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Issue 17, 2014
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RNA intrusions change DNA elastic properties and structure

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Abstract

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.

Graphical abstract: RNA intrusions change DNA elastic properties and structure

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Supplementary files

Article information


Submitted
02 Apr 2014
Accepted
10 May 2014
First published
19 May 2014

Nanoscale, 2014,6, 10009-10017
Article type
Paper
Author version available

RNA intrusions change DNA elastic properties and structure

H. Chiu, K. D. Koh, M. Evich, A. L. Lesiak, M. W. Germann, A. Bongiorno, E. Riedo and F. Storici, Nanoscale, 2014, 6, 10009
DOI: 10.1039/C4NR01794C

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