Published in Q Rev Biophys on October 16, 2006
Following translation by single ribosomes one codon at a time. Nature (2008) 4.14
Stability and kinetics of G-quadruplex structures. Nucleic Acids Res (2008) 2.75
Frameshifting RNA pseudoknots: structure and mechanism. Virus Res (2008) 2.02
RNA folding: conformational statistics, folding kinetics, and ion electrostatics. Annu Rev Biophys (2008) 2.00
DNA curvature and flexibility in vitro and in vivo. Q Rev Biophys (2010) 1.63
Quantitative guidelines for force calibration through spectral analysis of magnetic tweezers data. Biophys J (2010) 1.33
Capturing the essence of folding and functions of biomolecules using coarse-grained models. Nat Commun (2011) 1.32
Biological mechanisms, one molecule at a time. Genes Dev (2011) 1.19
Single-molecule mechanical unfolding and folding of a pseudoknot in human telomerase RNA. RNA (2007) 1.17
Unwinding RNA's secrets: advances in the biology, physics, and modeling of complex RNAs. Curr Opin Struct Biol (2008) 1.10
Direct observation of a force-induced switch in the anisotropic mechanical unfolding pathway of a protein. Proc Natl Acad Sci U S A (2012) 1.05
Torque measurements reveal sequence-specific cooperative transitions in supercoiled DNA. Proc Natl Acad Sci U S A (2012) 1.01
Predicting ribosomal frameshifting efficiency. Phys Biol (2008) 0.96
An RNA toolbox for single-molecule force spectroscopy studies. Nucleic Acids Res (2007) 0.96
When microbial conversations get physical. Trends Microbiol (2011) 0.91
Mechanical unfolding of two DIS RNA kissing complexes from HIV-1. J Mol Biol (2009) 0.86
The essential role of stacking adenines in a two-base-pair RNA kissing complex. J Am Chem Soc (2013) 0.86
The Amber ff99 Force Field Predicts Relative Free Energy Changes for RNA Helix Formation. J Chem Theory Comput (2012) 0.84
RNA reactions one molecule at a time. Cold Spring Harb Perspect Biol (2010) 0.83
Single-Molecule Fluorescence Studies of RNA: A Decade's Progress. Chem Phys Lett (2009) 0.81
A new computational approach for mechanical folding kinetics of RNA hairpins. Biophys J (2009) 0.81
Mimicking Ribosomal Unfolding of RNA Pseudoknot in a Protein Channel. J Am Chem Soc (2015) 0.76
Probing the mechanisms of translation with force. Chem Rev (2014) 0.75
Nanomanipulation of single RNA molecules by optical tweezers. J Vis Exp (2014) 0.75
Folding behavior of a T-shaped, ribosome-binding translation enhancer implicated in a wide-spread conformational switch. Elife (2017) 0.75
Mfold web server for nucleic acid folding and hybridization prediction. Nucleic Acids Res (2003) 77.89
Expanded sequence dependence of thermodynamic parameters improves prediction of RNA secondary structure. J Mol Biol (1999) 41.48
Models for the specific adhesion of cells to cells. Science (1978) 28.03
Estimation of secondary structure in ribonucleic acids. Nature (1971) 20.52
Reversible unfolding of individual titin immunoglobulin domains by AFM. Science (1997) 19.62
Overstretching B-DNA: the elastic response of individual double-stranded and single-stranded DNA molecules. Science (1996) 18.53
Entropic elasticity of lambda-phage DNA. Science (1994) 15.40
Dynamic strength of molecular adhesion bonds. Biophys J (1997) 14.93
Incorporating chemical modification constraints into a dynamic programming algorithm for prediction of RNA secondary structure. Proc Natl Acad Sci U S A (2004) 10.35
Biological applications of optical forces. Annu Rev Biophys Biomol Struct (1994) 10.00
The elasticity of a single supercoiled DNA molecule. Science (1996) 8.58
Observation of a single-beam gradient force optical trap for dielectric particles. Opt Lett (1986) 8.31
Reversible unfolding of single RNA molecules by mechanical force. Science (2001) 8.14
Optical trapping. Rev Sci Instrum (2004) 7.15
Force-clamp spectroscopy monitors the folding trajectory of a single protein. Science (2004) 6.82
Direct observation of base-pair stepping by RNA polymerase. Nature (2005) 6.29
