Revealing the base pair stepping dynamics of nucleic acid motor proteins with optical traps.
暂无分享,去创建一个
[1] W. Greenleaf,et al. High-resolution, single-molecule measurements of biomolecular motion. , 2007, Annual review of biophysics and biomolecular structure.
[2] V. Rao,et al. The DNA translocating ATPase of bacteriophage T4 packaging motor. , 2006, Journal of molecular biology.
[3] S. Kowalczykowski,et al. Characterization of the helicase activity of the Escherichia coli RecBCD enzyme using a novel helicase assay. , 1989, Biochemistry.
[4] A. Mehta,et al. Single-molecule biomechanics with optical methods. , 1999, Science.
[5] Christoph F. Schmidt,et al. Direct observation of kinesin stepping by optical trapping interferometry , 1993, Nature.
[6] Jens Michaelis,et al. Mechanism of Force Generation of a Viral DNA Packaging Motor , 2005, Cell.
[7] I. Tinoco,et al. RNA translocation and unwinding mechanism of HCV NS3 helicase and its coordination by ATP , 2006, Nature.
[8] C. Cameron,et al. Multiple Full-length NS3 Molecules Are Required for Optimal Unwinding of Oligonucleotide DNA in Vitro* , 2005, Journal of Biological Chemistry.
[9] I. Tinoco,et al. Simulation and analysis of single-ribosome translation , 2009, Physical biology.
[10] A. Kwong,et al. Structure of the hepatitis C virus RNA helicase domain , 1997, Nature Structural Biology.
[11] L. Black,et al. Mechanistic Coupling of Bacteriophage T4 DNA Packaging to Components of the Replication-dependent Late Transcription Machinery* , 2006, Journal of Biological Chemistry.
[12] G. Shivashankar,et al. RecA polymerization on double-stranded DNA by using single-molecule manipulation: the role of ATP hydrolysis. , 1999, Proceedings of the National Academy of Sciences of the United States of America.
[13] Polly M Fordyce,et al. Simultaneous, coincident optical trapping and single-molecule fluorescence , 2004, Nature Methods.
[14] Carlos Bustamante,et al. Recent advances in optical tweezers. , 2008, Annual review of biochemistry.
[15] Carlos Bustamante,et al. Supplemental data for : The Bacteriophage ø 29 Portal Motor can Package DNA Against a Large Internal Force , 2001 .
[16] Carlos Bustamante,et al. Differential detection of dual traps improves the spatial resolution of optical tweezers. , 2006, Proceedings of the National Academy of Sciences of the United States of America.
[17] Dwight L. Anderson,et al. Substrate Interactions and Promiscuity in a Viral DNA Packaging Motor , 2009, Nature.
[18] T. Lohman,et al. Non-hexameric DNA helicases and translocases: mechanisms and regulation , 2008, Nature Reviews Molecular Cell Biology.
[19] Michelle D. Wang,et al. Single molecule analysis of RNA polymerase elongation reveals uniform kinetic behavior , 2002, Proceedings of the National Academy of Sciences of the United States of America.
[20] Nancy R Forde,et al. Mechanical processes in biochemistry. , 2004, Annual review of biochemistry.
[21] C. Bustamante,et al. Ten years of tension: single-molecule DNA mechanics , 2003, Nature.
[22] Marc C. Morais,et al. Structure of the bacteriophage φ29 DNA packaging motor , 2000, Nature.
[23] Polly M Fordyce,et al. Combined optical trapping and single-molecule fluorescence , 2003, Journal of biology.
[24] L. Bird,et al. Crystal structure of a DExx box DNA helicase , 1996, Nature.
[25] V. Serebrov,et al. Periodic cycles of RNA unwinding and pausing by hepatitis C virus NS3 helicase , 2004, Nature.
[26] S. Velankar,et al. Crystal Structures of Complexes of PcrA DNA Helicase with a DNA Substrate Indicate an Inchworm Mechanism , 1999, Cell.
[27] D. Wigley,et al. Structure and mechanism of helicases and nucleic acid translocases. , 2007, Annual review of biochemistry.
