Determination of base binding strength and base stacking interaction of DNA duplex using atomic force microscope

Scientific Reports
Tian-biao ZhangYi-fu Guan

Abstract

As one of the most crucial properties of DNA, the structural stability and the mechanical strength are attracting a great attention. Here, we take advantage of high force resolution and high special resolution of Atom Force Microscope and investigate the mechanical force of DNA duplexes. To evaluate the base pair hydrogen bond strength and base stacking force in DNA strands, we designed two modes (unzipping and stretching) for the measurement rupture forces. Employing k-means clustering algorithm, the ruptured force are clustered and the mean values are estimated. We assessed the influence of experimental parameters and performed the force evaluation for DNA duplexes of pure dG/dC and dA/dT base pairs. The base binding strength of single dG/dC and single dA/dT were estimated to be 20.0 ± 0.2 pN and 14.0 ± 0.3 pN, respectively, and the base stacking interaction was estimated to be 2.0 ± 0.1 pN. Our results provide valuable information about the quantitative evaluation of the mechanical properties of the DNA duplexes.

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Citations

May 10, 2015·The Journal of Chemical Physics·R K MishraS Kumar
Jul 21, 2016·Analytical Chemistry·Seungyeop ChoiSang Woo Lee
Dec 13, 2017·Physical Chemistry Chemical Physics : PCCP·Weibin RenJiang Zhao
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Jun 19, 2021·Biotechnology and Applied Biochemistry·Tijjani AdamM N A Uda
Oct 12, 2021·Journal of Biomolecular Structure & Dynamics·Cristian OrdóñezRuben Santamaria

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