Bustamante Lab Recent Publications List

2008

  • 231. Ptacin, J.L., Nšllmann, M., Becker, E.C., Cozzarelli, N.R., Pogliano, K., and C. Bustamante,
    Sequence-directed DNA export guides chromosome translocation during sporulation in Bacillus subtilis
    Nat Struct Mol Biol. 2008 Apr 6; [Epub ahead of print] PDF
  • Jin-Der Wen, Laura Lancaster, Courtney Hodges, Ana-Carolina Zeri, Shige H. Yoshimura, Harry F. Noller, Carlos Bustamante and Ignacio Tinoco
    Following translation by single ribosomes one codon at a time
    Nature 452, 598-603 (3 April 2008) PDF
  • Chemla YR, Moffitt JR, Bustamante C,
    Exact Solutions for Kinetic Models of Macromolecular Dynamics
    Journal of Physical Chemistry B (2008); Articles ASAP (10.1021/jp076153r) PDF
  • Moffitt JR, Chemla YR, Smith SB, Bustamante C.
    Recent Advances in Optical Tweezers
    Annual Review of Biochemistry (2008) 77: 19.1-19.4 (Reviews in Advance) PDF
  • Green L, Kim CH, Bustamante C, Tinoco I Jr.
    Characterization of the Mechanical Unfolding of RNA pseudoknots
    J Mol Biol 375(2):511-28 (Jan. 11, 2008: Epub May 26, 2007) PDF
  • C. Bustamante, Y.R. Chemla, and J.R. Moffitt.
    High-Resolution Dual-Trap Optical Tweezers with Differential Detection
    Ch 14 in Single-Molecule Techniques: A Laboratory Manual. P. Selvin and T. Ha, Eds. (CSHL, 2008)

    • 2007

    2006

    • Ignacio Tinoco Jr., Pan T. X. Li and Carlos Bustamante
      Determination of thermodynamics and kinetics of RNA reactions by force
      Quarterly Reviews of Biophysics 39(4):325-360 (November 2006). PDF
    • Jerod L. Ptacin, Marcelo Nöllmann, Carlos Bustamante and Nicholas Cozzarelli
      Identification of the FtsK sequence-recognition domain
      Nature Structural and Molecular Biology 13: 1023-1025 (2006) PDF
      Supplementary Information: materials and methods, data, figure 3, figure 2, figure 1,
    • Yongli Zhang, Corey L. Smith, Anjanabha Saha, Stephan W. Grill, Shirley Mihardja, Steven B. Smith, Bradley R. Cairns, Craig L. Peterson, Carlos Bustamante
      DNA Translocation and Loop Formation Mechanism of Chromatin Remodeling by SWI/SNF and RSC
      Molecular Cell 24: 559-568 (2006) PDF
      Summary from Cell
    • Mihardja S, Spakowitz A, Zhang Y, Bustamante C
      Effect of force on mononucleosomal dynamics
      PNAS 103 (43): 15871-15876 (2006) PDF
    • Li P XT, Bustamante C, Tinoco I Jr.
      Unusual mechanical stability of a minimal RNA kissing complex
      PNAS 103: 15847-15852 (2006) PDF
    • Gore J, Bryant Z, Nöllmann M, Le MU, Cozzarelli NR, Bustamante C
      DNA overwinds when stretched
      Nature 442: 836-839 (2006) PDF
    • Moffitt JR, Chemla YR, Izhaky D, Bustamante C
      Differential detection of dual traps improves the spatial resolution of optical tweezers
      PNAS, 103 (24): 9006-11 (2006) PDF
    • Ritort F, Mihardja S, Smith SB, Bustamante C
      Condensation transition in DNA-polyaminoamide dendrimer fibers studied using optical tweezers
      Phys. Rev. Lett. 96 (11): 118301-4 (2006) PDF
    • Gore J, Bryant Z, Stone MD, Nöllmann M, Cozzarelli NR and Bustamante C
      Mechanochemical analysis of DNA gyrase using rotor bead tracking
      Nature 439: 100-104 (2006) PDF
    • Dumont S, Cheng W, Serebrov V, Beran RK, Tinoco I Jr., Pyle AM and Bustamante C
      RNA translocation and unwinding mechanism of HCV NS3 helicase and its coordination by ATP
      Nature 439: 105-108 (2006) PDF
    • Li PT, Collin D, Smith SB, Bustamante C, Tinoco I Jr.
      Probing the mechanical folding kinetics of TAR RNA by hopping, force-jump, and force-ramp methods
      Biophysics Journal, 90 (1): 250-60 (2006) PDF

