Yongli Zhang

Summary

Affiliation: Lawrence Berkeley National Laboratory
Country: USA

Publications

  1. pmc Analysis of in-vivo LacR-mediated gene repression based on the mechanics of DNA looping
    Yongli Zhang
    Departments of Chemistry and Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut, United States of America
    PLoS ONE 1:e136. 2006
  2. pmc Statistical-mechanical theory of DNA looping
    Yongli Zhang
    Department of Molecular Biophysics, Yale University, New Haven, Connecticut, USA
    Biophys J 90:1903-12. 2006
  3. pmc Anomalous DNA binding by E2 regulatory protein driven by spacer sequence TATA
    Zhiqun Xi
    Department of Chemistry, Yale University, New Haven, CT 06511, USA
    Nucleic Acids Res 38:3827-33. 2010
  4. ncbi request reprint DNA translocation of ATP-dependent chromatin remodeling factors revealed by high-resolution optical tweezers
    Yongli Zhang
    Department of Cell Biology, Yale University School of Medicine, New Haven, Connecticut, USA
    Methods Enzymol 513:3-28. 2012
  5. pmc Predicting indirect readout effects in protein-DNA interactions
    Yongli 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
  6. pmc Statistical mechanics of sequence-dependent circular DNA and its application for DNA cyclization
    Yongli Zhang
    Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06511, USA
    Biophys J 84:136-53. 2003
  7. pmc High-throughput approach for detection of DNA bending and flexibility based on cyclization
    Yongli 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
  8. pmc High-resolution optical tweezers for single-molecule manipulation
    Xinming Zhang
    Department of Cell Biology, Yale School of Medicine, New Haven, Connecticut
    Yale J Biol Med 86:367-83. 2013

Collaborators

Detail Information

Publications8

  1. pmc Analysis of in-vivo LacR-mediated gene repression based on the mechanics of DNA looping
    Yongli Zhang
    Departments of Chemistry and Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut, United States of America
    PLoS ONE 1:e136. 2006
    ....
  2. pmc Statistical-mechanical theory of DNA looping
    Yongli 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...
  3. pmc Anomalous DNA binding by E2 regulatory protein driven by spacer sequence TATA
    Zhiqun 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...
  4. ncbi request reprint DNA translocation of ATP-dependent chromatin remodeling factors revealed by high-resolution optical tweezers
    Yongli 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...
  5. pmc Predicting indirect readout effects in protein-DNA interactions
    Yongli 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...
  6. pmc Statistical mechanics of sequence-dependent circular DNA and its application for DNA cyclization
    Yongli 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...
  7. pmc High-throughput approach for detection of DNA bending and flexibility based on cyclization
    Yongli 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...
  8. pmc High-resolution optical tweezers for single-molecule manipulation
    Xinming 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. ..