Expression of the Rous sarcoma virus pol gene by ribosomal frameshifting. Science (1985) 5.90
Equilibrium information from nonequilibrium measurements in an experimental test of Jarzynski's equality. Science (2002) 5.76
Sequence-dependent mechanics of single DNA molecules. Nat Struct Biol (1999) 5.72
Free energy reconstruction from nonequilibrium single-molecule pulling experiments. Proc Natl Acad Sci U S A (2001) 4.56
Magnetic tweezers: micromanipulation and force measurement at the molecular level. Biophys J (2002) 4.49
Verification of the Crooks fluctuation theorem and recovery of RNA folding free energies. Nature (2005) 3.71
RNA translocation and unwinding mechanism of HCV NS3 helicase and its coordination by ATP. Nature (2006) 3.67
An automated two-dimensional optical force clamp for single molecule studies. Biophys J (2002) 3.57
Nanomechanical measurements of the sequence-dependent folding landscapes of single nucleic acid hairpins. Proc Natl Acad Sci U S A (2006) 3.56
Identifying kinetic barriers to mechanical unfolding of the T. thermophila ribozyme. Science (2003) 3.32
Entropy production fluctuation theorem and the nonequilibrium work relation for free energy differences. Phys Rev E Stat Phys Plasmas Fluids Relat Interdiscip Topics (1999) 3.25
Passive all-optical force clamp for high-resolution laser trapping. Phys Rev Lett (2005) 3.13
Optical-trap force transducer that operates by direct measurement of light momentum. Methods Enzymol (2003) 2.86
A mechanical explanation of RNA pseudoknot function in programmed ribosomal frameshifting. Nature (2006) 2.41
Single-molecule assay reveals strand switching and enhanced processivity of UvrD. Proc Natl Acad Sci U S A (2004) 2.24
Simultaneous, coincident optical trapping and single-molecule fluorescence. Nat Methods (2004) 2.20
Force spectroscopy with single bio-molecules. Curr Opin Chem Biol (2000) 2.18
The 9-A solution: how mRNA pseudoknots promote efficient programmed -1 ribosomal frameshifting. RNA (2003) 2.14
Entropy and heat capacity of DNA melting from temperature dependence of single molecule stretching. Biophys J (2001) 1.99
Preferential relaxation of positively supercoiled DNA by E. coli topoisomerase IV in single-molecule and ensemble measurements. Genes Dev (2000) 1.94
Exact theory of kinkable elastic polymers. Phys Rev E Stat Nonlin Soft Matter Phys (2005) 1.90
Stretching of single collapsed DNA molecules. Biophys J (2000) 1.90
Probing the mechanical folding kinetics of TAR RNA by hopping, force-jump, and force-ramp methods. Biophys J (2005) 1.86
Single-molecule optomechanical cycle. Science (2002) 1.83
Mechanochemical analysis of DNA gyrase using rotor bead tracking. Nature (2006) 1.83
Signals and noise in micromechanical measurements. Methods Cell Biol (1998) 1.81
Interlaced optical force-fluorescence measurements for single molecule biophysics. Biophys J (2006) 1.75
Temperature control methods in a laser tweezers system. Biophys J (2005) 1.70
Single-molecule measurements of the persistence length of double-stranded RNA. Biophys J (2005) 1.67
Elastic properties of a single-stranded charged homopolymeric ribonucleotide. Phys Rev Lett (2004) 1.66
A two-state kinetic model for the unfolding of single molecules by mechanical force. Proc Natl Acad Sci U S A (2002) 1.57
Mechanical unfolding of RNA hairpins. Proc Natl Acad Sci U S A (2005) 1.57
Slow nucleic acid unzipping kinetics from sequence-defined barriers. Eur Phys J E Soft Matter (2003) 1.55
Forced-unfolding and force-quench refolding of RNA hairpins. Biophys J (2006) 1.42
Force as a useful variable in reactions: unfolding RNA. Annu Rev Biophys Biomol Struct (2004) 1.39
Thermodynamic and kinetic aspects of RNA pulling experiments. Biophys J (2005) 1.38
Single-molecule analysis of RNA polymerase transcription. Annu Rev Biophys Biomol Struct (2006) 1.37
Chair-boat transitions in single polysaccharide molecules observed with force-ramp AFM. Proc Natl Acad Sci U S A (2002) 1.27
