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 journalArticle

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.

Original languageEnglish (US)
Pages (from-to)10009-10017
Number of pages9
JournalNanoscale
Volume6
Issue number17
DOIs
StatePublished - Sep 7 2014

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RNA
Ribonucleosides
DNA
Mechanical properties
Molecules
Nucleotides
Nanotechnology
Nuclear magnetic resonance spectroscopy
Molecular dynamics
Elasticity
Atomic force microscopy
Defects

ASJC Scopus subject areas

  • Materials Science(all)

Cite this

Chiu, H. C., Koh, K. D., Evich, M., Lesiak, A. L., Germann, M. W., Bongiorno, A., ... Storici, F. (2014). RNA intrusions change DNA elastic properties and structure. Nanoscale, 6(17), 10009-10017. https://doi.org/10.1039/c4nr01794c

RNA intrusions change DNA elastic properties and structure. / Chiu, Hsiang Chih; Koh, Kyung Duk; Evich, Marina; Lesiak, Annie L.; Germann, Markus W.; Bongiorno, Angelo; Riedo, Elisa; Storici, Francesca.

In: Nanoscale, Vol. 6, No. 17, 07.09.2014, p. 10009-10017.

Research output: Contribution to journalArticle

Chiu, HC, Koh, KD, Evich, M, Lesiak, AL, Germann, MW, Bongiorno, A, Riedo, E & Storici, F 2014, 'RNA intrusions change DNA elastic properties and structure', Nanoscale, vol. 6, no. 17, pp. 10009-10017. https://doi.org/10.1039/c4nr01794c
Chiu HC, Koh KD, Evich M, Lesiak AL, Germann MW, Bongiorno A et al. RNA intrusions change DNA elastic properties and structure. Nanoscale. 2014 Sep 7;6(17):10009-10017. https://doi.org/10.1039/c4nr01794c
Chiu, Hsiang Chih ; Koh, Kyung Duk ; Evich, Marina ; Lesiak, Annie L. ; Germann, Markus W. ; Bongiorno, Angelo ; Riedo, Elisa ; Storici, Francesca. / RNA intrusions change DNA elastic properties and structure. In: Nanoscale. 2014 ; Vol. 6, No. 17. pp. 10009-10017.
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