Bustamante Lab Recent Publications List

2009

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