Relating single-molecule measurements to thermodynamics. Biophys J (2003) 1.26
Application of optical traps in vivo. Methods Enzymol (2003) 1.24
Resource Letter: LBOT-1: Laser-based optical tweezers. Am J Phys (2003) 1.17
Single-molecule DNA nanomanipulation: detection of promoter-unwinding events by RNA polymerase. Methods Enzymol (2003) 1.08
Force-extension behavior of folding polymers. Eur Phys J E Soft Matter (2003) 1.06
Biomolecular force measurements and the atomic force microscope. Curr Opin Biotechnol (2002) 1.01
Forces of a single-beam gradient laser trap on a dielectric sphere in the ray optics regime. Methods Cell Biol (1998) 0.99
The surface apparatus--a tool for probing molecular protein interactions. Nature (1995) 0.96
Analysis of RNA flexibility by scanning force spectroscopy. Nucleic Acids Res (2002) 0.91
Weakly bound water molecules shorten single-stranded DNA. J Am Chem Soc (2006) 0.84
Modelling RNA folding under mechanical tension. Mol Phys (2006) 0.83
Single-molecule investigations of RNA dissociation. Biophys J (2004) 0.80
A new interpolation formula for semiflexible polymers. Biophys Chem (2005) 0.76
A scan for positively selected genes in the genomes of humans and chimpanzees. PLoS Biol (2005) 8.32
Genomic scans for selective sweeps using SNP data. Genome Res (2005) 6.43
Equilibrium information from nonequilibrium measurements in an experimental test of Jarzynski's equality. Science (2002) 5.76
Rapid spontaneous accessibility of nucleosomal DNA. Nat Struct Mol Biol (2004) 5.00
Recent and ongoing selection in the human genome. Nat Rev Genet (2007) 4.62
Direct observation of the three-state folding of a single protein molecule. Science (2005) 4.48
Following translation by single ribosomes one codon at a time. Nature (2008) 4.14
Structural transitions and elasticity from torque measurements on DNA. Nature (2003) 3.71
Direct measure of the de novo mutation rate in autism and schizophrenia cohorts. Am J Hum Genet (2010) 3.69
RNA translocation and unwinding mechanism of HCV NS3 helicase and its coordination by ATP. Nature (2006) 3.67
Nucleosomal fluctuations govern the transcription dynamics of RNA polymerase II. Science (2009) 3.60
Identifying kinetic barriers to mechanical unfolding of the T. thermophila ribozyme. Science (2003) 3.32
Recent advances in optical tweezers. Annu Rev Biochem (2008) 3.08
Intersubunit coordination in a homomeric ring ATPase. Nature (2009) 2.93
Optical-trap force transducer that operates by direct measurement of light momentum. Methods Enzymol (2003) 2.86
Mechanism of force generation of a viral DNA packaging motor. Cell (2005) 2.81
Backtracking determines the force sensitivity of RNAP II in a factor-dependent manner. Nature (2007) 2.64
Differential detection of dual traps improves the spatial resolution of optical tweezers. Proc Natl Acad Sci U S A (2006) 2.48
Experimental test of connector rotation during DNA packaging into bacteriophage phi29 capsids. PLoS Biol (2007) 2.39
Genetic architecture of aluminum tolerance in rice (Oryza sativa) determined through genome-wide association analysis and QTL mapping. PLoS Genet (2011) 2.34
Evolutionary history of GS3, a gene conferring grain length in rice. Genetics (2009) 2.33
ClpX(P) generates mechanical force to unfold and translocate its protein substrates. Cell (2011) 2.31
DNA overwinds when stretched. Nature (2006) 2.27
DNA translocation and loop formation mechanism of chromatin remodeling by SWI/SNF and RSC. Mol Cell (2006) 2.25
Sequence-directed DNA translocation by purified FtsK. Science (2005) 2.22
Chirality sensing by Escherichia coli topoisomerase IV and the mechanism of type II topoisomerases. Proc Natl Acad Sci U S A (2003) 2.15
Effect of force on mononucleosomal dynamics. Proc Natl Acad Sci U S A (2006) 2.03
Replication of mitochondrial DNA occurs by strand displacement with alternative light-strand origins, not via a strand-coupled mechanism. Genes Dev (2005) 1.94
