On the Structure and Dynamics of Duplex GNA

Glycol nucleic acid (GNA), with a nucleotide backbone comprising of just three carbons and the stereocenter derived from propylene glycol (1,2-propanediol), is a structural analog of nucleic acids with intriguing biophysical properties, such as formation of highly stable antiparallel duplexes with high Watson–Crick base pairing fidelity. Previous crystallographic studies of double stranded GNA (dsGNA) indicated two forms of backbone conformations, an elongated M-type (containing metallo-base pairs) and the condensed N-type (containing brominated base pairs). A herein presented new crystal structure of a GNA duplex at 1.8 Å resolution from self-complementary 3′-CTCBrUAGAG-2′ GNA oligonucleotides reveals an N-type conformation with alternating gauche–anti torsions along its (O3′–C3′–C2′–O2′) backbone. To elucidate the conformational state of dsGNA in solution, molecular dynamic simulations over a period of 20 ns were performed with the now available repertoire of structural information. Interestingly, dsGNA adopts conformational states in solution intermediate between experimentally observed backbone conformations: simulated dsGNA shows the all-gauche conformation characteristic of M-type GNA with the higher helical twist common to N-type GNA structures. The so far counterintuitive, smaller loss of entropy upon duplex formation as compared to DNA can be traced back to the conformational flexibility inherent to dsGNA but missing in dsDNA. Besides extensive interstrand base stacking and conformational preorganization of single strands, this flexibility contributes to the extraordinary thermal stability of GNA.乙二醇核酸（Glycol nucleic acid, GNA）是一类核酸结构类似物，其核苷酸主链仅含3个碳原子，手性中心源自丙二醇（1,2-丙二醇），展现出诸多引人关注的生物物理特性，例如可形成具有高沃森-克里克（Watson–Crick）碱基配对保真度的高度稳定反平行双链结构。此前针对双链GNA（double stranded GNA, dsGNA）的晶体学研究已揭示两种主链构象：一种是含金属碱基对的伸长型M构象，另一种是含溴化碱基对的紧凑型N构象。本研究报道的分辨率为1.8 Å的GNA双链晶体结构，源自自身互补的3′-CTCBrUAGAG-2′ GNA寡核苷酸链，其主链沿(O3′–C3′–C2′–O2′)键呈现交替的旁式-反式（gauche–anti）扭转角，属于N型构象。为阐明dsGNA在溶液中的构象状态，本研究结合现有结构信息库开展了时长20纳秒的分子动力学模拟。值得注意的是，dsGNA在溶液中采取的构象状态介于两种实验观测到的主链构象之间：模拟得到的dsGNA同时兼具M型GNA标志性的全旁式构象，以及N型GNA结构特有的高螺旋扭角。相较于脱氧核糖核酸（DNA），双链形成过程中熵的损失更小——这一迄今看似违背直觉的现象，可归因于dsGNA固有的构象灵活性，而该特性在双链DNA（dsDNA）中并不存在。除了广泛的链间碱基堆积与单链的构象预组织作用外，这种构象灵活性也是GNA具备优异热稳定性的重要原因。