studies of DNA mechanics and DNA/protein interactions......Page 186
Introduction......Page 190
Ease of handling......Page 191
DNA as a model polymer......Page 192
Strategies and forces involved......Page 193
Measurement techniques......Page 195
Measuring forces with Brownian motion......Page 197
Advantages and disadvantages of the manipulation techniques......Page 199
Tertiary structures in DNA......Page 200
Topological formalism......Page 201
DNA topoisomerases......Page 202
DNA elasticity in the absence of torsion (sigma=0)......Page 203
Results......Page 204
Mechanical properties of supercoiled DNA......Page 205
Interpretation......Page 206
The buckling instability in DNA......Page 208
Stretching single-strand DNA......Page 209
Conclusions on the mechanical properties of nucleic acids......Page 210
An introduction to transcription......Page 211
Historical overview: transcription elongation, or RNA polymerase as a linear motor......Page 213
RNA polymerase as a torquing device: the case of transcription initiation......Page 214
Type I and Type II topoisomerases......Page 218
Enzymatic cycle......Page 220
Calibrating the experiment......Page 221
Crossover clamping in the absence of ATP......Page 222
Low ATP concentrations: detecting a single enzymatic cycle......Page 223
High ATP concentration......Page 224
Determining Vsat, the saturated reaction velocity......Page 225
Effect of the stretching force......Page 226
Topo II only removes crossovers in DNA......Page 227
A comparison with E. coli topo IV......Page 228
Conclusions on type II topoisomerases......Page 229
References......Page 230
Introduction to single-DNA micromechanics......Page 236
Introduction......Page 240
Structure......Page 242
Discrete-segment model of a semiflexible polymer......Page 244
Bending elasticity and the persistence length......Page 246
End-to-end distance......Page 247
DNA loop bending energies......Page 248
Site-juxtaposition probabilities......Page 249
Stretching out the double helix......Page 250
Larger forces (> kB T/A = 0.08 pN)......Page 252
Free energy of the semiflexible polymer......Page 254
Really large forces (> 10 pN)......Page 255
Strand separation......Page 256
Free-energy models of strand separation......Page 257
Sequence-dependent models......Page 258
Free energy of internal `bubbles\'......Page 259
Small internal bubbles may facilitate sharp bending......Page 260
Stretching single-stranded nucleic acids......Page 261
Unzipping the double helix......Page 263
Effect of torque on dsDNA end......Page 265
Fixed extension versus fixed force for unzipping......Page 266
Twist rigidity of the double helix......Page 267
Writhing of the double helix......Page 268
Simple model of plectonemic supercoiling......Page 269
Twisted DNA under tension......Page 273
Forces and torques can drive large structural reorganizations of the double helix......Page 275
DNA knotting......Page 276
Knotting a molecule is surprisingly unlikely......Page 277
Condensation-resolution mechanism for disentangling long molecules......Page 278
DNA-protein interactions......Page 279
Three-dimensional diffusion to the target......Page 280
Nonspecific interactions can accelerate targeting......Page 281
DNA-looping protein: equilibrium `length-loss\' model......Page 282
Loop formation kinetics......Page 283
DNA-bending proteins......Page 284
Analytical calculation for compaction by DNA-bending proteins......Page 287
Effects of twisting of DNA by proteins......Page 289
Surprising results of experiments......Page 290
Conclusion......Page 291
References......Page 293
The analysis of regulatory sequences......Page 296
The non-coding genome......Page 300
Transcriptional regulation......Page 301
String-based representations......Page 304
Matrix-based representation......Page 305
Study cases......Page 308
Analysis of word occurrences......Page 309
Analysis of dyad occurrences (spaced pairs of words)......Page 316
Strengths and weaknesses of word- and dyad-based pattern discovery......Page 318
String-based pattern matching......Page 319
Matrix-based pattern discovery......Page 321
Gibbs sampling......Page 322
Strengths and weaknesses of matrix-based pattern discovery......Page 324
Concluding remarks......Page 326
IUPAC ambiguous nucleotide code......Page 327
A survey of gene circuit approach applied to modelling of segment determination in fruitfly......Page 330
Introduction......Page 334
The biology of segment determination......Page 335
The gene circuit modelling framework......Page 336
Quantitative expression data......Page 338
Selection of gene circuits......Page 339
Regulatory interactions in gap gene system......Page 340
Pattern formation and nuclear divisions are uncoupled in Drosophila segmentation......Page 343
Conclusions......Page 345
References......Page 346
Modeling, analysis, and simulation of genetic regulatory networks: from differential equations to logical models......Page 350
Introduction......Page 354
Models and analysis......Page 356
Analysis of regulatory networks involved in cell-cycle control, circadian rhythms, and development......Page 359
Models and analysis......Page 360
Simulation of the initiation of sporulation in Bacillus subtilis......Page 364
Models and analysis......Page 368
Modeling of the lysis-lysogeny decision during the infection of Escherichia coli by bacteriophage lambda......Page 370
Extensions of logical modeling......Page 374
Conclusions......Page 375
References......Page 376