    2005

    • Bustamante C
      Unfolding single RNA molecules: bridging the gap between equilibrium and non-equilibrium statistical thermodynamics.
      Quarterly Reviews of Biophysics, 38(4):291-301 (November 2005, published online in 2006) PDF
    • O Levy, JL Ptacin, PJ Pease, J Gore, MB Eisen, C Bustamante, and NR Cozzarelli
      Identification of oligonucleotide sequences that direct the movement of the Escherichia coli FtsK translocase
      PNAS, 102 (49):17618 - 17623 (2005) PDF
    • Gorostiza P, Tombola F, Verdaguer A, Smith SB, Bustamante C, Isacoff EY
      Molecular handles for the mechanical manipulation of single-membrane proteins in living cells
      IEEE Trans Nanobioscience. 4 (4): 269-76 (2005) PDF
    • J Martinez, TD Yuzvinsky, AM Fennimore, A Zettl, R Garcia 3 and C Bustamante
      Length control and sharpening of atomic force microscope carbon nanotube tips assisted by an electron beam.
      Nanotechnology, 16, 2493 - 2496 (September 2005) PDF
    • Wilcox AJ, Choy J, Bustamante C, and Matouschek A
      Effect of protein structure on mitochondrial import
      PNAS 102 (43): 15435 - 15440 OCT 25 (2005) PDF
    • Brown TA, Cecconi C, Tkachuk AN, Bustamante C, and Clayton DA
      Replication of mitochondrial DNA occurs by strand displacement with alternative light-strand origins, not via a strand-coupled mechanism
      Genes & Development 19 (20): 2466-2476 OCT 15 (2005) PDF
    • Mao HB, Arias-Gonzalez JR, Smith SB, Tinoco I, and Bustamante C
      Temperature control methods in a laser tweezers system 
      Biophysical Journal 89 (2): 1308-1316 AUG (2005) PDF
    • Bustamante C, Liphardt J, Ritort F
      The nonequilibrium thermodynamics of small systems 
      Physics Today 58 (7): 43-48 JUL (2005) PDF
    • Tang M, Cecconi C, Kim H, Bustamante C, and Rio DC
      Guanosine triphosphate acts as a cofactor to promote assembly of initial P-element transposase-DNA synaptic complexes 
      Genes & Development 19 (12): 1422-1425 JUN 15 (2005) PDF
    • Cecconi C, Shank EA, Bustamante C, and Marqusee S
      Direct Observation of the Three-State Folding of a Single Protein Molecule
      Science 23: 2057-2060 (2005) PDF
    • Chemla YR, Aathavan K, Michaelis J, Grimes S, Jardine PJ, Anderson DL and Bustamante C
      Mechanism of Force Generation of a Viral DNA Packaging Motor
      Cell 122 (5): 683-692 (2005) PDF
    • Collin D, Ritort F, Jarzynski C, Smith SB, Tinoco (Jr) I, and Bustamante C
      Verification of the Crooks fluctuation theorem and recovery of RNA folding free energies
      Nature 437: 231-234 (2005) PDF (see accompanying Nature News and Views article)
    • Paul J. Pease, Oren Levy, Gregory J. Cost, Jeff Gore, Jerod L. Ptacin, David Sherratt, Carlos Bustamante, and Nicholas R. Cozzarelli
      Sequence-Directed DNA Translocation by Purified FtsK
      Science 307: 586-590 (2005) PDF REPRINT (see News & Views in NSMB)
    • Gu Li, Marcia Levitus, Carlos Bustamante & Jonathan Widom
      Rapid spontaneous accessibility of nucleosomal DNA
      Nature Structural & Molecular Biology 12, 46 - 53 (2005) PDF

