El-Khoury Roberto, Macaluso Veronica, Hennecker Christopher, Mittermaier Anthony K, Orozco Modesto, González Carlos, Garavís Miguel, Damha Masad J
Department of Chemistry, McGill University, Montréal, H3A0B8, Canada.
Institute for Research in Biomedicine (IRB Barcelona), Barcelona, 08028, Spain.
Commun Chem. 2023 Feb 16;6(1):31. doi: 10.1038/s42004-023-00831-7.
G-quadruplex and i-motif nucleic acid structures are believed to fold through kinetic partitioning mechanisms. Such mechanisms explain the structural heterogeneity of G-quadruplex metastable intermediates which have been extensively reported. On the other hand, i-motif folding is regarded as predictable, and research on alternative i-motif folds is limited. While TC normally folds into a stable tetrameric i-motif in solution, we report that 2'-deoxy-2'-fluoroarabinocytidine (araF-C) substitutions can prompt TC to form an off-pathway and kinetically-trapped dimeric i-motif, thereby expanding the scope of i-motif folding landscapes. This i-motif is formed by two strands, associated head-to-head, and featuring zero-nucleotide loops which have not been previously observed. Through spectroscopic and computational analyses, we also establish that the dimeric i-motif is stabilized by fluorine and non-fluorine hydrogen bonds, thereby explaining the superlative stability of araF-C modified i-motifs. Comparative experimental findings suggest that the strength of these interactions depends on the flexible sugar pucker adopted by the araF-C residue. Overall, the findings reported here provide a new role for i-motifs in nanotechnology and also pose the question of whether unprecedented i-motif folds may exist in vivo.
G-四链体和i-基序核酸结构被认为是通过动力学分配机制折叠的。这种机制解释了已被广泛报道的G-四链体亚稳态中间体的结构异质性。另一方面，i-基序折叠被认为是可预测的，而对替代性i-基序折叠的研究有限。虽然TC在溶液中通常折叠成稳定的四聚体i-基序，但我们报道2'-脱氧-2'-氟阿拉伯糖胞苷（araF-C）取代可以促使TC形成一条非典型的、动力学捕获的二聚体i-基序，从而扩大了i-基序折叠格局的范围。这种i-基序由两条链形成，头对头相连，具有零核苷酸环，这是以前未曾观察到的。通过光谱和计算分析，我们还确定二聚体i-基序由氟和非氟氢键稳定，从而解释了araF-C修饰的i-基序的卓越稳定性。比较实验结果表明，这些相互作用的强度取决于araF-C残基所采用的灵活糖环构象。总体而言，此处报道的研究结果为i-基序在纳米技术中的新作用提供了依据，同时也提出了体内是否可能存在前所未有的i-基序折叠的问题。
