Publications

61. Thayaparan Paramanathan, Ioana Vladescu, Micah J. McCauley, Ioulia Rouzina, and Mark C. Williams. Force spectroscopy reveals the DNA structural dynamics that govern the slow binding of Actinomycin D. Nucleic Acids Research (in press, 2012).

60. Jingyun Zhang, Micah J McCauley, L. James Maher III, Mark C Williams, and Nathan E Israeloff.Basic N-terminus of yeast Nhp6A regulates the mechanism of its DNA flexibility enhancement. Journal of Molecular Biology 416: 10–20 (2012).

59. Kathy R. Chaurasiya, Hylkje Geertsema, Gaël Cristofari, Jean-Luc Darlix, and Mark C. Williams.A single zinc finger optimizes the DNA interactions of the nucleocapsid protein of the yeast retrotransposon Ty3 Nucleic Acids Research 40: 751–760 (2012).

58. Micah J. McCauley and Mark C. Williams. Single-molecule biophysics: Untying a nanoscale knot. Nature Chemistry 3: 754–755 (2011).

57. James D. Evans, Suresh Peddigari, Kathy R. Chaurasiya, Mark C. Williams, and Sandra L. Martin. Paired mutations abolish and restore the balanced annealing and melting activities of ORF1p that are required for LINE-1 retrotransposition Nucleic Acids Research 39: 5611-5621 (2011).

56. Thayaparan Paramanathan, Micah J. McCauley, and Mark C. Williams. Studying Nucleic Acid - Drug Interactions at the Single Molecule Level Using Optical Tweezers. In “Methods for Studying DNA/Drug Interactions”, Meni Wanunu and Yitzhak Tor, eds. CRC Press (2011).

55. Micah J. McCauley and Mark C. Williams. Measuring DNA-Protein Binding Affinity on a Single Molecule Using Optical Tweezers. In DNA Nanotechnology, Giampaolo Zuccheri and Bruno Samorì, eds. Humana Press, Springer, New York (2011).

54. Mark C. Williams and Ioulia Rouzina. Force spectroscopy reveals DNA interactions with single-stranded DNA binding proteins and retroviral nucleic acid chaperones. In “Biophysics of DNA-protein interactions: From single molecules to biological systems”, Mark C. Williams and L. James Maher, III, eds. Springer, New York, pages 163-189 (2011).

53. Book: “Biophysics of DNA-protein interactions: From single molecules to biological systems”, Mark C. Williams and L. James Maher, III, eds. Springer, New York (2011).

52. Hao Wu, Ioulia Rouzina, and Mark C. Williams. "Single molecule stretching studies of RNA Chaperones". RNA Biology 7: 712-723 (2010).

51. Micah J. McCauley, Kathy R. Chaurasiya, Thayaparan Paramanathan, Ioulia Rouzina, and Mark C. Williams. "DNA stretching as a probe for nucleic acid interactions: Reply to Comments on 'Biophysical characterization of DNA binding from single molecule
force measurements'". Physics of Life Reviews 7: 358-361 (2010).

50. Kathy R. Chaurasiya, Thayaparan Paramanathan, Micah J. McCauley, and Mark C. Williams. Biophysical characterization of DNA binding from single molecule force measurements. Physics of Life Reviews 7: 299-341 (2010).

49. Dominic F. Qualley, Kristen M. Stewart-Maynard, Fei Wang, Mithun Mitra, Robert J. Gorelick, Ioulia Rouzina, Mark C. Williams and Karin Musier-Forsyth. C-terminal domain modulates the nucleic acid chaperone activity of human T-cell leukemia virus type 1 (HTLV-1) nucleocapsid protein (NC) via an electrostatic mechanism. Journal of Biological Chemistry 285: 295-307 (2010).

48. Mark C. Williams, Ioulia Rouzina, and Micah J. McCauley. Peeling back the mystery of DNA overstretching (Commentary). Proceedings of the National Academy of Sciences USA 106: 18047-18048 (2009).

47. Leila Shokri, Ioulia Rouzina, and Mark C. Williams. Interaction of bacteriophage T4 and T7 single-stranded DNA binding proteins with DNA. Physical Biology 6: 025002 (2009).

