RNA•DNA:DNA Triplex Formation Modulates Individual Base Pair Stabilities in the DNA Target Duplex.

IF 5 3区生物学 Q2 BIOCHEMISTRY & MOLECULAR BIOLOGY

RNA Pub Date : 2026-05-05 DOI:10.1261/rna.080909.125

Nina M Krause, Julia Wirmer-Bartoschek, Christian Richter, Matthias S Leisegang, Ralf P Brandes, Harald Schwalbe

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引用次数: 0

Abstract

Long non-coding RNAs (lncRNAs) play key roles in gene regulation. One potential regulation mechanism involves the formation of RNA•DNA:DNA triplexes. In these triplexes, the lncRNA binds in the major groove of a target DNA via Hoogsteen base pair formation. Here, we investigated the impact of the underlying RNA binding on the on the stability of the DNA duplex target to gain insights into the triplex stability at base pair resolution. Quantification of the temperature-dependent exchange of imino hydrogen atoms with solvent of the target DNA duplex allows determination of the changes of the stability of individual DNA duplex base pairs upon triplex formation. The data shown here investigates an antiparallel triplex, formed between the lncRNA hypoxia-inducible factor 1-alpha Antisense RNA 1 (HIF1α-AS1) and the DNA target Adrenomedullin (ADM), important in cardiovascular diseases. Triplex formation alters DNA structure and stability by affecting both hydrogen bonding strength and nucleobase-stacking interactions. These thermodynamic insights support bioinformatic methods to predict triplex stability and enhance our understanding of RNA•DNA:DNA triplex formation.

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RNA•DNA:DNA三重结构调节DNA靶双工中单个碱基对的稳定性。

长链非编码rna （lncRNAs）在基因调控中发挥着关键作用。一种潜在的调控机制涉及RNA•DNA的形成：DNA三联体。在这些三联体中，lncRNA通过Hoogsteen碱基对形成结合在目标DNA的主要凹槽中。在这里，我们研究了潜在的RNA结合对DNA双工靶稳定性的影响，以深入了解碱基对分辨率下的三工稳定性。定量的温度依赖交换的亚胺氢原子与溶剂的目标DNA双工允许确定的稳定性的变化，个别DNA双工碱基对的三聚体形成。这里显示的数据研究了在lncRNA缺氧诱导因子1- α反义RNA 1 （HIF1α-AS1）和DNA靶点肾上腺髓质素（ADM）之间形成的反平行三联体，这在心血管疾病中很重要。三聚体的形成通过影响氢键强度和核碱基堆叠相互作用来改变DNA的结构和稳定性。这些热力学见解支持生物信息学方法来预测三联体的稳定性，并增强我们对RNA•DNA:DNA三联体形成的理解。

本文章由计算机程序翻译，如有差异，请以英文原文为准。

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来源期刊

RNA 生物-生化与分子生物学

CiteScore

8.30

自引率

2.20%

发文量

101

审稿时长

2.6 months

期刊介绍： RNA is a monthly journal which provides rapid publication of significant original research in all areas of RNA structure and function in eukaryotic, prokaryotic, and viral systems. It covers a broad range of subjects in RNA research, including: structural analysis by biochemical or biophysical means; mRNA structure, function and biogenesis; alternative processing: cis-acting elements and trans-acting factors; ribosome structure and function; translational control; RNA catalysis; tRNA structure, function, biogenesis and identity; RNA editing; rRNA structure, function and biogenesis; RNA transport and localization; regulatory RNAs; large and small RNP structure, function and biogenesis; viral RNA metabolism; RNA stability and turnover; in vitro evolution; and RNA chemistry.