Mismatch Induced DNA "Unbending" Upon Duplex Opening

¹ School of Chemical and Biomolecular Engineering, Cornell University
² Department of Applied and Engineering Physics, Cornell University
³ Department of Materials Science and Engineering, Cornell University
⁴ Cornell University

^* To whom correspondence should be addressed. E-mail: laa25{at}cornell.edu.

Submitted on May 3, 2005
Revised on June 3, 2005
Accepted on 18 July 2005

	Abstract

A DNA duplex can be torn open at a specific position by introducing a branch or bulge to create an asymmetric three way junction (TWJ). The opened duplex manifests a bent conformation (bending angle 60°, relative to the unopened form), which leads to a dramatic decrease in gel electrophoretic mobility. In the presence of a base pair mismatch at the opening position, the DNA backbone becomes less bent and assumes a distorted T-shaped structure, resulting in an increase in polyacrylamide (PA) gel electrophoretic mobility. In this manuscript, both conformational changes are confirmed using fluorescence resonance energy transfer (FRET) experiments and found to be similar to the signature conformational changes of DNA duplex upon MutS protein binding. Our results imply that some structural rearrangements essential for mismatch recognition are achievable without protein interference. The gel electrophoretic mobility data of TWJ with and without mismatch correlates well with rotational diffusivity data, computed by taking into account the conformational change of TWJ induced by base mismatch.

Key Words: FRET, Mutations, Three Way Junctions, electrophoresis, p53, protein dna interaction

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