Journal ArticleDOI
The locus of sequence-directed and protein-induced DNA bending
Hen-Ming Wu,Donald M. Crothers +1 more
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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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Rational Design of Sequence-Specific DNA Alkylating Agents Based on Duocarmycin A and Pyrrole−Imidazole Hairpin Polyamides
TL;DR: The alkylation of non-self-complementary duplex decanucleotides, ODN1 and ODN2, was investigated and HPLC and ESMS analyses of the reaction of these ODNs demonstrated that both conjugates efficiently and selectively alkylate N3 of the purine bases of their target sequences.
Journal ArticleDOI
An introduction to the mechanics of DNA.
A. A. Travers,J. M. T. Thompson +1 more
TL;DR: This article gives an overview of recent research on the mechanical properties and spatial deformations of the DNA molecule.
Journal ArticleDOI
Repression of the klebsiella aerogenes nac promoter
TL;DR: Transcription of the nitrogen-regulated nac promoter of Klebsiella aerogenes requires sigma54 RNA polymerase, is activated by the phosphorylated form of the transcription factor nitrogen regulator I (NRI) (NtrC), and is repressed by the product of the nac gene, Nac.
Journal ArticleDOI
Indirect Readout of DNA Sequence at the Primary-kink Site in the CAP-DNA Complex: DNA Binding Specificity Based on Energetics of DNA Kinking
TL;DR: In this article, the authors show that the main determinant of DNA conformation in this system is protein-DNA interaction, and not DNA sequence, and further infer that indirect readout does not involve differences in the geometry of DNA kinking but, rather, solely differ in the energetics of DNA bending.
Journal ArticleDOI
Isolation of intermediates in the binding of the FLP recombinase of the yeast plasmid 2-micron circle to its target sequence.
TL;DR: On the basis of the behavior of various FLP target sequences in the gel-binding assay, a model describing the steps that lead to the formation of a stable FLP-DNA complex is proposed.
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.
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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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