Institute of Biochemistry, Universität Greifswald, D-17489 Greifswald, Germany.
Nucleic Acids Res. 2022 Jul 8;50(12):7161-7175. doi: 10.1093/nar/gkac549.
A G-rich sequence was designed to allow folding into either a stable parallel or hybrid-type topology. With the parent sequence featuring coexisting species, various related sequences with single and double mutations and with a shortened central propeller loop affected the topological equilibrium. Two simple modifications, likewise introduced separately to all sequences, were employed to lock folds into one of the topologies without noticeable structural alterations. The unique combination of sequence mutations, high-resolution NMR structural information, and the thermodynamic stability for both topological competitors identified critical loop residue interactions. In contrast to first loop residues, which are mostly disordered and exposed to solvent in both propeller and lateral loops bridging a narrow groove, the last loop residue in a lateral three-nucleotide loop is engaged in stabilizing stacking interactions. The propensity of single-nucleotide loops to favor all-parallel topologies by enforcing a propeller-like conformation of an additional longer loop is shown to result from their preference in linking two outer tetrads of the same tetrad polarity. Taken together, the present studies contribute to a better structural and thermodynamic understanding of delicate loop interactions in genomic and artificially designed quadruplexes, e.g. when employed as therapeutics or in other biotechnological applications.
设计了一个富含 G 的序列，使其能够折叠成稳定的平行或混合拓扑结构。由于原始序列存在共存的物种，因此具有单个和双突变以及缩短中央螺旋桨环的各种相关序列会影响拓扑平衡。两个简单的修饰同样分别引入到所有序列中，用于将折叠锁定在一种拓扑结构中，而不会引起明显的结构改变。序列突变、高分辨率 NMR 结构信息和两种拓扑竞争者的热力学稳定性的独特组合确定了关键环残基相互作用。与第一个环残基不同，第一个环残基在桨叶和横向环中大多无序且暴露在溶剂中，连接狭窄沟槽的三个核苷酸环的最后一个环残基参与稳定的堆积相互作用。单核苷酸环通过强制额外较长环的桨叶状构象来优先采用全平行拓扑的倾向，是由于它们偏爱连接相同四联体极性的两个外四联体。总的来说，这些研究有助于更好地理解基因组和人工设计的四联体中精细环相互作用的结构和热力学，例如，当用作治疗剂或在其他生物技术应用中。