Multiple modes of Escherichia coli DNA gyrase activity revealed by force and torque. Nat Struct Mol Biol (2007) 1.91
The effect of force on thermodynamics and kinetics of single molecule reactions. Biophys Chem (2002) 1.90
Probing the mechanical folding kinetics of TAR RNA by hopping, force-jump, and force-ramp methods. Biophys J (2005) 1.86
Retracted The bacterial condensin MukBEF compacts DNA into a repetitive, stable structure. Science (2004) 1.83
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) 1.77
The folding cooperativity of a protein is controlled by its chain topology. Nature (2010) 1.76
The ribosome uses two active mechanisms to unwind messenger RNA during translation. Nature (2011) 1.74
Laminin and biomimetic extracellular elasticity enhance functional differentiation in mammary epithelia. EMBO J (2008) 1.74
Development of a panel of genome-wide ancestry informative markers to study admixture throughout the Americas. PLoS Genet (2012) 1.74
Temperature control methods in a laser tweezers system. Biophys J (2005) 1.70
Bias and error in estimates of equilibrium free-energy differences from nonequilibrium measurements. Proc Natl Acad Sci U S A (2003) 1.66
Identification of oligonucleotide sequences that direct the movement of the Escherichia coli FtsK translocase. Proc Natl Acad Sci U S A (2005) 1.66
Force unfolding kinetics of RNA using optical tweezers. I. Effects of experimental variables on measured results. Biophys J (2007) 1.61
Light-powering Escherichia coli with proteorhodopsin. Proc Natl Acad Sci U S A (2007) 1.59
Sequence-directed DNA export guides chromosome translocation during sporulation in Bacillus subtilis. Nat Struct Mol Biol (2008) 1.58
Proofreading dynamics of a processive DNA polymerase. EMBO J (2009) 1.58
Counting single photoactivatable fluorescent molecules by photoactivated localization microscopy (PALM). Proc Natl Acad Sci U S A (2012) 1.56
Single-molecule derivation of salt dependent base-pair free energies in DNA. Proc Natl Acad Sci U S A (2010) 1.53
The ribosome modulates nascent protein folding. Science (2011) 1.51
NS3 helicase actively separates RNA strands and senses sequence barriers ahead of the opening fork. Proc Natl Acad Sci U S A (2007) 1.50
Conformational flexibility in the chromatin remodeler RSC observed by electron microscopy and the orthogonal tilt reconstruction method. Proc Natl Acad Sci U S A (2007) 1.49
Identification of the FtsK sequence-recognition domain. Nat Struct Mol Biol (2006) 1.49
Three-dimensional architecture of the bacteriophage phi29 packaged genome and elucidation of its packaging process. Virology (2007) 1.48
Nucleosomal elements that control the topography of the barrier to transcription. Cell (2012) 1.46
Substrate interactions and promiscuity in a viral DNA packaging motor. Nature (2009) 1.41
High degree of coordination and division of labor among subunits in a homomeric ring ATPase. Cell (2012) 1.35
SpoIIIE strips proteins off the DNA during chromosome translocation. Genes Dev (2008) 1.31
Single-base pair unwinding and asynchronous RNA release by the hepatitis C virus NS3 helicase. Science (2011) 1.31
Thermal probing of E. coli RNA polymerase off-pathway mechanisms. J Mol Biol (2008) 1.29
Protein-DNA chimeras for single molecule mechanical folding studies with the optical tweezers. Eur Biophys J (2008) 1.29
Mechanochemistry of a viral DNA packaging motor. J Mol Biol (2010) 1.29
Unusual mechanical stability of a minimal RNA kissing complex. Proc Natl Acad Sci U S A (2006) 1.29
Relating single-molecule measurements to thermodynamics. Biophys J (2003) 1.26
Triplex structures in an RNA pseudoknot enhance mechanical stability and increase efficiency of -1 ribosomal frameshifting. Proc Natl Acad Sci U S A (2009) 1.25
Characterization of the mechanical unfolding of RNA pseudoknots. J Mol Biol (2007) 1.20
Mechanics and structure of titin oligomers explored with atomic force microscopy. Biochim Biophys Acta (2003) 1.19
