Laboratory of Single Molecule Biological Physics

exp_img magnetic tweezers
Lab Group nucleosome


sarkar
Abhijit Sarkar
Assistant Professor

211 Hannan Hall
Physics Department

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


Office: (202) 319-6740
Lab: (202) 319-5330
Fax: (202) 319-4448


Email: sarkar@cua.edu

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Research Interests

My lab studies protein-DNA 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. A stiff glass pipette is used to aspirate on the poly-bead while using a permanent magnet to pull on the magnetic bead. 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 it's being pulled with. Using microspray protocols and other approaches, we can introduce DNA-binding proteins of interest allowing them to bind to the DNA which is held extended with 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. Tension on DNA can also be applied using a combination of stiff & flexible pipettes, with each pipette aspirating on one of the two beads. Holding one of the pipettes fixed, the other pipette can be stepped away from or towards the fixed pipette thereby extending the DNA molecule. The length of the DNA tether is determined be tracking the position of a reference point on each pipette; the bending of flexible pipette is used to determine the pulling force.

I am 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
Christopher Tyson, M.S.
Ryan Vilbig

Post-Doctoral Research Associate
Ping Lu

Collaborators
Patrick Mehl
Pamela Tuma
Mark Knepper
Andre X.C.N. Valente

Teaching

PHYS 215-216
University Physics I-II

PHYS 569-669
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

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 J. F. 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
Former Lab Members

Christopher McAndrew
[Graduate Student, 2008-2012]
[Ph.D. 2012]
[Federal Employee GS-12]

Tara Lakeman
[Intern, Summer 2012]
[Senior Physics major, CUA]

Benjamin Buckeye
[Intern, Summer 2010]
[Sophomore BioEngineering Major, Mount Union College]

Christine Dedoulis
[Intern, Summer 2012]
[Senior, St Johns College High School]

Jonathan Luke
[Intern, Summer 2009, 2010]
[Junior Biology major, University of Maryland - College Park]

Philip Allen
[Intern, Summer 2012]
[Freshman Biology major, University of Notre Dame]

Joseph Zischkau
[Intern, Summer 2009, 2010, 2011]
[Software Developer, YinzCam Inc]

William Kraemer
[Intern, Summer 2011]
[Freshman Bioengineering major, Rochester Institute of Technology]

Helen DeCelles-Zwerneman
[Intern, Summer 2010]
[Junior Physics major, Georgetown University]

Nazanin Ghassamian
[Intern, Summer-Fall 2011]
[Junior Biomedical Engineering major, CUA]

Angeline Premraj
[Intern, Summer 2012]
[Junior Biomedical Engineering major, CUA]

Matthew Dion
[Intern, Summer 2011]
[Graduate Student, Rensselear Polytechnic Institute]