Effect of Inert Tails on the Thermodynamics of DNA Hybridization

Di Michele, Lorenzo and Mognetti, Bortolo M. and Yanagishima, Taiki and Varilly, Patrick and Ruff, Zachary and Frenkel, Daan and Eiser, Erika (2014) Effect of Inert Tails on the Thermodynamics of DNA Hybridization. Journal of the American Chemical Society, 136 (18). pp. 6538-6541.

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Official URL: http://dx.doi.org/10.1021/ja500027v

Abstract

The selective hybridization of DNA is of key importance for many practical applications such as gene detection and DNA-mediated self-assembly. These applications require a quantitative prediction of the hybridization free energy. Existing methods ignore the effects of non-complementary ssDNA tails beyond the first unpaired base. We use experiments and simulations to show that the binding strength of complementary ssDNA oligomers is altered by these sequences of non-complementary nucleotides. Even a small number of non-binding bases are enough to raise the hybridization free energy by approximately 1 kcal/mol at physiological salt concentrations. We propose a simple analytical expression that accounts quantitatively for this variation as a function of tail length and salt concentration.

Item Type: Article
Uncontrolled Keywords: 2014AREP; IA67;
Subjects: 99 - Other
Divisions: 99 - Other
Journal or Publication Title: Journal of the American Chemical Society
Volume: 136
Page Range: pp. 6538-6541
Depositing User: Sarah Humbert
Date Deposited: 27 Jun 2014 16:49
Last Modified: 03 Jul 2014 17:09
URI: http://eprints.esc.cam.ac.uk/id/eprint/3070

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