Nano-mechanical measurements of protein-DNA interactions with a silicon nitride pulley

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Nano-mechanical measurements of protein-DNA interactions with a silicon nitride pulley

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Title: Nano-mechanical measurements of protein-DNA interactions with a silicon nitride pulley
Author: Shon, Min Ju; Cohen, Adam E.

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Citation: Shon, Min Ju, and Adam E. Cohen. 2016. “Nano-mechanical measurements of protein-DNA interactions with a silicon nitride pulley.” Nucleic Acids Research 44 (1): e7. doi:10.1093/nar/gkv866. http://dx.doi.org/10.1093/nar/gkv866.
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Abstract: Proteins adhere to DNA at locations and with strengths that depend on the protein conformation, the underlying DNA sequence and the ionic content of the solution. A facile technique to probe the positions and strengths of protein-DNA binding would aid in understanding these important interactions. Here, we describe a ‘DNA pulley’ for position-resolved nano-mechanical measurements of protein-DNA interactions. A molecule of λ DNA is tethered by one end to a glass surface, and by the other end to a magnetic bead. The DNA is stretched horizontally by a magnet, and a nanoscale knife made of silicon nitride is manipulated to contact, bend and scan along the DNA. The mechanical profile of the DNA at the contact with the knife is probed via nanometer-precision optical tracking of the magnetic bead. This system enables detection of protein bumps on the DNA and localization of their binding sites. We study theoretically the technical requirements to detect mechanical heterogeneities in the DNA itself.
Published Version: doi:10.1093/nar/gkv866
Other Sources: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4705685/pdf/
Terms of Use: This article is made available under the terms and conditions applicable to Other Posted Material, as set forth at http://nrs.harvard.edu/urn-3:HUL.InstRepos:dash.current.terms-of-use#LAA
Citable link to this page: http://nrs.harvard.edu/urn-3:HUL.InstRepos:24984010
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