Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, 612 65 Brno, Czech Republic.
Regional Centre of Advanced Technologies and Materials, Faculty of Science, Palacký University, tř. 17 listopadu 12, 771 46 Olomouc, Czech Republic.
J Chem Theory Comput. 2020 Jun 9;16(6):3447-3463. doi: 10.1021/acs.jctc.9b01068. Epub 2020 May 4.
G-quadruplexes (GQs) are four-stranded noncanonical DNA and RNA architectures that can be formed by guanine-rich sequences. The stability of GQs increases with the number of G-quartets, and three G-quartets generally form stable GQs. However, the stability of two-quartet GQs is an open issue. To understand the intrinsic stability of two-quartet GQ stems, we have carried out a series of unbiased molecular dynamics (MD) simulations (505 μs in total) of two- and four-quartet DNA and RNA GQs, with attention paid mainly to parallel-stranded arrangements. We used AMBER DNA parmOL15 and RNA parmOL3 force fields and tested different ion and water models. Two-quartet parallel-stranded DNA GQs unfolded in all the simulations, while the equivalent RNA GQ was stable in most of the simulations. GQs composed of two stacked units of two-quartet GQs were stable for both DNA and RNA. The simulations suggest that a minimum of three quartets are needed to form an intrinsically stable all- parallel-stranded DNA GQ. Parallel two-quartet DNA GQ may exist if substantially stabilized by another molecule or structural element, including multimerization. On the other hand, we predict that isolated RNA two-quartet parallel GQs may form, albeit being weakly stable. We also show that ionic parameters and water models should be chosen with caution because some parameter combinations can cause spurious instability of GQ stems. Some in-so-far unnoticed limitations of force-field description of multiple ions inside the GQs are discussed, which compromise the capability of simulations to fully capture the effect of increase in the number of quartets on the GQ stability.
G-四链体（GQs）是由富含鸟嘌呤的序列形成的四条链非经典 DNA 和 RNA 结构。GQs 的稳定性随 G-四聚体的数量增加而增加，通常三个 G-四聚体形成稳定的 GQs。然而，双 G-四聚体 GQs 的稳定性是一个悬而未决的问题。为了了解双 G-四聚体 GQ 茎的内在稳定性，我们对双 G-四聚体和四 G-四聚体 DNA 和 RNA GQs 进行了一系列无偏分子动力学（MD）模拟（总计 505 μs），主要关注平行链排列。我们使用 AMBER DNA parmOL15 和 RNA parmOL3 力场，并测试了不同的离子和水模型。在所有模拟中，双 G-四聚体平行 DNA GQs 均发生解折叠，而等效的 RNA GQ 在大多数模拟中均稳定。由两个双 G-四聚体堆叠单元组成的 GQs 对 DNA 和 RNA 均稳定。模拟表明，形成内在稳定的全平行链 DNA GQ 至少需要三个四聚体。如果通过另一个分子或结构元件（包括多聚化）得到实质性稳定，平行双 G-四聚体 DNA GQ 可能存在。另一方面，我们预测孤立的 RNA 双 G-四聚体平行 GQ 可能形成，尽管其稳定性较弱。我们还表明，应谨慎选择离子参数和水模型，因为某些参数组合可能导致 GQ 茎的虚假不稳定性。讨论了力场对 GQs 内多个离子的描述存在一些迄今为止未被注意到的局限性，这限制了模拟充分捕捉 GQ 稳定性随四聚体数量增加的效果的能力。
