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DNA topoisomerase II selects DNA cleavage sites based on reactivity rather than binding affinity

DNA topoisomerase II modulates DNA topology by relieving supercoil stress and by unknotting or decatenating entangled DNA. During its reaction cycle, the enzyme creates a transient double-strand break in one DNA segment, the G-DNA. This break serves as a gate through which another DNA segment is tra...

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Autores principales: Mueller-Planitz, Felix, Herschlag, Daniel
Formato: Texto
Lenguaje:English
Publicado: Oxford University Press 2007
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1920260/
https://www.ncbi.nlm.nih.gov/pubmed/17517767
http://dx.doi.org/10.1093/nar/gkm335
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author Mueller-Planitz, Felix
Herschlag, Daniel
author_facet Mueller-Planitz, Felix
Herschlag, Daniel
author_sort Mueller-Planitz, Felix
collection PubMed
description DNA topoisomerase II modulates DNA topology by relieving supercoil stress and by unknotting or decatenating entangled DNA. During its reaction cycle, the enzyme creates a transient double-strand break in one DNA segment, the G-DNA. This break serves as a gate through which another DNA segment is transported. Defined topoisomerase II cleavage sites in genomic and plasmid DNA have been previously mapped. To dissect the G-DNA recognition mechanism, we studied the affinity and reactivity of a series of DNA duplexes of varied sequence under conditions that only allow G-DNA to bind. These DNA duplexes could be cleaved to varying extents ranging from undetectable (<0.5%) to 80%. The sequence that defines a cleavage site resides within the central 20 bp of the duplex. The DNA affinity does not correlate with the ability of the enzyme to cleave DNA, suggesting that the binding step does not contribute significantly to the selection mechanism. Kinetic experiments show that the selectivity interactions are formed before rather than subsequent to cleavage. Presumably the binding energy of the cognate interactions is used to promote a conformational change that brings the enzyme into a cleavage competent state. The ability to modulate the extent of DNA cleavage by varying the DNA sequence may be valuable for future structural and mechanistic studies that aim to determine topoisomerase structures with DNA bound in pre- and post-cleavage states and to understand the conformational changes associated with DNA binding and cleavage.
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spelling pubmed-19202602007-07-19 DNA topoisomerase II selects DNA cleavage sites based on reactivity rather than binding affinity Mueller-Planitz, Felix Herschlag, Daniel Nucleic Acids Res Nucleic Acid Enzymes DNA topoisomerase II modulates DNA topology by relieving supercoil stress and by unknotting or decatenating entangled DNA. During its reaction cycle, the enzyme creates a transient double-strand break in one DNA segment, the G-DNA. This break serves as a gate through which another DNA segment is transported. Defined topoisomerase II cleavage sites in genomic and plasmid DNA have been previously mapped. To dissect the G-DNA recognition mechanism, we studied the affinity and reactivity of a series of DNA duplexes of varied sequence under conditions that only allow G-DNA to bind. These DNA duplexes could be cleaved to varying extents ranging from undetectable (<0.5%) to 80%. The sequence that defines a cleavage site resides within the central 20 bp of the duplex. The DNA affinity does not correlate with the ability of the enzyme to cleave DNA, suggesting that the binding step does not contribute significantly to the selection mechanism. Kinetic experiments show that the selectivity interactions are formed before rather than subsequent to cleavage. Presumably the binding energy of the cognate interactions is used to promote a conformational change that brings the enzyme into a cleavage competent state. The ability to modulate the extent of DNA cleavage by varying the DNA sequence may be valuable for future structural and mechanistic studies that aim to determine topoisomerase structures with DNA bound in pre- and post-cleavage states and to understand the conformational changes associated with DNA binding and cleavage. Oxford University Press 2007-06 2007-05-21 /pmc/articles/PMC1920260/ /pubmed/17517767 http://dx.doi.org/10.1093/nar/gkm335 Text en © 2007 The Author(s) http://creativecommons.org/licenses/by-nc/2.0/uk/ This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Nucleic Acid Enzymes
Mueller-Planitz, Felix
Herschlag, Daniel
DNA topoisomerase II selects DNA cleavage sites based on reactivity rather than binding affinity
title DNA topoisomerase II selects DNA cleavage sites based on reactivity rather than binding affinity
title_full DNA topoisomerase II selects DNA cleavage sites based on reactivity rather than binding affinity
title_fullStr DNA topoisomerase II selects DNA cleavage sites based on reactivity rather than binding affinity
title_full_unstemmed DNA topoisomerase II selects DNA cleavage sites based on reactivity rather than binding affinity
title_short DNA topoisomerase II selects DNA cleavage sites based on reactivity rather than binding affinity
title_sort dna topoisomerase ii selects dna cleavage sites based on reactivity rather than binding affinity
topic Nucleic Acid Enzymes
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1920260/
https://www.ncbi.nlm.nih.gov/pubmed/17517767
http://dx.doi.org/10.1093/nar/gkm335
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