Koch Lab:Publications
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Paper Drafts
Probing Protein-DNA Interactions by Unzipping DNA with Optical Tweezers
Our initial proof-of-principle publication in the Wang Lab at Cornell
Koch SJ, Shundrovsky A, Jantzen BC, Wang MD. Probing protein-DNA interactions by unzipping a single DNA double helix. Biophys J. 2002 Aug;83(2):1098-105. PMID 12124289
Our follow-on paper showing that unbinding forces can be analyzed nicely with Evan Evans' Dynamic Force Spectrosocpy (DFS) model
Koch SJ, Wang MD. Dynamic force spectroscopy of protein-DNA interactions by unzipping DNA. Phys Rev Lett. 2003 Jul 11;91(2):028103. PMID 12906513
- Buried in this paper is the "loading rate clamp" that we used and which greatly simplifies data analysis as well as provides much cleaner data. Also, our maximum likelihood method for data analysis is better than the typical method of fitting Gaussians to histograms, but this was also buried in footnotes. It's been while since published, but the Koch lab would like to publish the details of these methods, as they would be very helpful to others doing DFS.
DNA in porous nanochannels
Initial passive transport of DNA in porous nanochannels fabricated from silica nanoparticles
We have been consulting with the Brueck and Lopez labs at UNM on a project for transporting DNA in nanochannels where the walls are formed from silica nanoparticles are are thus porous on the nanoscale. Initial work of Deying Xia and Thomas Gamble were recently published in Nanoletters:
Xia Deying, Gamble Thomas C., Mendoza Edgar A., Koch Steven J., He Xiang, Lopez Gabriel P., and Brueck S. R. J. "DNA Transport in Hierarchically-Structured Colloidal-Nanoparticle Porous-Wall Nanochannels." Nano Lett., 8 (6) 1610 - 1618, 2008
MEMS Force Sensor for Biophysics
Work done with Gayle Thayer, Alex Corwin, Maarten de Boer at Sandia, finished up after Koch moved to UNM, Physics & CHTM
Koch SJ, Thayer GE, Corwin AD, de Boer MP. Micromachined piconewton force sensor for biophysics investigations. Appl. Phys. Let. 2006 Oct 23;89(17):173901 (PDF)
Kinesin / Microtubule Molecular Motor System
In George Bachand's lab with Susan Rivera, fungal kinesin from Thermomyces lanuginosus
Rivera SB, Koch SJ, Bauer JM, Edwards JM, Bachand GD. 2007. "Temperature dependent properties of a kinesin-3 motor protein from Thermomyces lanuginosus." Fungal Genetics and Biology 44:1170-1179. PMID 17398126