Dyubankova N, Sochacka E, Kraszewska K, Nawrot B, Herdewijn P, Lescrinier E
Medicinal Chemistry, Department of Pharmaceutical Sciences, Rega Institute for Medical Research, KU Leuven, Minderbroedersstraat 10, 3000 Leuven, Belgium.
Org Biomol Chem. 2015 May 7;13(17):4960-6. doi: 10.1039/c5ob00164a.
Posttranscriptional modifications of transfer RNAs (tRNAs) are proven to be critical for all core aspects of tRNA function. While the majority of tRNA modifications were discovered in the 1970s, their contribution in tRNA folding, stability, and decoding often remains elusive. In this work an NMR study was performed to obtain more insight in the role of the dihydrouridine (D) modification in the D-arm of tRNAi(Met) from S. pombe. While the unmodified oligonucleotide adopted several undefined conformations that interconvert in solution, the presence of a D nucleoside triggered folding into a hairpin with a stable stem and flexible loop region. Apparently the D modification is required in the studied sequence to fold into a stable hairpin. Therefore we conclude that D contributes to the correct folding and stability of D-arm in tRNA. In contrast to what is generally assumed for nucleic acids, the sharp 'imino' signal for the D nucleobase at 10 ppm in 90% H2O is not indicative for the presence of a stable hydrogen bond. The strong increase in pKa upon loss of the aromatic character in the modified nucleobase slows down the exchange of its 'imino' proton significantly, allowing its observation even in an isolated D nucleoside in 90% H2O in acidic to neutral conditions.
转运RNA（tRNA）的转录后修饰已被证明对tRNA功能的所有核心方面都至关重要。虽然大多数tRNA修饰是在20世纪70年代发现的，但它们在tRNA折叠、稳定性和解码中的作用往往仍不明确。在这项工作中，进行了一项核磁共振研究，以更深入地了解来自粟酒裂殖酵母的tRNAi(Met)的D臂中二氢尿嘧啶（D）修饰的作用。未修饰的寡核苷酸在溶液中呈现出几种未定义的构象，它们之间可以相互转换，而D核苷的存在则促使其折叠成一个具有稳定茎和灵活环区域的心形结构。显然，在所研究的序列中，D修饰是折叠成稳定心形结构所必需的。因此，我们得出结论，D有助于tRNA中D臂的正确折叠和稳定性。与核酸通常的情况相反，在90% H2O中，D核苷酸碱基在10 ppm处尖锐的“亚氨基”信号并不表明存在稳定的氢键。修饰核苷酸碱基失去芳香性后pKa的大幅增加显著减缓了其“亚氨基”质子的交换，甚至在酸性至中性条件下90% H2O中的孤立D核苷中也能观察到该信号。