[28] David I. Stuart,et al. A mechanical explanation of RNA pseudoknot function in programmed ribosomal frameshifting , 2006, Nature.
[29] T. Ha,et al. Bridging conformational dynamics and function using single-molecule spectroscopy. , 2006, Structure.
[30] Wei Yang,et al. UvrD Helicase Unwinds DNA One Base Pair at a Time by a Two-Part Power Stroke , 2006, Cell.
[31] J. Michaelis,et al. Mechanisms of nucleic acid translocases: lessons from structural biology and single-molecule biophysics. , 2007, Current opinion in structural biology.
[32] R. T. Dame. Single-molecule micromanipulation studies of DNA and architectural proteins. , 2008, Biochemical Society transactions.
[33] Carlos Bustamante,et al. Inter-Subunit Coordination in a Homomeric Ring-ATPase , 2009, Nature.
[34] Carlos Bustamante,et al. Exact solutions for kinetic models of macromolecular dynamics. , 2008, The journal of physical chemistry. B.
[35] V. Serebrov,et al. Establishing a Mechanistic Basis for the Large Kinetic Steps of the NS3 Helicase* , 2009, Journal of Biological Chemistry.
[36] M. Rossmann,et al. Defining molecular and domain boundaries in the bacteriophage phi29 DNA packaging motor. , 2008, Structure.
[37] Michelle D. Wang,et al. Optical torque wrench: angular trapping, rotation, and torque detection of quartz microparticles. , 2004, Physical review letters.
[38] E. Mancini,et al. Atomic Snapshots of an RNA Packaging Motor Reveal Conformational Changes Linking ATP Hydrolysis to RNA Translocation , 2004, Cell.
[39] Ignacio Tinoco,et al. How RNA unfolds and refolds. , 2008, Annual review of biochemistry.
[40] Steven M. Block,et al. Kinesin Moves by an Asymmetric Hand-OverHand Mechanism , 2003 .
[41] S. Grimes,et al. Bacteriophage φ29 DNA packaging , 2002 .
[42] M. Schnitzer,et al. Statistical kinetics of processive enzymes. , 1995, Cold Spring Harbor symposia on quantitative biology.
[43] Derek N. Fuller,et al. Single phage T4 DNA packaging motors exhibit large force generation, high velocity, and dynamic variability , 2007, Proceedings of the National Academy of Sciences.
[44] Carlos Bustamante,et al. Backtracking determines the force sensitivity of RNAP II in a factor-dependent manner , 2007, Nature.
[45] Michael G. Rossmann,et al. The Structure of the Phage T4 DNA Packaging Motor Suggests a Mechanism Dependent on Electrostatic Forces , 2008, Cell.
[46] Steven M. Block,et al. Sequence-Resolved Detection of Pausing by Single RNA Polymerase Molecules , 2006, Cell.
[47] S. Chu,et al. Observation of a single-beam gradient force optical trap for dielectric particles. , 1986, Optics letters.
[48] Matthew J Lang,et al. Interlaced optical force-fluorescence measurements for single molecule biophysics. , 2006, Biophysical journal.
[49] Robert Landick,et al. RNA Polymerase as a Molecular Motor , 1998, Cell.
[50] G. Wuite,et al. Visualizing single DNA-bound proteins using DNA as a scanning probe , 2007, Nature Methods.
[51] Carlos Bustamante,et al. Direct Observation of the Three-State Folding of a Single Protein Molecule , 2005, Science.
[52] Andrew J. Spakowitz,et al. Effect of force on mononucleosomal dynamics , 2006, Proceedings of the National Academy of Sciences.
[53] H. Noller,et al. mRNA Helicase Activity of the Ribosome , 2005, Cell.
[54] C. Bustamante,et al. The mechanochemistry of molecular motors. , 2000, Biophysical journal.
[55] Ashley R. Carter,et al. Stabilization of an Optical Microscope to 0.1 Nm in Three Dimensions , 2022 .
[56] Ravindra V Dalal,et al. Pulling on the nascent RNA during transcription does not alter kinetics of elongation or ubiquitous pausing. , 2006, Molecules and Cells.
