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Measuring the Elasticity of Ribonucleotide(s)-Containing DNA Molecules Using AFM

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RNA Nanotechnology and Therapeutics

Part of the book series: Methods in Molecular Biology ((MIMB,volume 1297))

Abstract

Ribonucleotides, ribonucleoside monophosphates (rNMPs), have been revealed as possibly the most noncanonical nucleotides in genomic DNA. rNMPs, either not removed from Okazaki fragments during DNA replication or incorporated and scattered throughout the genome, pose a perturbation to the structure and a threat to the stability of DNA. The instability of DNA is mainly due to the extra 2′-hydroxyl (OH) group of rNMPs which give rise to local structural effects, which may disturb various molecular interactions in cells. As a result of these structural perturbations by rNMPs, the elastic properties of DNA are also affected. Here, we show the approach to test whether the presence of rNMPs in DNA duplexes could alter the elasticity of DNA by implementing atomic force microscopy (AFM)-based single molecule force-measurements of short rNMP(s)-containing oligonucleotides (oligos).

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Acknowledgment

This work was supported by the Integrative Biosystems Institute grant IBSI-4 to F.S. and E.R., and the NSF grant MCB-1021763 to F.S.

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Authors and Affiliations

  1. School of Biology, Georgia Institute of Technology, Atlanta, GA, 30332, USA

    Kyung Duk Koh & Francesca Storici

  2. School of Physics, Georgia Institute of Technology, Atlanta, GA, 30332, USA

    Hsiang-Chih Chiu & Elisa Riedo

  3. Department of Physics, National Taiwan Normal University, 116, Taipei, Taiwan

    Hsiang-Chih Chiu

Authors
  1. Kyung Duk Koh
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  2. Hsiang-Chih Chiu
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  3. Elisa Riedo
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  4. Francesca Storici
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Correspondence to Francesca Storici .

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Editors and Affiliations

  1. Nanobiotechnology Center, Markey Cancer Center, Department of Pharmaceutical Sciences, University of Kentucky, Lexington, Kentucky, USA

    Peixuan Guo

  2. Nanobiotechnology Center, Markey Cancer Center, Department of Pharmaceutical Sciences, University of Kentucky, Lexington, Kentucky, USA

    Farzin Haque

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Koh, K.D., Chiu, HC., Riedo, E., Storici, F. (2015). Measuring the Elasticity of Ribonucleotide(s)-Containing DNA Molecules Using AFM. In: Guo, P., Haque, F. (eds) RNA Nanotechnology and Therapeutics. Methods in Molecular Biology, vol 1297. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-2562-9_3

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  • DOI: https://doi.org/10.1007/978-1-4939-2562-9_3

  • Publisher Name: Humana Press, New York, NY

  • Print ISBN: 978-1-4939-2561-2

  • Online ISBN: 978-1-4939-2562-9

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