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Reference: Julien Bischerour and Ronald Chalmers, (2007). Base-flipping dynamics in a DNA hairpin processing reaction. Nucleic Acids Research, 35 (8), 2584-2595.Citable link to this page:


Base-flipping dynamics in a DNA hairpin processing reaction

Abstract: Many enzymes that repair or modify bases in double-stranded DNA gain access to their substrates by base flipping. Although crystal structures provide stunning snap shots, biochemical approaches addressing the dynamics have proven difficult, particularly in complicated multi-step reactions. Here, we use protein-DNA crosslinking and potassium permanganate reactivity to explore the base-flipping step in tN5 transposition. We present a model to suggest that base flipping is driven by a combination of factors including DNA bending and the intrusion of a probe residue. The forces are postulated to act early in the reaction to create a state of tension, relieved by base flipping after cleavage of the first strand of DNA at the transposon end. Elimination of the probe residue retards the kinetics of nicking and reduces base flipping by 50%. Unexpectedly, the probe residue is even more important during the hairpin resolution step. Overall, base flipping is pivotal to the hairpin processing reaction because it performs two opposite but closely related functions. On one hand it disrupts the double helix, providing the necessary strand separation and steric freedom. While on the other, transposase appears to position the second DNA strand in the active site for cleavage using the flipped base as a handle.

Publication status:PublishedPeer Review status:Peer reviewedVersion:Publisher's version Funder: Wellcome Trust   Notes:Citation: Bischerour, J. & Chalmers, R. (2007). 'Base-flipping dynamics in a DNA hairpin processing reaction', Nucleic Acids Research, 35(8), 2584-2595. [Available at]. This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License ( which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

Bibliographic Details

Publisher: Oxford University Press

Publisher Website:

Host: Nucleic Acids Researchsee more from them

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Issue Date: 2007-April

Copyright Date: 2007



Issn: 0305-1048

Eissn: 1362-4962

Urn: uuid:0cae0044-30d3-498c-94b9-d38efc28e5b2 Item Description

Type: Article: post-print;

Language: en

Version: Publisher's versionKeywords: base flipping DNASubjects: Biochemistry Tiny URL: ora:3020


Autor: Julien Bischerour - institutionUniversity of Oxford facultyMedical Sciences Division - Biochemistry - - - Ronald Chalmers - insti



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