[57] Steven M Block,et al. Passive all-optical force clamp for high-resolution laser trapping. , 2005, Physical review letters.
[58] W. Gelbart,et al. Physical chemistry of DNA viruses. , 2009, Annual review of physical chemistry.
[59] J P Griffith,et al. Hepatitis C virus NS3 RNA helicase domain with a bound oligonucleotide: the crystal structure provides insights into the mode of unwinding. , 1998, Structure.
[60] Ignacio Tinoco,et al. Following translation by single ribosomes one codon at a time , 2008, Nature.
[61] J. Liphardt,et al. Reversible Unfolding of Single RNA Molecules by Mechanical Force , 2001, Science.
[62] O. Gileadi,et al. Compaction of single DNA molecules induced by binding of integration host factor (IHF) , 2001, Proceedings of the National Academy of Sciences of the United States of America.
[63] W. Greenleaf,et al. Direct observation of base-pair stepping by RNA polymerase , 2005, Nature.
[64] Peixuan Guo,et al. Prohead and DNA-gp3-dependent ATPase activity of the DNA packaging protein gp16 of bacteriophage phi 29. , 1987, Journal of molecular biology.
[65] Martin Depken,et al. The origin of short transcriptional pauses. , 2009, Biophysical journal.
[66] Halina Rubinsztein-Dunlop,et al. Optical torque on microscopic objects. , 2007, Methods in cell biology.
[67] Scott Forth,et al. Nanofabricated quartz cylinders for angular trapping: DNA supercoiling torque detection , 2007, Nature Methods.
[68] Gijs J. L. Wuite,et al. Bacterial chromatin organization by H-NS protein unravelled using dual DNA manipulation , 2006, Nature.
[69] C. Catalano,et al. Biochemical characterization of bacteriophage lambda genome packaging in vitro. , 2003, Virology.
[70] Gijs J. L. Wuite,et al. DNA-tension dependence of restriction enzyme activity reveals mechanochemical properties of the reaction pathway , 2005, Nucleic acids research.
[71] Gerhard A Blab,et al. Stretching submicron biomolecules with constant-force axial optical tweezers. , 2009, Biophysical journal.
[72] D. Herschlag,et al. Direct Measurement of the Full, Sequence-Dependent Folding Landscape of a Nucleic Acid , 2006, Science.
[73] Sotaro Uemura,et al. Peptide bond formation destabilizes Shine–Dalgarno interaction on the ribosome , 2007, Nature.
[74] K. Schulten,et al. Fluorescence-Force Spectroscopy Maps Two-Dimensional Reaction Landscape of the Holliday Junction , 2007, Science.
[75] Shimon Weiss,et al. Initial Transcription by RNA Polymerase Proceeds Through a DNA-Scrunching Mechanism , 2006, Science.
[76] H. Noller,et al. Ribosomes and translation. , 1997, Annual review of biochemistry.
[77] C. Catalano,et al. Packaging of a unit-length viral genome: the role of nucleotides and the gpD decoration protein in stable nucleocapsid assembly in bacteriophage lambda. , 2008, Journal of molecular biology.
[78] E. Schäffer,et al. Optical tweezers with millikelvin precision of temperature-controlled objectives and base-pair resolution. , 2009, Optics express.
[79] Carlos Bustamante,et al. Optical-trap force transducer that operates by direct measurement of light momentum. , 2003, Methods in enzymology.
[80] Paul Matsudaira,et al. Detecting force-induced molecular transitions with fluorescence resonant energy transfer. , 2007, Angewandte Chemie.
[81] S. Block,et al. Versatile optical traps with feedback control. , 1998, Methods in enzymology.
[82] Taekjip Ha,et al. Spring-Loaded Mechanism of DNA Unwinding by Hepatitis C Virus NS3 Helicase , 2007, Science.
[83] H Fujisawa,et al. Phage DNA packaging , 1997, Genes to cells : devoted to molecular & cellular mechanisms.
[84] S. Patel,et al. Structure and function of hexameric helicases. , 2000, Annual review of biochemistry.
[85] Ignacio Tinoco,et al. Determination of thermodynamics and kinetics of RNA reactions by force , 2006, Quarterly Reviews of Biophysics.
