DNA-Protein Interactions

1 DNA structure.- 1.1 Structural features of DNA.- 1.2 DNA polymorphism.- 1.3 Conformational variability of DNA.- 1.4 Intrinsic bending of DNA.- 1.5 DNA supercoiling and topology.- 1.6 The topology of protein-bound DNA.- 1.7 Structure of supercoiled DNA.- References.- 2 DNA—protein interactions: The three-dimensional architecture of DNA—protein complexes.- 2.1 General principles.- 2.2 Local DNA conformation and protein binding.- 2.3 DNA wrapping.- 2.4 DNA configuration and sequence periodicity.- 2.5 The establishment of DNA architecture.- References.- 3 DNA—protein interactions: Sequence specific recognition.- 3.1 General principles of sequence specific recognition.- 3.2 Structural motifs for sequence specific binding.- 3.3 Co-operative binding to DNA.- 3.4 Co-operativity at a distance: DNA looping.- 3.5 Protein flexibility in DNA—protein complexes.- References.- 4 The mechanism of RNA chain initiation.- 4.1 The promoter.- 4.2 RNA polymerases.- 4.3 The kinetics of transcription initiation.- 4.4 The molecular interactions of RNA polymerase with a promoter site.- 4.5 The topological consequences of transcription.- 4.6 Transcriptional activators.- 4.7 Transcriptional activation by negative superhelicity.- 4.8 How does RNA polymerase melt promoter DNA?.- References.- 5 The regulation of promoter selectivity in eubacteria.- 5.1 Control of stable RNA synthesis.- 5.2 Stable RNA promoters.- 5.3 The transition from exponential growth to stationary phase and vice versa.- 5.4 Sigma factors and promoter recognition.- 5.5 The heat shock response.- 5.6 ?54: A target for transcriptional enhancers.- 5.7 The transcriptional programmes of bacterial viruses.- References.- 6 The mechanism of eukaryotic transcription.- 6.1 Eukaryotic transcriptional regulatory elements.- 6.2Eukaryotic transcriptional regulators: structure.- 6.3 Specificity and selectivity of eukaryotic transcription factors.- 6.4 Sp1 transcription factor.- 6.5 Heat shock transcription factor (HSF).- 6.6 How do transcriptional activators work?.- 6.7 Transcription by RNA polymerase III.- 6.8 The establishment of repression.- References.- 7 Chromatin and transcription.- 7.1 Local control of chromatin structure.- 7.2 The structural organization of chromatin.- 7.2.1 Chromosomal superstructure.- 7.3 Heterochromatin.- 7.4 The regulation of transcriptional competence.- References.

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