Structural analysis of ribonucleopeptide aptamer against ATP.

Tsukasa Mashima, Akimasa Matsugami, Shun Nakano, Masafumi Inoue, Masatora Fukuda, Takashi Morii, Masato Katahira
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引用次数: 1

Abstract

A ribonucleopeptide aptamer against ATP was obtained by the in vitro selection method. This ribonucleopeptide aptamer comprises a randomized and selected RNA linked to the Rev-responsive element (RRE) in complex with a peptide derived from an HIV Rev protein. The ribonucleopeptide aptamer selectively binds ATP in the presence of the Rev-derived peptide, exclusively. Here, we present the structural analysis of the ribonucleopeptide aptamer with NMR. The secondary structure of the RNA part of the aptamer, the selected RNA region linked to RRE, in the presence of the Rev-derived peptide was determined in an Ado-bound form. G:A and G:G base pairs, together with canonical base pairs, are formed in a duplex of RRE. The selected RNA region plays a crucial role in target binding. It has been found that the two U residues located in the selected RNA region trap Ado through the formation of the U:A:U base triple. This was directly confirmed by the HNN-COSY experiment through the detection of spin-spin couplings across the hydrogen bonds for Watson-Crick and Hoogsteen A:U base pairs in the U:A:U base triple.

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抗ATP核糖核肽适配体的结构分析。
通过体外筛选获得了一个抗ATP的核糖核肽适配体。该核糖核肽适配体包括一个随机选择的RNA,与Rev-responsive element (RRE)结合,并与HIV Rev蛋白衍生的肽相结合。核糖核肽适配体在rev衍生肽存在的情况下选择性地结合ATP。本文采用核磁共振技术对该核糖核苷酸适配体进行了结构分析。在rev衍生肽存在的情况下,适体RNA部分的二级结构(与RRE连接的选定RNA区域)以ado结合形式确定。G:A和G:G碱基对与正则碱基对一起构成RRE的双工结构。选择的RNA区域在靶标结合中起着至关重要的作用。已经发现,位于选定RNA区域的两个U残基通过形成U:A:U碱基三重体来捕获Ado。HNN-COSY实验通过检测U:A:U碱基三元组中Watson-Crick和Hoogsteen A:U碱基对氢键上的自旋-自旋耦合直接证实了这一点。
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