Weak tension accelerates hybridization and dehybridization of short oligonucleotides.
Weak tension accelerates hybridization and dehybridization of short oligonucleotides.
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DOI：
10.1093/nar/gkad118
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发表时间：
2023-04-24
影响因子：
14.9
通讯作者：
中科院分区：
文献类型：
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DNA 在张力作用下的杂交和去杂交与基本遗传过程和基于 DNA 的机械生物学检测的设计相关。虽然强张力会加速 DNA 熔化并减缓 DNA 退火，但低于 5pN 的张力的影响尚不清楚。在这项研究中，我们开发了一种 DNA 弓测定法，它利用双链 DNA (dsDNA) 的弯曲刚度对单链 DNA (ssDNA) 目标施加 2–6 pN 范围内的微弱张力。将此测定与单分子 FRET 相结合，我们测量了张力下 15 nt ssDNA 与 8-9 nt 寡核苷酸之间的杂交和去杂交动力学，发现对于测试的各种核苷酸序列，杂交和去杂交速率均随着张力单调增加。这些发现表明，过渡态的有核双链体比纯 dsDNA 或 ssDNA 对应物延伸得更多。基于粗粒度 oxDNA 模拟，我们提出过渡态延伸的增加是由于彼此非常接近的未配对 ssDNA 片段之间的空间排斥所致。利用通过短 DNA 片段模拟验证的线性力-延伸关系，我们推导出力到速率转换的解析方程，该方程与我们的测量结果非常吻合。
The hybridization and dehybridization of DNA subject to tension is relevant to fundamental genetic processes and to the design of DNA-based mechanobiology assays. While strong tension accelerates DNA melting and decelerates DNA annealing, the effects of tension weaker than 5 pN are less clear. In this study, we developed a DNA bow assay, which uses the bending rigidity of double-stranded DNA (dsDNA) to exert weak tension on a single-stranded DNA (ssDNA) target in the range of 2–6 pN. Combining this assay with single-molecule FRET, we measured the hybridization and dehybridization kinetics between a 15 nt ssDNA under tension and a 8–9 nt oligonucleotide, and found that both the hybridization and dehybridization rates monotonically increase with tension for various nucleotide sequences tested. These findings suggest that the nucleated duplex in its transition state is more extended than the pure dsDNA or ssDNA counterpart. Based on coarse-grained oxDNA simulations, we propose that this increased extension of the transition state is due to steric repulsion between the unpaired ssDNA segments in close proximity to one another. Using linear force-extension relations verified by simulations of short DNA segments, we derived analytical equations for force-to-rate conversion that are in good agreement with our measurements.
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影响因子：
48
作者：
Brockman JM;Blanchard AT;Pui-Yan V Ma;Derricotte WD;Zhang Y;Fay ME;Lam WA;Evangelista FA;Mattheyses AL;Salaita K
通讯作者：
Salaita K
DOI：
10.1126/science.aar7831
发表时间：
2018-04-06
期刊：
Science (New York, N.Y.)
影响因子：
--
作者：
Ganji M;Shaltiel IA;Bisht S;Kim E;Kalichava A;Haering CH;Dekker C
通讯作者：
Dekker C
影响因子：
12.6
作者：
Mustafa G;Chuang CY;Roy WA;Farhath MM;Pokhrel N;Ma Y;Nagasawa K;Antony E;Comstock MJ;Basu S;Balci H
通讯作者：
Balci H
DOI：
10.1073/pnas.0806085105
发表时间：
2008-10-14
影响因子：
11.1
作者：
Dudko, Olga K.;Hummer, Gerhard;Szabo, Attila
通讯作者：
Szabo, Attila
影响因子：
3.4
作者：
Aitken, Colin Echeverria;Marshall, R. Andrew;Puglisi, Joseph D.
通讯作者：
Puglisi, Joseph D.