    2004

    • Bustamante C
      Of torques, forces and protein machines.
      Protein Sci. 2004 13(11): 3061-3065 (2004) PDF
    • Trepagnier EH, Jarzynski C, Ritort F, Crooks GE, Bustamante C, and Liphardt J
      Experimental Test of Hatano and Sasa's Nonequilibrium Steady-state Equality
      PNAS 101 (42) 15038-15041 (2004) PDF
    • Bustamante C, Chemla YR, Forde NR & Izhaky D
      Mechanical processes in biochemistry
      Annual Review of Biochemistry (2004) 73: 705-748 PDF
    • Goedken ER, Levitus M, Johnson A, Bustamante C, O'Donnell M, Kuriyan J
      Fluorescence measurements on the E-coli DNA polymerase clamp loader:
      Implications for conformational changes during ATP and clamp binding
      Journal Of Molecular Biology 336 (5): 1047-1059 (MAR 5 2004) PDF

    2003

    • Gore J, Ritort F & Bustamante C
      Bias and error in estimates of equilibrium free-energy differences from nonequilibrium measurements
      Proc Natl Acad Sci U S A (2003) 100: 12564-12569 PDF
      (see accompanying PNAS Commentary)
    • Matouschek A & Bustamante C
      Finding a protein's Achilles heel
      Nat Struct Biol. (2003) 10(9):674-6 PDF
    • Bryant Z, Stone MD, Gore J, Smith SB,Cozzarelli NR Bustamante C
      Structural transitions and elasticity from torque measurements on DNA
      Nature (2003) 424: 338-341 PDF
    • Stone MD, Bryant Z, Crisona NJ, Smith SB, Vologodskii A, Bustamante C, and Cozzarelli NR
      Chirality sensing by Escherichia coli topoisomerase IV and the mechanism of type II topoisomerases Proc Natl Acad Sci U S A (2003) 100: 8654-8659 PDF
    • Smith SB, Cui Y, Bustamante C.
      Optical-Trap Force Transducer that Operates by Direct Measurement of Light Momentum
      Methods in Enzymology (2003), 361:134-162 PDF
    • Onoa B, Dumont S, Liphardt J, Smith SB, Tinoco, I Jr., Bustamante C
      Identifying the kinetic barriers to mechanical unfolding of the T. thermophila ribozyme
      Science (2003): 1892-1895 PDF
    • Rivetti C, Codeluppi S., Dieci G.and Bustamante C
      Visualizing RNA Extrusion and DNA Wrapping in Transcription Elongation Complexes of Bacterial and Eukaryotic RNA Polymerases
      J. Mol. Bio. (2003) 5:1413-1426 PDF
    • Keller D, Swigon D, Bustamante C
      Relating Single-Molecule Measurements to Thermodynamics
      Biophys. J. (2003) 84: 733-738 PDF
    • Bustamante C, Bryant Z, Smith SB
      Ten years of tension: single-molecule DNA mechanics
      Nature (2003) 421: 423 - 427 PDF
    • Kellermayer MSZ, Bustamante C, Granzier HL
      Mechanics and structure of titin oligomers explored with atomic force microscopy
      Biochimica Et Biophysica Acta-Bioenergetics 1604 (2): 105-114 (JUN 5 2003) PDF