[86] M. Tasaka,et al. DNA packaging ATPase of bacteriophage T3. , 1993, Virology.
[87] Rae M. Robertson,et al. Measurements of single DNA molecule packaging dynamics in bacteriophage lambda reveal high forces, high motor processivity, and capsid transformations. , 2007, Journal of molecular biology.
[88] John F. Atkins,et al. Ribosomal frameshifting in decoding antizyme mRNAs from yeast and protists to humans: close to 300 cases reveal remarkable diversity despite underlying conservation , 2007, Nucleic acids research.
[89] K. Neuman,et al. Single-molecule force spectroscopy: optical tweezers, magnetic tweezers and atomic force microscopy , 2008, Nature Methods.
[90] Ashley R. Carter,et al. Precision surface-coupled optical-trapping assay with one-basepair resolution. , 2009, Biophysical journal.
[91] W. Greenleaf,et al. Single-molecule studies of RNA polymerase: motoring along. , 2008, Annual review of biochemistry.
[92] Colin Echeverría Aitken,et al. Translation at the single-molecule level. , 2008, Annual review of biochemistry.
[93] M. Emmett,et al. Functional visualization of viral molecular motor by hydrogen-deuterium exchange reveals transient states , 2005, Nature Structural &Molecular Biology.
[94] Mark J. Schnitzer,et al. Kinesin hydrolyses one ATP per 8-nm step , 1997, Nature.
[95] Michael G Rossmann,et al. The structure of the ATPase that powers DNA packaging into bacteriophage T4 procapsids. , 2007, Molecular cell.
[96] D. Wigley,et al. Demonstration of unidirectional single-stranded DNA translocation by PcrA helicase: measurement of step size and translocation speed. , 2000, Biochemistry.
[97] H. Flyvbjerg,et al. Power spectrum analysis for optical tweezers , 2004 .
[98] M. Feiss,et al. The bacteriophage DNA packaging motor. , 2008, Annual review of genetics.
[99] Gabriel Waksman,et al. Major Domain Swiveling Revealed by the Crystal Structures of Complexes of E. coli Rep Helicase Bound to Single-Stranded DNA and ADP , 1997, Cell.
[100] Elio A. Abbondanzieri,et al. Ubiquitous Transcriptional Pausing Is Independent of RNA Polymerase Backtracking , 2003, Cell.
[101] J. Lakowicz,et al. Viral DNA packaging studied by fluorescence correlation spectroscopy. , 2007, Biophysical journal.
[102] R. Landick. The regulatory roles and mechanism of transcriptional pausing. , 2006, Biochemical Society transactions.
[103] Joshua W. Shaevitz,et al. Backtracking by single RNA polymerase molecules observed at near-base-pair resolution , 2003, Nature.
[104] C. Joo,et al. Advances in single-molecule fluorescence methods for molecular biology. , 2008, Annual review of biochemistry.
[105] T. Lohman,et al. A nonuniform stepping mechanism for E. coli UvrD monomer translocation along single-stranded DNA. , 2007, Molecular cell.
[106] J. Allemand,et al. Stretching DNA and RNA to probe their interactions with proteins. , 2003, Current opinion in structural biology.
[107] Nancy R Forde,et al. Thermal probing of E. coli RNA polymerase off-pathway mechanisms. , 2008, Journal of molecular biology.
[108] M. Fisher,et al. Molecular motors: a theorist's perspective. , 2007, Annual review of physical chemistry.
[109] P. Nelson,et al. Elasticity of short DNA molecules: theory and experiment for contour lengths of 0.6-7 microm. , 2007, Biophysical journal.
[110] S. Smith,et al. Polymerization and mechanical properties of single RecA-DNA filaments. , 1999, Proceedings of the National Academy of Sciences of the United States of America.
[111] Michelle D. Wang,et al. Mechanical disruption of individual nucleosomes reveals a reversible multistage release of DNA , 2002, Proceedings of the National Academy of Sciences of the United States of America.
[112] Joshua W Shaevitz,et al. Statistical kinetics of macromolecular dynamics. , 2005, Biophysical journal.