DNA-Protein Interactions

Our understanding of the mechanisms regulating gene expression, which determine the patterns of growth and development in all living organisms, ultimately involves the elucidation of the detailed and dy namic interactions of proteins with nucleic acids -both DNA and RNA. Until recently the commonly presented view of the DNA double helix as visualized on the covers of many textbooks and journals - was as a monotonous static straight rod incapable in its own right of directing the processes necessary for the conservation and selective reading of genetic information. This view, although perhaps extreme, was reinforced by the necessary linearity of genetic maps. The reality is that the biological functions of both DNA and RNA are dependent on complex, and sometimes transient, three-dimensional nucleoprotein structures in which genetically distant elements are brought into close spatial proximity. It is in such structures that the enzymatic manipulation of DNA in the essential biological processes as DNA replication, transcription and recombination are effected - the complexes are the mediators of the 'DNA transactions' of Hatch Echols.

Inhalt
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 DNAprotein interactions: The three-dimensional architecture of DNAprotein 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 DNAprotein 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 DNAprotein 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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