RNA intrusions change DNA elastic properties and structure

Hsiang Chih Chiu, Kyung Duk Koh, Marina Evich, Annie L. Lesiak, Markus W. Germann, Angelo Bongiorno, Elisa Riedo, Francesca Storici

Research output: Contribution to journalArticlepeer-review


The units of RNA, termed ribonucleoside monophosphates (rNMPs), have been recently found as the most abundant defects present in DNA. Despite the relevance, it is largely unknown if and how rNMPs embedded in DNA can change the DNA structure and mechanical properties. Here, we report that rNMPs incorporated in DNA can change the elastic properties of DNA. Atomic force microscopy (AFM)-based single molecule elasticity measurements show that rNMP intrusions in short DNA duplexes can decrease-by 32%-or slightly increase the stretch modulus of DNA molecules for two sequences reported in this study. Molecular dynamics simulations and nuclear magnetic resonance spectroscopy identify a series of significant local structural alterations of DNA containing embedded rNMPs, especially at the rNMPs and nucleotide 3′ to the rNMP sites. The demonstrated ability of rNMPs to locally alter DNA mechanical properties and structure may help in understanding how such intrusions impact DNA biological functions and find applications in structural DNA and RNA nanotechnology.

Original languageEnglish (US)
Pages (from-to)10009-10017
Number of pages9
Issue number17
StatePublished - Sep 7 2014

ASJC Scopus subject areas

  • General Materials Science


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