Doherty E A, Batey R T, Masquida B, Doudna J A
Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520, USA.
Nat Struct Biol. 2001 Apr;8(4):339-43. doi: 10.1038/86221.
RNA molecules fold into specific three-dimensional shapes to perform structural and catalytic functions. Large RNAs can form compact globular structures, but the chemical basis for close helical packing within these molecules has been unclear. Analysis of transfer, catalysis, in vitro-selected and ribosomal RNAs reveal that helical packing predominantly involves the interaction of single-stranded adenosines with a helix minor groove. Using the Tetrahymena thermophila group I ribozyme, we show here that the near-perfect shape complementarity between the adenine base and the minor groove allows for optimal van der Waals contacts, extensive hydrogen bonding and hydrophobic surface burial, creating a highly energetically favorable interaction. Adenosine is recognized in a chemically similar fashion by a combination of protein and RNA components in the ribonucleoprotein core of the signal recognition particle. These results provide a thermodynamic explanation for the noted abundance of conserved adenosines within the unpaired regions of RNA secondary structures.
RNA分子折叠成特定的三维形状以执行结构和催化功能。大型RNA可以形成紧密的球状结构，但这些分子内紧密螺旋堆积的化学基础尚不清楚。对转移RNA、催化性RNA、体外筛选的RNA和核糖体RNA的分析表明，螺旋堆积主要涉及单链腺苷与螺旋小沟的相互作用。利用嗜热四膜虫I组核酶，我们在此表明腺嘌呤碱基与小沟之间近乎完美的形状互补性允许最佳的范德华接触、广泛的氢键形成和疏水表面埋藏，从而产生高度有利的能量相互作用。在信号识别颗粒的核糖核蛋白核心中，蛋白质和RNA成分以化学相似的方式识别腺苷。这些结果为RNA二级结构未配对区域中显著丰富的保守腺苷提供了热力学解释。
