Laboratory of Single-Molecule Biophysics

tether extension sample cell Tweezers Photo Protein Steps Nucleosome DNA


sarkar
Abhijit Sarkar
Associate Professor

Physics Department

Catholic University of America
620 Michigan Ave NE
Washington, DC 20064


Office: 211 Hannan Hall
(202)319-6740

Lab: 431 Hannan Hall
(202)319-5330

Fax: (202)319-4448

Email: sarkar@cua.edu

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Research Interests

Our lab studies DNA-protein interactions using single molecule micromanipulation techniques. We do experiments on λ-DNA modified with a polystyrene bead on one end and a magnetic bead on the other. By altering the separation between the DNA and a permanent magnet, we can apply various forces to the DNA molecule. You can see some movies of experiments done in our lab using this technique. Image processing methods allow us to extract the extension of the DNA and the force with which it's being pulled. Using microspray protocols and other approaches, we can introduce DNA-binding proteins of interest and observe as they bind to the DNA which is held at a fixed force. When proteins bind and produce changes in the DNA length, say by forming loops in the DNA, the resulting force-extesion curves can be used to infer a great deal of information about the physics of the DNA-protein interaction. Our lab has developed several novel experimental and computational methods to precisely quantify these interactions.

We are also interested in developing statistical mechanical models of single molecule experiments. In general, I have an interest in applying ideas from condensed matter physics to better understand how genetic processes work on a variety of scales.


Current Members

Principal Investigator
Abhijit Sarkar

Graduate Students
Roberto Fabian
Barbara Medvar

Undergraduate Interns
Kiera Lyons
Jeremy Burgos

Collaborators
Bhupesh Taneja
Pamela Tuma
Mark Knepper
Andre X.C.N. Valente

Teaching

PHYS 215-216
University Physics I-II

PHYS 469/669
Intro to Biophysics

PHYS 611 & 612
Mathematical Methods

PHYS 615
Advanced Mechanics

PHYS 621 & 622
Statistical Mechanics
sm1999-1986-600-level
sm2010-2000-600level

Publications

McAndrew C., Tyson C., Zischkau J., Mehl P., Tuma P.L., Pegg I., and Sarkar A. (2016) "A Simple, Low-Cost, Horizontal Magnetic Tweezers for Micromanipulation of Single DNA Molecules and DNA-Protein Complexes." BioTechniques. (Accepted, in press)

Tyson C., McAndrew C., Tuma P.L., Pegg I., Sarkar A. (2015) "Automated nonparametric method for detection of step-like features in biological data sets." Cytometry A. 87;5:393-404

Valente A. X.C.N., Sarkar A., Gao Y. (2014) Recent Advances in Systems Biology Research. Nova Science Publishers Inc., Hauppauge, N.Y.

Lu P., Pegg I.L., Sarkar A. (2013) "Mechanically Unzipping dsDNA with Built-in Sequence Inhomogeneities and Bound Proteins." Eur. Phys. J. E 36(2):9825

Vilbig R., Sarkar A., Zischkau J., Knepper M., Pitiskun, T. (2012) "An online tool for calculation of free-energy balance for the renal inner medulla." Am. J. Physiol. Renal Physiol. Aug;303(3):F366-72. Epub 2012 May 30

Valente A.X., Shin J.H., Sarkar A., Gao Y. (2012) "Rare coding SNP in DZIP1 gene associated with late-onset sporadic Parkinson's disease." Nat. Sci. Rep. 2, 256

McAndrew, C. (2012) "Studies of Single DNA-Histone Binding Events Using a Novel Magnetic Tweezer." Ph.D. Thesis, Catholic University of America

Davis D., Akhtar U., Keaster B., Grozinger K., Washington L., Kelsey S., Sarkar A., and DeLong R.K. (2009) "Challenges and potential for RNA nanoparticles (RNPs)." J. Biomed. Nanotechnol. 5, 36

Valente A. X. C. N., Sarkar A., and Stone H. (2004) "Two-peak and three-peak optimal complex networks." Phys. Rev. Lett. 92, 118702

Cocco S., Marko J. F., Monasson R., Sarkar A., and Yan J. (2003) "Force-extension behavior of folding polymers." Euro. Phys. J. E 10, 249

Sarkar A., Eroglu S., Poirier M., Nemani A., Gupta P., and Marko J. F. (2002) "Dynamics of chromosome compaction during mitosis." Expt. Cell Res. 277, 48

Sarkar A. and Marko J. F. (2001) "Removal of DNA-bound proteins by DNA twisting." Phys. Rev. E 63, 61909

Sarkar A., Leger J. F., Chatenay D., and Marko J. F. (2001) "Structural transitions in DNA driven by force and torque." Phys. Rev. E 63, 51903

Leger J. F., Romano G., Sarkar A., Robert J., Bourdieu L., Chatenay D., and Marko J. F. (1999) "Structural transition of a twisted and stretched DNA molecule." Phys. Rev. Lett. 83, 1066


Computational Methods

Former Lab Members

Christopher Tyson
[Ph.D. 2015]

Christopher McAndrew
[Ph.D. 2012]

Ping Lu
[Post-doctoral associate 2013]

Margaret Wheeler
[Intern, Summer 2015]

Jacob Perreira
[Intern, Summer 2015]

Vishal Mummareddy
[Intern, Summer 2014]

Edward "Rhett" Cheek
[Intern, Summer 2014]

Catherine Premraj
[Intern, Summer 2014]

German Uritskiy
[Intern, Summer 2013]

Matheus Galvez
[Intern, Summer 2013]

Casey Vantucci
[Intern, Summer 2013]

Tara Lakeman
[Intern, Summer 2012]

Philip Allen
[Intern, Summer 2012]

Christine Dedoulis
[Intern, Summer 2012]

Angeline Premraj
[Intern, Summer 2012]

William Kraemer
[Intern, Summer 2011]

Nazanin Ghassamian
[Intern, Summer-Fall 2011]

Matthew Dion
[Intern, Summer 2011]

Joseph Zischkau
[Intern, Summers of 2009, 2010, 2011]

Helen DeCelles-Zwerneman
[Intern, Summer 2010]

Benjamin Buckeye
[Intern, Summer 2010]

Jonathan Luke
[Intern, Summers 2009 and 2010]