Molecular pathways in DNA-DNA hybridization of surface-bound oligonucleotides

Moritz Julian Hoefert; Edward John Sambriski; Juan José de Pablo

doi:10.1039/C0SM00729C

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Soft Matter

Issue 2, 2011

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Molecular pathways in DNA-DNA hybridization of surface-bound oligonucleotides

Moritz Julian Hoefert,^a Edward John Sambriski^b and Juan José de Pablo*^a

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Department of Chemical and Biological Engineering, University of Wisconsin-Madison, Madison, United States of America
E-mail: depablo@engr.wisc.edu ;
Fax: (+608) 262-5434 ;
Tel: (+608) 262-7727

Department of Chemistry and Biochemistry, Delaware Valley College, Doylestown, United States of America

Soft Matter, 2011,7, 560-566

DOI: 10.1039/C0SM00729C
Received 26 Jul 2010, Accepted 27 Sep 2010
First published online 12 Nov 2010

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Abstract
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A molecular model of DNA, that has been shown to reproduce hybridization, is used here to study the transition from two single-stranded molecules to a double-helical complex in situations where one strand is attached to a surface. Transition Path Sampling simulations reveal that hybridization is initiated by forming specific contacts between distinct bases of the molecule. Molecules with repetitive sequences form double helices by sliding along each other after having formed initial contacts. For random sequences, it is shown that the pathway that molecules follow to hybridization depends on the linker length as well as the temperature, and is significantly different from that observed in the bulk.

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