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 | |
| Publication status | Published - 2015 Jan 1 |
Fingerprint
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 journal › Article
}
TY - JOUR
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
UR - http://www.scopus.com/inward/record.url?scp=84928492136&partnerID=8YFLogxK
UR - http://www.scopus.com/inward/citedby.url?scp=84928492136&partnerID=8YFLogxK
U2 - 10.1007/978-1-4939-2562-9_3
DO - 10.1007/978-1-4939-2562-9_3
M3 - Article
C2 - 25895994
AN - SCOPUS:84928492136
VL - 1297
SP - 43
EP - 57
JO - Methods in Molecular Biology
JF - Methods in Molecular Biology
SN - 1064-3745
ER -