Affiliation: Lawrence Berkeley National Laboratory
- Analysis of in-vivo LacR-mediated gene repression based on the mechanics of DNA loopingYongli Zhang
Departments of Chemistry and Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut, United States of America
PLoS ONE 1:e136. 2006....
- Statistical-mechanical theory of DNA loopingYongli Zhang
Department of Molecular Biophysics, Yale University, New Haven, Connecticut, USA
Biophys J 90:1903-12. 2006..We derive a rigorous theory of loop formation that connects global mechanical and geometric properties of both DNA and protein and demonstrates the importance of protein flexibility in loop-mediated protein-DNA interactions...
- Anomalous DNA binding by E2 regulatory protein driven by spacer sequence TATAZhiqun Xi
Department of Chemistry, Yale University, New Haven, CT 06511, USA
Nucleic Acids Res 38:3827-33. 2010..In the case of Mg(2+), additional ions are bound to TATA that require displacement for protein binding. We suggest that the TATA sequence may bias the DNA structure towards a conformation that binds the protein relatively weakly...
- DNA translocation of ATP-dependent chromatin remodeling factors revealed by high-resolution optical tweezersYongli Zhang
Department of Cell Biology, Yale University School of Medicine, New Haven, Connecticut, USA
Methods Enzymol 513:3-28. 2012..We show that optical tweezer force microscopy is a powerful and friendly tool for studies of chromatin structures and remodeling...
- Predicting indirect readout effects in protein-DNA interactionsYongli Zhang
Departments of Chemistry and Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06511, USA
Proc Natl Acad Sci U S A 101:8337-41. 2004..The sole exception was traced to differential magnesium ion binding...
- Statistical mechanics of sequence-dependent circular DNA and its application for DNA cyclizationYongli Zhang
Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06511, USA
Biophys J 84:136-53. 2003..J factors calculated by our new approach are well consistent with Monte Carlo simulations, whereas the new theory has much greater efficiency in computations. Simulation of experimental results has been demonstrated...
- High-throughput approach for detection of DNA bending and flexibility based on cyclizationYongli Zhang
Departments of Molecular Biophysics and Biochemistry and Chemistry, Yale University, New Haven, CT 06511, USA
Proc Natl Acad Sci U S A 100:3161-6. 2003..We found that, although the nicks hardly alter the bending flexibility, they significantly increase the torsional flexibility, and that the AT repeat has 28% (+/-12%) lower bending rigidity than a generic DNA sequence...
- High-resolution optical tweezers for single-molecule manipulationXinming Zhang
Department of Cell Biology, Yale School of Medicine, New Haven, Connecticut
Yale J Biol Med 86:367-83. 2013..These past and future applications demonstrate the unique advantages of high-resolution optical tweezers in quantitatively characterizing complex multi-scale dynamics of biomacromolecules. ..