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RNA Nanotechnology and Therapeutics

Volume 1297 of the series Methods in Molecular Biology pp 43-57

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

  • Kyung Duk KohAffiliated withSchool of Biology, Georgia Institute of Technology
  • , Hsiang-Chih ChiuAffiliated withSchool of Physics, Georgia Institute of TechnologyDepartment of Physics, National Taiwan Normal University
  • , Elisa RiedoAffiliated withSchool of Physics, Georgia Institute of Technology
  • , Francesca StoriciAffiliated withSchool of Biology, Georgia Institute of Technology Email author 

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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).

Key words

Ribonucleoside monophosphates (rNMP) RNA elasticity Atomic force microscopy (AFM) Single molecule force spectroscopy Stretch modulus