Vladimir Tchernaenko

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Numerous biological processes are regulated by DNA elements that communicate with their targets over a distance via formation of protein-bridged DNA loops. One of the first questions arising in studies of DNA looping is whether the rate of loop formation is limited by diffusion of the DNA sites. We addressed this question by comparing the in vitro measured(More)
Electrophoretic mobility shift (bandshift) phasing analysis and rotational variant topological analysis were performed on initiation complexes formed on the bacteriophage lambda PR promoter. Both the open complex and an abortive complex containing a short RNA primer extending to +3 were characterized. The two methods were used to analyze a series of(More)
It is well established that an A-tract imparts curvature to the DNA double helix. Constructs of such A-tracts have been used as bend standards in a large number of both structural and functional studies, and A-tracts can confer significant activation in transcription. An accurate value for the bend angle induced by an A-tract is centrally important to all(More)
Sequences of four to six adenine residues, termed A-tracts, have been shown to produce curvature in the DNA double helix. A-tracts have been used extensively as reference standards to quantify bending induced by other sequences as well as by DNA binding proteins when they bind to their sites. However, the ability of an A-tract to serve as such a standard is(More)
The properties of the DNA bubble in the transcription open complex have been characterized by topological analysis of DNA circles containing the lac UV5 promoter or the PR promoter from bacteriophage lambda. Topological analysis is particularly well suited to this purpose since it quantifies the changes in DNA duplex geometry caused by bubble formation as(More)
The rotational variant method of Lutter et al. was developed to measure the bend angle induced when a protein binds to DNA. To measure the intrinsic bend conferred by a sequence of six adenine bases (an A6 tract), the method was modified by relaxing at high temperature to remove the bend. We describe here an alternative approach that involves unwinding the(More)
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