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

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

doi:10.1007/978-1-4939-2562-9_3

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

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

Department of Physics

Research output: Contribution to journal › Article

5 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 language	English
Pages (from-to)	43-57
Number of pages	15
Journal	Methods in Molecular Biology
Volume	1297
DOIs	https://doi.org/10.1007/978-1-4939-2562-9_3
Publication status	Published - 2015 Jan 1

Keywords

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

ASJC Scopus subject areas

Molecular Biology
Genetics

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10.1007/978-1-4939-2562-9_3

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title = "Measuring the elasticity of ribonucleotide(S)-containing DNA molecules using AFM",

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).",

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

author = "Koh, {Kyung Duk} and Hsiang-Chih Chiu and Elisa Riedo and Francesca Storici",

year = "2015",

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T1 - Measuring the elasticity of ribonucleotide(S)-containing DNA molecules using AFM

AU - Koh, Kyung Duk

AU - Chiu, Hsiang-Chih

AU - Riedo, Elisa

AU - Storici, Francesca

PY - 2015/1/1

Y1 - 2015/1/1

N2 - 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).

AB - 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).

KW - Atomic force microscopy(AFM)

KW - RNA elasticity

KW - Ribonucleoside monophosphates (rNMP)

KW - Single molecule force spectroscopy

KW - Stretch modulus

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