    2002

    • Tinoco I Jr., Bustamante, C
      The effect of force on thermodynamics and kinetics of single molecule reactions
      Biophysical Chemistry (2002) 102: 513-533 PDF
    • Ritort F, Bustamante C, Tinoco I Jr
      A two-state kinetic model for the unfolding of single molecules by mechanical force.
      Proc Natl Acad Sci U S A (2002) 99:13544-8 PDF
    • Forde NR, Izhaky D, Woodcock GR, Wuite GJ, Bustamante C
      Using mechanical force to probe the mechanism of pausing and arrest during continuous elongation by Escherichia coli RNA polymerase.
      Proc Natl Acad Sci U S A (2002) 99:11682-7 PDF
    • Liphardt J, Dumont S, Smith SB, Tinoco I Jr, Bustamante C
      Equilibrium information from nonequilibrium measurements in an experimental test of Jarzynski's equality.
      Science (2002) 296:1832-5 PDF
    • Parak WJ, Gerion D, Zanchet D, Woerz AS, Pellegrino T, Micheel C, Williams SC, Seitz M, Bruehl RE, Bryant Z, Bustamante C, Bertozzi CR, Alivisatos AP
      Conjugation of DNA to silanized colloidal semiconductor nanocrystalline quantum dots
      Chemistry Of Materials 14 (5): 2113-2119 (MAY 2002) PDF

    2001

    • Smith DE, Tans SJ, Smith SB, Grimes S, Anderson DL, Bustamante C
      The bacteriophage phi29 portal motor can package DNA against a large internal force
      Nature (2001) 413:748-52 (October 2001) PDF [Supplementary Info]
    • Bustamante C, Keller D, Oster G
      The physics of molecular motors.
      Acc Chem Res (2001) 34:412-20 PDF
    • d'Erme M, Yang G, Sheagly E, Palitti F, Bustamante C
      Effect of poly(ADP-ribosyl)ation and Mg2+ ions on chromatin structure revealed by scanning force microscopy.
      Biochemistry (2001) 40:10947-55 PDF
    • Liphardt J, Onoa B, Smith SB, Tinoco I JR, Bustamante C
      Reversible unfolding of single RNA molecules by mechanical force.
      Science (2001) 292:733-7 PDF
    • Kellermayer MS, Smith SB, Bustamante C, Granzier HL
      Mechanical fatigue in repetitively stretched single molecules of titin.
      Biophys J (2001) 80:852-63 PDF

    2000

    • Keller D., and Bustamante C.
      The Mechanochemistry of Molecular Motors
      Biophys. J. 78: 541-556, (2000)
      PDF
    • Bustamante C, Macosko JC, Wuite GJ
      Grabbing the cat by the tail: manipulating molecules one by one.
      Nat Rev Mol Cell Biol (2000) 1:130-6 PDF
    • Wuite GJ, Smith SB, Young M, Keller D, Bustamante C
      Single-molecule studies of the effect of template tension on T7 DNA polymerase activity.
      Nature (2000) 404:103-6 PDF
    • Kellermayer MS, Smith S, Bustamante C, Granzier HL
      Mechanical manipulation of single titin molecules with laser tweezers.
      Adv Exp Med Biol (2000) 481:111-26; discussion 127-8
    • Wuite GJ, Davenport RJ, Rappaport A, Bustamante C
      An integrated laser trap/flow control video microscope for the study of single biomolecules.
      Biophys J (2000) 79:1155-67 PDF
    • Baumann CG, Bloomfield VA, Smith SB, Bustamante C, Wang MD, Block SM
      Stretching of single collapsed DNA molecules.
      Biophys J (2000) 78:1965-78 PDF
    • Davenport RJ, Wuite GJ, Landick R, Bustamante C
      Single-molecule study of transcriptional pausing and arrest by E. coli RNA polymerase.
      Science (2000) 287:2497-500 PDF
    • Yang GL, Cecconi C, Baase WA, Vetter IR, Breyer WA, Haack, JA, Matthews BW, Dahlquist FW, Bustamante C
      Solid-state synthesis and mechanical unfolding of polymers of T4 lysozyme.
      Proc. Nat. Acad. Sci., 2000, V97(N1):139-144 PDF
    • Cui Y, Bustamante C
      Pulling a single chromatin fiber reveals the forces that maintain its higher-order structure.
      Proc Natl Acad Sci U S A (2000) 97(1):127-32 PDF

    1999

    • Tinoco I, Bustamante C
      How RNA folds
      J. Mol. Biol., 1999, V293(N2):271-281 PDF
    • Leuba SH, Bustamante C
      Analysis of chromatin by scanning force microscopy
      Methods Mol Biol (1999) 119:143-60