Department of Chemical Engineering and Materials Science, University of Minnesota, 421 Washington Ave SE, Minneapolis, Minnesota 55455, USA.
J Chem Phys. 2011 Nov 28;135(20):205102. doi: 10.1063/1.3662137.
DNA produces a wide range of structures in addition to the canonical B-form of double-stranded DNA. Some of these structures are stabilized by Hoogsteen bonds. We developed an experimentally parameterized, coarse-grained model that incorporates such bonds. The model reproduces many of the microscopic features of double-stranded DNA and captures the experimental melting curves for a number of short DNA hairpins, even when the open state forms complicated secondary structures. We demonstrate the utility of the model by simulating the folding of a thrombin aptamer, which contains G-quartets, and strand invasion during triplex formation. Our results highlight the importance of including Hoogsteen bonding in coarse-grained models of DNA.
DNA 除了产生双链 DNA 的典型 B 构象外，还能产生多种结构。其中一些结构由 Hoogsteen 键稳定。我们开发了一个实验参数化的粗粒模型，其中包含了这种键。该模型再现了双链 DNA 的许多微观特征，并捕捉到了许多短 DNA 发夹的实验熔化曲线，即使在开环状态形成复杂的二级结构时也是如此。我们通过模拟包含 G-四联体的凝血酶适体的折叠和三链体形成时的链入侵，展示了该模型的实用性。我们的结果强调了在 DNA 的粗粒模型中包含 Hoogsteen 键合的重要性。
