The overall long-range objective is to quantitatively understand the mechanics of transcriptional control through DNA looping. This will not only elucidate the relationship between the structure, dynamics and function of such regulatory loops, but also improve our understanding of a wide range of fundamental life processes in which proteins interact with multiple sites on a DNA molecule, such as site-specific recombination and the regulation of replication.For this aim, a simplified model system for DNA looping based on the lac repressor and the lac operon in E. coli will be studied in vitro in a series of single-molecule experiments. Specifically, state-of-the-art single-molecule techniques, such as an optical-tweezer based femtoNewton force spectroscopy technique and total-internal-reflection fluorescence microscopy methods will be adapted and further improved to allow the measurement of forces that are associated with the loop formation process with femtoNewton sensitivity and millisecond time resolution while the substrate DNA is subjected to mechanical constraints that are ubiquitous in a living cell, such as tension, twist and supercoiling. The dependence of protein-mediated loop formation rates on these mechanical features will be studied, and quantitatively interpreted in the framework of statistical mechanics of DNA molecules. In the end, it will be attempted to directly control transcription by mechanically opening and closing the repressor loop through the application of tension. This will test current models of how DNA looping regulates transcription and explore the role of mechanical constraints on this important process. This will help to bridge the gap between oversimplified models for DNA looping such as in-vitro DNA ring cyclization, and transcriptional repression in a living cell, which is currently inaccessible to a quantitatively accurate theoretical description. On the side, the instrument development efforts will pave the way for a multitude of other ultra-sensitive single-molecules studies in fields as diverse as the dynamics of protein- and RNA folding or improved studies of molecular motors.

Agency
National Institute of Health (NIH)
Institute
National Institute of General Medical Sciences (NIGMS)
Type
Research Project (R01)
Project #
5R01GM065934-03
Application #
6796364
Study Section
Biophysical Chemistry Study Section (BBCB)
Program Officer
Lewis, Catherine D
Project Start
2002-09-01
Project End
2007-08-31
Budget Start
2004-09-01
Budget End
2005-08-31
Support Year
3
Fiscal Year
2004
Total Cost
$241,210
Indirect Cost
Name
University of Michigan Ann Arbor
Department
Physics
Type
Schools of Arts and Sciences
DUNS #
073133571
City
Ann Arbor
State
MI
Country
United States
Zip Code
48109
Milstein, J N; Chen, Y F; Meiners, J-C (2011) Bead size effects on protein-mediated DNA looping in tethered-particle motion experiments. Biopolymers 95:144-50
Chen, Yih-Fan; Milstein, J N; Meiners, Jens-Christian (2010) Femtonewton entropic forces can control the formation of protein-mediated DNA loops. Phys Rev Lett 104:048301
Chen, Yih-Fan; Milstein, J N; Meiners, Jens-Christian (2010) Protein-mediated DNA loop formation and breakdown in a fluctuating environment. Phys Rev Lett 104:258103
Chen, Yih-Fan; Wilson, David P; Raghunathan, Krishnan et al. (2009) Entropic boundary effects on the elasticity of short DNA molecules. Phys Rev E Stat Nonlin Soft Matter Phys 80:020903
Chen, Yih-Fan; Blab, Gerhard A; Meiners, Jens-Christian (2009) Stretching submicron biomolecules with constant-force axial optical tweezers. Biophys J 96:4701-8
Chen, Hao; Gu, Wei; Cellar, Nick et al. (2008) Electromechanical properties of pressure-actuated poly(dimethylsiloxane) microfluidic push-down valves. Anal Chem 80:6110-3
Goyal, Sachin; Lillian, Todd; Blumberg, Seth et al. (2007) Intrinsic curvature of DNA influences LacR-mediated looping. Biophys J 93:4342-59
Newby Lambert, Meredith; Vocker, Eva; Blumberg, Seth et al. (2006) Mg2+-induced compaction of single RNA molecules monitored by tethered particle microscopy. Biophys J 90:3672-85
Blumberg, Seth; Tkachenko, Alexei V; Meiners, Jens-Christian (2005) Disruption of protein-mediated DNA looping by tension in the substrate DNA. Biophys J 88:1692-701
Blumberg, Seth; Gajraj, Arivalagan; Pennington, Matthew W et al. (2005) Three-dimensional characterization of tethered microspheres by total internal reflection fluorescence microscopy. Biophys J 89:1272-81