Nanotubes: Sliding on a Nanotube: Interplay of Friction, Deformations and Structure (Adv. Mater. 21/2012)

Chiu, Hsiang-Chih; Ritz, Beate; Kim, Suenne; Tosatti, Erio; Klinke, Christian

doi:10.1002/adma.201290122

Cited by 2 publications

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“…S6, † and the literature. [58][59][60][61][62] In the retracting force curve (red in Fig. 2d), it is possible to observe that the tip has to overcome an initial adhesion force F adh to detach from the substrate.…”

Section: Resultsmentioning

confidence: 99%

RNA intrusions change DNA elastic properties and structure

et al. 2014

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The units of RNA, termed ribonucleoside monophosphates (rNMPs), have been recently found as the most abundant defects present in DNA. Despite the relevance, it is largely unknown if and how rNMPs embedded in DNA can change the DNA structure and mechanical properties. Here, we report that rNMPs incorporated in DNA can change the elastic properties of DNA. Atomic force microscopy (AFM)-based single molecule elasticity measurements show that rNMP intrusions in short DNA duplexes can decrease--by 32%--or slightly increase the stretch modulus of DNA molecules for two sequences reported in this study. Molecular dynamics simulations and nuclear magnetic resonance spectroscopy identify a series of significant local structural alterations of DNA containing embedded rNMPs, especially at the rNMPs and nucleotide 3' to the rNMP sites. The demonstrated ability of rNMPs to locally alter DNA mechanical properties and structure may help in understanding how such intrusions impact DNA biological functions and find applications in structural DNA and RNA nanotechnology.

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Section: Resultsmentioning

confidence: 99%

RNA intrusions change DNA elastic properties and structure

et al. 2014

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

Koh

Chiu

Storici

2015

Methods in Molecular Biology

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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).

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Nanotubes: Sliding on a Nanotube: Interplay of Friction, Deformations and Structure (Adv. Mater. 21/2012)

Cited by 2 publications

References 0 publications

RNA intrusions change DNA elastic properties and structure

RNA intrusions change DNA elastic properties and structure

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

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