46. Jingyun Zhang, Micah J. McCauley, L. James Maher, III, Mark C. Williams, and N. E. Israeloff. Mechanism of DNA flexibility enhancement by HMGB proteins. Nucleic Acids Research 37: 1107-1114 (2009).

45. Micah J. McCauley and Mark C. Williams. Optical Tweezers Experiments Resolve Distinct Modes of DNA-Protein Binding. Biopolymers 91: 265–282 (2009).

44. Sandra L. Martin, Diane Bushman, Fei Wang, Patrick Wai-Lun Li, Ann Walker, Jessica Cummiskey, Dan Branciforte, and Mark C. Williams. A single amino acid substitution in ORF1 dramatically decreases L1 retrotransposition and provides insight into nucleic acid chaperone activity. Nucleic Acids Research 36: 5845-5854 (2008).

43. Leila Shokri, Boriana Marintcheva, Mootaz Eldib, Andreas Hanke, Ioulia Rouzina, and Mark C. Williams. Kinetics and thermodynamics of salt-dependent T7 gene 2.5 protein binding to single- and double-stranded DNA. Nucleic Acids Research 36: 5668-5677 (2008).

42.  Kristen M. Stewart-Maynard, Margareta Cruceanu, Fei Wang, My-Nuong Vo, Robert J. Gorelick, Mark C. Williams, Ioulia Rouzina, and Karin Musier-Forsyth. Retroviral Nucleocapsid Proteins Display Non-equivalent Levels of Nucleic Acid Chaperone Activity. Journal of Virology 82: 10129-10142 (2008).

41.  Micah J. McCauley, Leila Shokri, Jana Sefcikova, Česlovas Venclovas, Penny J. Beuning, and Mark C.Williams. Distinct Double- and Single-Stranded DNA Binding of E. coli Replicative DNA Polymerase III Alpha Subunit. ACS Chemical Biology 3: 577–587 (2008). This work was also featured in a journal podcast.

40.  Kiran Pant, Leila Shokri, Richard L. Karpel, Scott W. Morrical, and Mark C. Williams. Modulation of T4 gene 32 protein DNA binding activity by the recombination mediator protein UvsY. Journal of Molecular Biology 380: 799-811 (2008).

39.  Leila Shokri, Micah J. McCauley, Ioulia Rouzina, and Mark C. Williams. DNA overstretching in the presence of glyoxal: Structural evidence of force–induced DNA melting. Biophysical Journal 95: 1248-1255 (2008).

38.  Thayaparan Paramanathan, Fredrik Westerlund, Micah J. McCauley, Ioulia Rouzina, Per Lincoln, and Mark C. Williams. Mechanically Manipulating the DNA Threading Intercalation Rate. Journal of the American Chemical Society (Communication) 130: 3752 -3753 (2008).

37.  Mark C. Williams, Ioulia Rouzina, and Richard L. Karpel. Quantifying DNA-protein interactions by single molecule stretching. Methods in Cell Biology 84: 517-540 (2008).

36. Yasumasa Iwatani, Denise S.B. Chan, F. Wang, Kristen Stewart Maynard, Wataru Sugiura, Angela Gronenborn, Ioulia Rouzina, Mark C. Williams, Karin Musier-Forsyth, and Judith G. Levin. Deaminase-independent inhibition of HIV-1 reverse transcription by APOBEC3G. Nucleic Acids Research 35: 7096-7108 (2007).

35. Micah J McCauley, Jeff Zimmerman, L. James Maher III, and Mark C Williams. HMGB Binding to DNA: Single and Double Box Motifs. Journal of Molecular Biology 374: 993-1004 (2007).

34. Micah McCauley, Philip R. Hardwidge, L. J. Maher III, and Mark C. Williams. DNA binding proteins that alter nucleic acid flexibility, Proceedings of SPIE 6644: 664405 (2007).

33. Mark C. Williams. Stuffing a virus with DNA: Dissecting viral genome packaging (Commentary). Proceedings of the National Academy of Sciences USA 104: 11125-11126 (2007).

32.  Ioana D. Vladescu, Micah J. McCauley, Megan E. Nuñez, Ioulia Rouzina, and Mark C. Williams. Quantifying force-dependent and zero-force DNA intercalation by single-molecule stretching. Nature Methods 4: 517-522 (2007). 

