Koch Lab:Publications

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==Probing Protein-DNA Interactions by Unzipping DNA with Optical Tweezers==
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===Our initial proof-of-principle publication in the Wang Lab at Cornell===
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[[Image:Paper_1_Fig2A.jpg|right|thumb|Figure 2A from the Biophys. J. paper.  The black trace shows unzipping force for a single DNA molecule in the absence of protein.  The red trace shows in the presence of a DNA-binding protein, with predicted binding curves shown as dotted lines.  Unoccupied binding sites marked with arrows.]]
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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
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===Our follow-on paper showing that unbinding forces can be analyzed nicely with Evan Evans' Dynamic Force Spectrosocpy (DFS) model===
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[[Image:PRL Fig 3, color.png|right|thumb|Fig. 3 from the PRL.  Orange bars are histograms of 449 total unbinding events.  Dashed curves are maximum likelihood fits of the PDF from Evan Evans' DFS model, each fit to a single rate.  Solid lines are PDFs from a single best fit for all rates.  Vertical dashed bars represent unaccessible ranges to our experiment.]]
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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
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*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.
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==MEMS Force Sensor for Biophysics==
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===Work done with Gayle Thayer, Alex Corwin, Maarten de Boer at Sandia, finished up after Koch moved to UNM, Physics & CHTM===
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[[Image:PN 186 sensor 45deg 08a big.PNG|right|thumb|Scanning Electron Microscope image of a force sensor similar that used for the research.]]
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[http://link.aip.org/link/?APL/89/173901 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] ([http://www.chtm.unm.edu/publications/APL%2089_173901_Koch,%20Thayer,%20Corwin,%20de%20Boer_MEMS%20force%20sensor%20for%20mag%20bead%20calibration.pdf PDF])
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Revision as of 12:21, 27 March 2007


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Contents

Probing Protein-DNA Interactions by Unzipping DNA with Optical Tweezers

Our initial proof-of-principle publication in the Wang Lab at Cornell

Figure 2A from the Biophys. J. paper.  The black trace shows unzipping force for a single DNA molecule in the absence of protein.  The red trace shows in the presence of a DNA-binding protein, with predicted binding curves shown as dotted lines.  Unoccupied binding sites marked with arrows.
Figure 2A from the Biophys. J. paper. The black trace shows unzipping force for a single DNA molecule in the absence of protein. The red trace shows in the presence of a DNA-binding protein, with predicted binding curves shown as dotted lines. Unoccupied binding sites marked with arrows.

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

Fig. 3 from the PRL.  Orange bars are histograms of 449 total unbinding events.  Dashed curves are maximum likelihood fits of the PDF from Evan Evans' DFS model, each fit to a single rate.  Solid lines are PDFs from a single best fit for all rates.  Vertical dashed bars represent unaccessible ranges to our experiment.
Fig. 3 from the PRL. Orange bars are histograms of 449 total unbinding events. Dashed curves are maximum likelihood fits of the PDF from Evan Evans' DFS model, each fit to a single rate. Solid lines are PDFs from a single best fit for all rates. Vertical dashed bars represent unaccessible ranges to our experiment.

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.


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

Scanning Electron Microscope image of a force sensor similar that used for the research.
Scanning Electron Microscope image of a force sensor similar that used for the research.

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)

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