GC-Content Dependence of Elastic and Overstretching Properties of DNA:RNA Hybrid Duplexes.
GC-Content Dependence of Elastic and Overstretching Properties of DNA:RNA Hybrid Duplexes.
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DNA:RNA 混合双链体的弹性和过度拉伸特性的 GC 含量依赖性。
DOI：
10.1016/j.bpj.2020.06.034
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发表时间：
2020-07
影响因子：
3.4
通讯作者：
Ma J
中科院分区：
文献类型：
--
作者：
Yang D;Liu W;Deng X;Xie W;Chen H;Zhong Z;Ma J
DNA：RNA杂交双链体在多种生物过程中起着重要作用。它的结构稳定性和与蛋白质的相互作用都是高度序列依赖性的。在这项研究中，我们利用自制的光镊研究如何GC内容的序列中的影响DNA：RNA杂交的结构和力学性质，通过测量其轮廓长度，弹性，和过度拉伸动力学。结果表明，DNA：RNA杂交体的构象介于A型和B型螺旋之间，在DNA：RNA杂交体发生过度拉伸转变之前，GC含量在40 ~ 60%范围内变化时，对DNA：RNA杂交体的结构和弹性参数没有明显影响。然而，在过度拉伸过渡，我们的研究揭示了显着的异质性和强烈的序列依赖性，这表明存在一个高度动态的两个过程之间的竞争，即S-形式的双链体形成（非滞后）和剥离（滞后）。分析过度拉伸过渡后留在DNA：RNA杂交体中的组分表明，RNA链比DNA链更容易剥离，而GC含量从40%增加到60%可以显着减少剥离。在拉伸和松弛过程之间观察到大的滞后，这也与DNA：RNA双链体中未剥离的百分比定量相关。盐浓度和GC含量的增加都可以有效地降低滞后，后者更显着。总之，我们的研究表明，DNA：RNA杂交双链体的机械性能显着不同于双链DNA和双链RNA，其过度拉伸行为是高度序列依赖性的。这些结果应考虑在未来的研究DNA：RNA杂交相关的功能结构和马达蛋白。
DNA:RNA hybrid duplex plays important roles in various biological processes. Both its structural stability and interactions with proteins are highly sequence dependent. In this study, we utilize homebuilt optical tweezers to investigate how GC contents in the sequence influence the structural and mechanical properties of DNA:RNA hybrid by measuring its contour length, elasticities, and overstretching dynamics. Our results support that the DNA:RNA hybrid adopts a conformation between the A- and B-form helix, and the GC content does not affect its structural and elastic parameters obviously when varying from 40 to 60% before the overstretching transition of DNA:RNA hybrid occurs. In the overstretching transition, however, our study unravels significant heterogeneity and strong sequence dependence, suggesting the presence of a highly dynamic competition between the two processes, namely the S-form duplex formation (nonhysteretic) and the unpeeling (hysteretic). Analyzing the components left in DNA:RNA hybrid after the overstretching transition suggests that the RNA strand is more easily unpeeled than the DNA strand, whereas an increase in the GC content from 40 to 60% can significantly reduce unpeeling. Large hysteresis is observed between the stretching and relaxation processes, which is also quantitatively correlated with the percentage of unpeeling in the DNA:RNA duplex. Increasing in both the salt concentration and GC content can effectively reduce the hysteresis with the latter being more significant. Together, our study reveals that the mechanical properties of DNA:RNA hybrid duplexes are significantly different from double-stranded DNA and double-stranded RNA, and its overstretching behavior is highly sequence dependent. These results should be taken into account in the future studies on DNA:RNA-hybrid-related functional structures and motor proteins.
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影响因子：
14.9
作者：
Y. Xiong;M. Sundaralingam
通讯作者：
Y. Xiong;M. Sundaralingam
双链体结构差异而非 2'-羟基解释了 HIV 逆转录酶与 RNA-DNA 的结合比 DNA-DNA 更稳定。
影响因子：
14.9
作者：
Olimpo, Jeffrey T.;DeStefano, Jeffrey J.
通讯作者：
DeStefano, Jeffrey J.
影响因子：
14.9
作者：
Penno C;Kumari R;Baranov PV;van Sinderen D;Atkins JF
通讯作者：
Atkins JF
DOI：
10.1074/jbc.m117.798256
发表时间：
2018-01-05
期刊：
The Journal of biological chemistry
影响因子：
--
作者：
Figiel M;Krepl M;Park S;Poznański J;Skowronek K;Gołąb A;Ha T;Šponer J;Nowotny M
通讯作者：
Nowotny M
影响因子：
56.9
作者：
ROBERTS, RW;CROTHERS, DM
通讯作者：
CROTHERS, DM