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Mismatch-Induced DNA Unbending upon Duplex Opening

Chongli Yuan ^*, Elizabeth Rhoades , Daniel M. Heuer ^*  and Lynden A. Archer ^*

^* School of Chemical and Biomolecular Engineering, Department of Applied and Engineering Physics, and Department of Materials Science and Engineering, Cornell University, Ithaca, New York 14853

Correspondence: Address reprint requests to Professor Lynden Archer, School of Chemical and Biomolecular Engineering, 120 Olin Hall, Cornell University, Ithaca, NY 14853. Fax: 607-255-9166; E-mail: laa25{at}cornell.edu.

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 basepair mismatch at the opening position, the DNA backbone becomes less bent and assumes a distorted T-shaped structure, resulting in an increase in polyacrylamide gel electrophoretic mobility. Both conformational changes are confirmed using fluorescence resonance energy transfer 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 for DNA TWJs with and without base mismatches correlates well with rotational diffusivity, computed by taking into account the conformational change of TWJ induced by base mismatch.

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