Effect of Inert Tails on the Thermodynamics of DNA Hybridization

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• 作者：Lorenzo Di Michele ; Bortolo M. Mognetti ; Taiki Yanagishima ; Patrick Varilly ; Zachary Ruff ; Daan Frenkel ; Erika Eiser
• 刊名：Journal of the American Chemical Society
• 出版年：2014
• 出版时间：May 7, 2014
• 年：2014
• 卷：136
• 期：18
• 页码：6538-6541
• 全文大小：308K
• 年卷期：v.136,no.18(May 7, 2014)
• ISSN：1520-5126

文摘

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.