Measuring the elasticity of ribonucleotide(S)-containing DNA molecules using AFM

Kyung Duk Koh, Hsiang-Chih Chiu, Elisa Riedo, Francesca Storici

Research output: Contribution to journalArticle

4 Citations (Scopus)

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).

Original languageEnglish
Pages (from-to)43-57
Number of pages15
JournalMethods in Molecular Biology
Volume1297
DOIs
Publication statusPublished - 2015 Jan 1

Fingerprint

Ribonucleosides
Ribonucleotides
Atomic Force Microscopy
Elasticity
DNA
DNA Replication
Oligonucleotides
Cell Communication
Hydroxyl Radical
Nucleotides
Genome

Keywords

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

ASJC Scopus subject areas

  • Molecular Biology
  • Genetics

Cite this

Measuring the elasticity of ribonucleotide(S)-containing DNA molecules using AFM. / Koh, Kyung Duk; Chiu, Hsiang-Chih; Riedo, Elisa; Storici, Francesca.

In: Methods in Molecular Biology, Vol. 1297, 01.01.2015, p. 43-57.

Research output: Contribution to journalArticle

Koh, Kyung Duk ; Chiu, Hsiang-Chih ; Riedo, Elisa ; Storici, Francesca. / Measuring the elasticity of ribonucleotide(S)-containing DNA molecules using AFM. In: Methods in Molecular Biology. 2015 ; Vol. 1297. pp. 43-57.
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