Laboratory for Computation and Visualisation in Mathematics and Mechanics, Institute of Mathematics, École Polytechnique Fédérale de Lausanne, Lausanne 1015, Switzerland.
Institute Lorentz for Theoretical Physics, Leiden University, Leiden, The Netherlands.
J Mol Biol. 2023 Jul 15;435(14):167978. doi: 10.1016/j.jmb.2023.167978. Epub 2023 Jan 25.
The sequence-dependent statistical mechanics of double-stranded nucleic acid, or dsNA, is believed to be essential in its biological functions. In turn, the equilibrium statistical mechanics behaviour of dsNA depends strongly both on sequence-dependent perturbations in its ground state shape away from an idealised, uniform, double-helical configuration, and on its fluctuations as governed by its sequence-dependent stiffness. We here describe the cgNA+web browser-based interactive tool for visualising the sequence-dependent ground states of dsNA fragments of arbitrary sequences, as predicted by the underlying cgNA+ coarse-grain model. Parameter sets are provided to model dsDNA, including the possibility of epigenetically modified CpG dinucleotide steps, dsRNA, and DNA:RNA Hybrid double helical fragments. The cgNA+web interface is specifically designed to compare ground state shapes of different sequences of the same dsNA, or analogous sequences of different dsNAs. The cgNA+web server is freely available at cgDNAweb.epfl.ch without any login requirement.
双链核酸（dsNA）的序列相关统计力学被认为对其生物功能至关重要。反过来，dsNA 的平衡统计力学行为强烈依赖于其基态形状的序列相关扰动，这些扰动偏离了理想的、均匀的双螺旋构象，以及由其序列相关刚度决定的波动。我们在这里描述了基于 cgNA+的网络浏览器交互工具，用于可视化由底层 cgNA+粗粒模型预测的任意序列的 dsNA 片段的序列相关基态。提供了参数集来模拟 dsDNA，包括表观遗传修饰的 CpG 二核苷酸步骤、dsRNA 和 DNA:RNA 杂交双链片段的可能性。cgNA+网络界面专门设计用于比较相同 dsNA 的不同序列或不同 dsNA 的类似序列的基态形状。cgNA+网络服务器可在 cgDNAweb.epfl.ch 上免费获得，无需登录要求。
