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A Novel Bipartite Mode of Binding of M.smegmatis Topoisomerase I to its Recognition Sequence

Sikder, Devanjan and Nagaraja, Valakunja (2001) A Novel Bipartite Mode of Binding of M.smegmatis Topoisomerase I to its Recognition Sequence. In: Journal of Molecular Biology, 314 . pp. 347-357.


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We have investigated interaction of Mycobacterium smegmatis topoisomerase I at its specific recognition sequence. DNase I foot printing demonstrates a large region of protection on both the scissile and non-scissile strands of DNA. Methylation protection and interference analyses reveal base-specific contacts within the recognition sequence. Missing contact analyses reveal additional interactions with the residues in both single and double-stranded DNA, and hence underline the role for the functional groups associated with those bases. These interactions are supplemented by phosphate contacts in the scissile strand. Conformation specific probes reveal protein-induced structural distortion of the DNA helix at the T-A-T-A sequence 11 bp upstream to the recognition sequence. Based on these foot printing analyses that define parameters of Topoisomerase I-DNA interactions, a model of topoisomerase I binding to its substrate is presented. Within the large protected region of 30 bp, the enzyme makes direct contact at two locations in the scissile strand, one around the leavage site and the other 8-12 bases upstream. Thus the enzyme makes asymmetric recognition of DNA and could carry out DNA relaxation by either of the two proposed mechanisms: enzyme bridged and restricted rotation.

Item Type: Journal Article
Publication: Journal of Molecular Biology
Publisher: Academic Press
Keywords: footprinting;mycobacteria;Sequence specificity; Topoisomerase I
Department/Centre: Division of Biological Sciences > Microbiology & Cell Biology
Date Deposited: 23 Jul 2004
Last Modified: 19 Sep 2010 04:13
URI: http://eprints.iisc.ac.in/id/eprint/1025

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