Jan 24 (Yasuda and others 1998)
Jan 31 (Yasuda and others 2001) Supplement Commentary: (Schnitzer 2001)
Feb 7 (Zhuang and others 2000) Supplement
Feb 14 (Zhuang and others 2002) Supplement
Feb 21 (Lu and others 1998)
Mar 14 (Strick and others 2000)
Mar 21 (Dekker and others 2002) Commentary: (Champoux 2002)
Mar 28 (Svoboda and others
1994)
Apr 4 (Ha and others 2002) Supplement
Apr 11 (Liphardt and others 2001) Supplement Commentary: (Fernandez and others 2001)
May 2 (Liphardt and others 2002) Supplement Commentary: (Egolf 2002)
Champoux JJ. 2002. Type IA DNA topoisomerases: Strictly one step at a time. PNAS 99(19):11998-12000.
Dekker NH, Rybenkov VV, Duguet M, Crisona NJ, Cozzarelli NR, Bensimon D, Croquette V. 2002. The mechanism of type IA topoisomerases. PNAS 99(19):12126-12131.
Egolf DA. 2002. STATISTICAL MECHANICS: Far from
Equilibrium. Science
296(5574):1813-1815.
Fernandez JM, Chu S, Oberhauser AF. 2001. RNA STRUCTURE: Pulling on Hair(pins). Science 292(5517):653-654.
Ha T, Rasnik I, Cheng W, Babcock HP, Gauss GH, Lohman TM, Chu S. 2002. Initiation and re-initiation of DNA unwinding by the Escherichia coli Rep helicase. Nature 419(6907):638-41.
Liphardt J, Dumont S, Smith SB, Tinoco I, Jr., Bustamante C. 2002. Equilibrium information from nonequilibrium measurements in an experimental test of Jarzynski's equality. Science 296(5574):1832-5.
Liphardt J, Onoa B, Smith SB, Tinoco IJ, Bustamante C. 2001. Reversible unfolding of single RNA molecules by mechanical force.
Science 292(5517):733-7.
Lu HP, Xun L, Xie XS. 1998. Single-Molecule Enzymatic Dynamics. Science 282(5395):1877-1882.
Schnitzer MJ. 2001. Molecular motors. Doing a rotary two-step. Nature 410(6831):878-9, 881.
Strick TR, Croquette V, Bensimon D. 2000. Single-molecule analysis of DNA uncoiling by a type II topoisomerase. Nature 404(6780):901-4.
Svoboda K, Mitra PP, Block SM. 1994. Fluctuation
analysis of motor protein movement and single enzyme kinetics. Proc Natl Acad Sci USA
91(25):11782-86.
Yasuda R, Noji H, Kinosita K, Jr., Yoshida M.
1998. F1-ATPase is a highly efficient molecular motor that rotates with
discrete 120 degree steps. Cell
93(7):1117-24.
Yasuda R, Noji H, Yoshida M, Kinosita K, Jr., Itoh H. 2001. Resolution of distinct rotational substeps by submillisecond kinetic analysis of F1-ATPase. Nature 410(6831):898-904.
Zhuang X, Bartley LE, Babcock HP, Russell R, Ha T, Herschlag D, Chu S. 2000. A single-molecule study of RNA catalysis and folding. Science 288(5473):2048-51.
Zhuang X, Kim H, Pereira MJB, Babcock HP, Walter NG, Chu S. 2002. Correlating Structural Dynamics and Function in Single Ribozyme Molecules. Science 296(5572):1473-1476.
The course will meet Fridays 2-4 on the dates shown above.
Each student is expected to attend every class prepared to give a full presentation on the paper being discussed. This means that each student before entering the classroom must know (and be able to clearly explain) the methods, results and interpretation of every experiment in the paper. Students should also be able to clearly describe the motivation for the paper: what problem does it address and how does it go beyond the existing literature. Please be prepared to defend your interpretation of the experiments; you should say what you think that the experimental results prove, not what the authors claim that they prove.
If an emergency has prevented you from properly preparing for one of the classes, please contact me before the start of the class. In general, I prefer that people who have not prepared not attend.
In the interest of fairness to students taking the class for credit, auditing by graduate students is not permitted. Postdocs can audit with the instructor's permission.