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

  • Kyung Duk Koh
  • Hsiang-Chih Chiu
  • Elisa Riedo
  • Francesca StoriciEmail author
Part of the Methods in Molecular Biology book series (MIMB, volume 1297)


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 



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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Copyright information

© Springer Science+Business Media New York 2015

Authors and Affiliations

  • Kyung Duk Koh
    • 1
  • Hsiang-Chih Chiu
    • 2
    • 3
  • Elisa Riedo
    • 2
  • Francesca Storici
    • 1
    Email author
  1. 1.School of BiologyGeorgia Institute of TechnologyAtlantaUSA
  2. 2.School of PhysicsGeorgia Institute of TechnologyAtlantaUSA
  3. 3.Department of PhysicsNational Taiwan Normal UniversityTaipeiTaiwan

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