He Weiwei, Chen Yen-Lin, Pollack Lois, Kirmizialtin Serdal
Chemistry Program, Science Division, New York University Abu Dhabi, Abu Dhabi, United Arab Emirates.
Department of Chemistry, New York University, New York, NY, USA.
Sci Adv. 2021 Apr 23;7(17). doi: 10.1126/sciadv.abf6106. Print 2021 Apr.
Double-stranded DNA (dsDNA) and RNA (dsRNA) helices display an unusual structural diversity. Some structural variations are linked to sequence and may serve as signaling units for protein-binding partners. Therefore, elucidating the mechanisms and factors that modulate these variations is of fundamental importance. While the structural diversity of dsDNA has been extensively studied, similar studies have not been performed for dsRNA. Because of the increasing awareness of RNA's diverse biological roles, such studies are timely and increasingly important. We integrate solution x-ray scattering at wide angles (WAXS) with all-atom molecular dynamics simulations to explore the conformational ensemble of duplex topologies for different sequences and salt conditions. These tightly coordinated studies identify robust correlations between features in the WAXS profiles and duplex geometry and enable atomic-level insights into the structural diversity of DNA and RNA duplexes. Notably, dsRNA displays a marked sensitivity to the valence and identity of its associated cations.
双链DNA（dsDNA）和RNA（dsRNA）螺旋呈现出不同寻常的结构多样性。一些结构变异与序列相关，可能作为蛋白质结合伴侣的信号单元。因此，阐明调节这些变异的机制和因素至关重要。虽然dsDNA的结构多样性已得到广泛研究，但对dsRNA尚未进行类似研究。由于对RNA多种生物学作用的认识不断提高，此类研究既及时又愈发重要。我们将广角溶液X射线散射（WAXS）与全原子分子动力学模拟相结合，以探索不同序列和盐条件下双链拓扑结构的构象集合。这些紧密配合的研究确定了WAXS图谱特征与双链几何结构之间的强相关性，并使我们能够从原子层面深入了解DNA和RNA双链的结构多样性。值得注意的是，dsRNA对其相关阳离子的价态和种类表现出显著的敏感性。
