Journal ArticleDOI
The locus of sequence-directed and protein-induced DNA bending
Hen-Ming Wu,Donald M. Crothers +1 more
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TLDR
The bending locus of trypanosome kinetoplast DNA, identified by gel electrophoresis, has tracts of a simple repeat sequence symmetrically distributed about it, with a repeat interval of 10 base pairs.Abstract:
The bending locus of trypanosome kinetoplast DNA, identified by gel electrophoresis, has tracts of a simple repeat sequence (CA5–6 T) symmetrically distributed about it, with a repeat interval of 10 base pairs The analogous bending induced when catabolite gene activating protein binds to its recognition sequence near the promoter of the Escherichia coli lac operon is centred on a site about 5–7 base pairs away from the centre of the protein binding siteread more
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Journal ArticleDOI
Repression and catabolite gene activation in the araBAD operon.
TL;DR: Data is presented showing that deletions generated by in vitro mutagenesis of the CAP site led to a five- to sixfold reduction in single-copy araBAD promoter activity in vivo.
Journal ArticleDOI
Purine and Pyrimidine-specific Repression of the Escherichia coli carAB Operon are Functionally and Structurally Coupled
TL;DR: The existence of an unprecedented functional and structural coupling between the modulation of P1 activity by purine and pyrimidine residues that appears to result from the unique position of the PUR box in the carAB control region, far upstream of the promoter is revealed.
Journal ArticleDOI
Distant neighbor base sequence context effects in human nucleotide excision repair of a benzo[a]pyrene-derived DNA lesion.
Yuqin Cai,Konstantin Kropachev,Rong Xu,Yijin Tang,Marina Kolbanovskii,Alexander Kolbanovskii,Shantu Amin,Dinshaw J. Patel,Suse Broyde,Nicholas E. Geacintov +9 more
TL;DR: Structural properties fit well with earlier findings that in the case of the family of minor groove 10S (+)-trans-anti-B[a]P-N(2)-dG lesions, flexible bends and enlarged minor groove widths constitute NER recognition signals, and extend the understanding of sequence context effects on NER to the neighbors that are distant to the lesion.
Journal ArticleDOI
Analysis of branched nucleic acid structure using comparative gel electrophoresis.
TL;DR: Two recent crystallographic structures show that the global structures were correctly deduced by electrophoresis, proving the worth of the method even in these rather complex systems.
Journal ArticleDOI
Localization of amino acids required for Fis to function as a class II transcriptional activator at the RpoS-dependent proP P2 promoter.
TL;DR: It is concluded that the same amino acids are used by Fis to activate transcription from a class I (-71, rrnB P1) and class II (-41, proP P2) location, but this region is distinct from that required to regulate the Hin site-specific DNA inversion reaction.
References
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Journal ArticleDOI
A rapid boiling method for the preparation of bacterial plasmids
David S. Holmes,Michael Quigley +1 more
TL;DR: A simple and rapid method for preparing plasmids for restriction enzyme analysis has been developed and can be readily adapted for the preparation of plasmid from liter cultures with quantitative yields.
Journal ArticleDOI
Structure of catabolite gene activator protein at 2.9 Å resolution suggests binding to left-handed B-DNA
David B. McKay,Thomas A. Steitz +1 more
TL;DR: The 2.9 Å resolution crystal structure of Escherichia coli catabolite gene activator protein (CAP) completed with cyclic AMP reveals two distinct structural domains separated by a cleft, suggesting that the CAP conversion of right- to left-handed DNA in a closed supercoil, is what activates transcription by RNA polymerase.
Journal ArticleDOI
Bent helical structure in kinetoplast DNA.
TL;DR: It is proposed that this molecule contains a region of systematically bent B-DNA, which accounts for the fragment's difficulty in snaking through the pores of a polyacrylamide gel, its ease in diffusing into Sephacryl beads, and its smaller rotational relaxation time.
Journal ArticleDOI
Genetic regulation: the Lac control region.
TL;DR: Identification of mutant variants of the sequence combined with the in vitro biochemical studies of others has allowed us to tentatively identify the recognition site for each of these proteins, and to suggest how CAP might act at a distance to affect the interaction of RNA polymerase with the promoter.
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Empirical estimation of protein-induced DNA bending angles: applications to λ site-specific recombination complexes
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