31.  Micah J. McCauley and Mark C. Williams, Mechanisms of DNA Binding Determined in Optical Tweezers Experiments. Biopolymers 85: 154-168 (2007).

30.  Leila Shokri, Boriana Marintcheva, Charles C. Richardson, Ioulia Rouzina, and Mark C. Williams. Single molecule force spectroscopy of salt-dependent bacteriophage T7 gene 2.5 protein binding to single-stranded DNA. Journal of Biological Chemistry 281: 38689-38696 (2006).

29.  Margareta Cruceanu, Andrew G. Stephen, Penny J. Beuning, Robert J. Gorelick, Robert J. Fisher, and Mark C. Williams. Single DNA molecule stretching measures the activity of chemicals that target the HIV-1 nucleocapsid protein Analytical Biochemistry 358: 159-170 (2006).

28.  Margareta Cruceanu, Robert J. Gorelick, Karin Musier-Forsyth, Ioulia Rouzina, and Mark C. Williams. Rapid kinetics of protein-nucleic acid interaction is a major component of HIV-1 nucleocapsid protein's nucleic acid chaperone function. Journal of Molecular Biology 363: 867-877 (2006).

27.  Aleksandra Mihailović, Ioana Vladescu, Micah McCauley, Elaine Ly, Mark C. Williams, Eileen M. Spain, and Megan E. Nuñez. Exploring the Interaction of Ruthenium(II) Polypyridyl Complexes with DNA Using Single-Molecule Techniques. Langmuir 22: 4699-4709 (2006).

26.  Margareta Cruceanu, Maria A. Urbaneja, Catherine V. Hixson, Donald G. Johnson, Siddhartha A. Datta, Matthew J. Fivash, Andrew G. Stephen, Robert J. Fisher, Robert J. Gorelick, Jose R. Casas-Finet, Alan Rein, Ioulia Rouzina, and Mark C. Williams. Nucleic acid binding and chaperone properties of HIV-1 Gag and nucleocapsid proteins. Nucleic Acids Research 34: 593-605 (2006).

25.  Mark C. Williams, Ioulia Rouzina, and Richard L. Karpel. Thermodynamics and kinetics of DNA-protein interactions from single molecule force spectroscopy measurements. Current Organic Chemistry 10: 419-432 (2006).

24. Igor M. Sokolov, Ralf Metzler, Kiran Pant, and Mark C. Williams. First passage time of N excluded-volume particles on a line. Physical Review E 72: 041102 (2005). 

23.  Ioana D. Vladescu, Micah J. McCauley, Ioulia Rouzina, and Mark C. Williams. Mapping the phase diagram of single DNA molecule force-induced melting in the presence of ethidium. Physical Review Letters 95: 158102 (2005).

22.  Ioulia Rouzina, Kiran Pant, Richard L. Karpel, and Mark C. Williams. Theory of electrostatically-regulated binding of T4 gene 32 protein to single- and double-stranded DNA. Biophysical Journal 89: 1941-1956 (2005).

21.  Igor M. Sokolov, Ralf Metzler, Kiran Pant, and Mark C. Williams. Target search of N sliding proteins on a DNA. Biophysical Journal 89: 895-902 (2005).

20.  Kiran Pant, Richard L. Karpel, Ioulia Rouzina, and Mark C. Williams. Salt dependent binding of T4 gene 32 protein to single- and double-stranded DNA: Single molecule force spectroscopy measurements. Journal of Molecular Biology 349: 317-330 (2005).

19.  Micah McCauley, Philip R. Hardwidge, L. James Maher III, and Mark C. Williams. Dual Binding Modes for an HMG Domain from Human HMGB2 on DNA. Biophysical Journal 89: 353-364 (2005).

18.  Sandra L. Martin, Margareta Cruceanu, Dan Branciforte, Patrick Wai-lun Li, Stanley C. Kwok, Robert S. Hodges, and Mark C. Williams. LINE-1 Retrotransposition Requires the Nucleic Acid Chaperone Activity of the ORF1 Protein. Journal of Molecular Biology 348: 549-561 (2005). 

17.  Kiran Pant, Richard L. Karpel, Ioulia Rouzina, and Mark C. Williams. Mechanical Measurement of Single Molecule Binding Rates: Kinetics of DNA Helix-Destabilization by T4 Gene 32 Protein. Journal of Molecular Biology 336: 851-870 (2004).

16.  Mark C. Williams, Kiran Pant, Ioulia Rouzina, and Richard L. Karpel. Single molecule force spectroscopy studies of DNA denaturation by T4 gene 32 protein. Spectroscopy – An International Journal 18: 203-211 (2004).

15.  Mark C. Williams. Review of “Thermodynamics of Pharmaceutical Systems”, by Kenneth A. Connors. Drug Discovery Today 8: 395 (2003). 

14.  Kiran Pant, Richard L. Karpel, and Mark C. Williams. Kinetic Regulation of Single DNA Molecule Denaturation by T4 Gene 32 Protein Structural Domains. Journal of Molecular Biology 327: 571-578 (2003).

13.  A. Wynveen, K. Lidke, M. C. Williams, C. F. Giese, and J. W. Halley. Dynamics of Low Energy Helium Vapor Pulses Physical Review E 67: 026311 (2003).

12.  Mark C. Williams, Robert J. Gorelick, and Karin Musier-Forsyth. Specific zinc finger architecture required for HIV-1 nucleocapsid protein’s nucleic acid chaperone function Proceedings of the National Academy of Sciences USA 99: 8614-8619 (2002).

11. Mark C. Williams. Optical Tweezers: Measuring Piconewton Forces, in Single Molecule Techniques, Petra Schwille, ed., a volume of the Biophysics Textbook Online, L. DeFelice, editor-in-chief, Biophysical Society, Bethesda, MD. Now available at http://www.biophysics.org/Portals/1/PDFs/Education/williams.pdf (2002).

10. Mark C. Williams and Ioulia Rouzina. Force Spectroscopy of Single DNA and RNA Molecules. Current Opinion in Structural Biology 12: 330-336 (2002).

9.   Mark C. Williams, Ioulia Rouzina, and Victor A. Bloomfield. Thermodynamics of DNA Interactions from Single Molecule Stretching Experiments. Accounts of Chemical Research 35: 159-166 (2002).

8.   Jay R. Wenner, Mark C. Williams, Ioulia Rouzina, and Victor A. Bloomfield. Salt dependence of the elasticity and overstretching transition of single DNA molecules Biophysical Journal 82: 3160-3169 (2002).

7.   Mark C. Williams, Ioulia Rouzina, Robert Gorelick, Karin Musier-Forsyth, and Victor A. Bloomfield. Mechanism for nucleic acid chaperone activity of HIV-1 nucleocapsid protein revealed by single molecule stretching. Proceedings of the National Academy of Sciences USA 98: 6121-6126 (2001).

6.   Mark C. Williams, Jay R. Wenner, Ioulia Rouzina, and Victor A. Bloomfield. Entropy and Heat Capacity of DNA Melting from Temperature Dependence of Single Molecule Stretching Biophysical Journal 80: 1932-1939 (2001).

5.   Mark C. Williams, Jay R. Wenner, Ioulia Rouzina, and Victor A. Bloomfield. The effect of pH on the overstretching transition of dsDNA: Evidence of force-induced DNA melting Biophysical Journal 80: 874-881 (2001).

4.   K. Lidke, M.C. Williams, A. Wynveen, and J.W. Halley. Gas Dynamics of Pulsed Low Energy Helium Beams. Journal of Low Temperature Physics 121: 351-356 (2000).

3.   Mark C. Williams, C.F. Giese, and J. W. Halley. Suspension of Superfluid Helium Using Cesium Coated Surfaces. Physical Review B 53: 6627-6633 (1996).

2.   C. F. Giese, K. Goetz, and M. C. Williams. Experimental Constraints on the Observation of the Condensate Fraction in Superfluid Helium Four by a new method. Physica B 194-196: 535-536 (1994).

1. Mark C. Williams and R. T. Brundage. Stimulated emission cross sections and nonradiative relaxation of the ⁵L_6' state of trivalent americium in fluorozirconate glass. Physical Review B 45: 4561-4565 (1992).