The elongation rate of RNA polymerase determines the fate of transcribed nucleosomes. Nat Struct Mol Biol (2011) 1.19
Real-time control of the energy landscape by force directs the folding of RNA molecules. Proc Natl Acad Sci U S A (2007) 1.15
Effect of protein structure on mitochondrial import. Proc Natl Acad Sci U S A (2005) 1.15
Tension induces a base-paired overstretched DNA conformation. Proc Natl Acad Sci U S A (2012) 1.13
The molten globule state is unusually deformable under mechanical force. Proc Natl Acad Sci U S A (2012) 1.07
Nascent RNA structure modulates the transcriptional dynamics of RNA polymerases. Proc Natl Acad Sci U S A (2012) 1.06
Randomized trial of personal genomics for preventive cardiology: design and challenges. Circ Cardiovasc Genet (2012) 1.06
Differential force microscope for long time-scale biophysical measurements. Rev Sci Instrum (2007) 1.06
Direct observation of a force-induced switch in the anisotropic mechanical unfolding pathway of a protein. Proc Natl Acad Sci U S A (2012) 1.05
Measurement of the effect of monovalent cations on RNA hairpin stability. J Am Chem Soc (2007) 1.05
Exact solutions for kinetic models of macromolecular dynamics. J Phys Chem B (2008) 1.04
Dynamic SpoIIIE assembly mediates septal membrane fission during Bacillus subtilis sporulation. Genes Dev (2010) 1.04
Ribosomal protein S1 unwinds double-stranded RNA in multiple steps. Proc Natl Acad Sci U S A (2012) 1.04
Inferring genome-wide patterns of admixture in Qataris using fifty-five ancestral populations. BMC Genet (2012) 1.01
A frameshifting stimulatory stem loop destabilizes the hybrid state and impedes ribosomal translocation. Proc Natl Acad Sci U S A (2014) 1.00
Finding a protein's Achilles heel. Nat Struct Biol (2003) 0.99
Molecular mechanisms of transcription through single-molecule experiments. Chem Rev (2014) 0.98
Visualizing RNA extrusion and DNA wrapping in transcription elongation complexes of bacterial and eukaryotic RNA polymerases. J Mol Biol (2003) 0.98
Methods in statistical kinetics. Methods Enzymol (2010) 0.97
Bayesian estimates of free energies from nonequilibrium work data in the presence of instrument noise. J Chem Phys (2008) 0.96
Single molecule transcription elongation. Methods (2009) 0.94
Transcription factors IIS and IIF enhance transcription efficiency by differentially modifying RNA polymerase pausing dynamics. Proc Natl Acad Sci U S A (2014) 0.89
Fluorescence measurements on the E.coli DNA polymerase clamp loader: implications for conformational changes during ATP and clamp binding. J Mol Biol (2004) 0.88
Mechanistic constraints from the substrate concentration dependence of enzymatic fluctuations. Proc Natl Acad Sci U S A (2010) 0.88
Peptide nucleic acids as tools for single-molecule sequence detection and manipulation. Nano Lett (2010) 0.88
Guanosine triphosphate acts as a cofactor to promote assembly of initial P-element transposase-DNA synaptic complexes. Genes Dev (2005) 0.88
Analysis of P element transposase protein-DNA interactions during the early stages of transposition. J Biol Chem (2007) 0.87
The essential role of stacking adenines in a two-base-pair RNA kissing complex. J Am Chem Soc (2013) 0.86
DNA molecular handles for single-molecule protein-folding studies by optical tweezers. Methods Mol Biol (2011) 0.86
Combining temperature and force to study folding of an RNA hairpin. Phys Chem Chem Phys (2013) 0.85
Suicidal ideation among students enrolled in healthcare training programs: a cross-sectional study. Rev Bras Psiquiatr (2009) 0.82
Extracting signal from noise: kinetic mechanisms from a Michaelis-Menten-like expression for enzymatic fluctuations. FEBS J (2013) 0.81
High-resolution dual-trap optical tweezers with differential detection: alignment of instrument components. Cold Spring Harb Protoc (2009) 0.81
High-resolution dual-trap optical tweezers with differential detection: instrument design. Cold Spring Harb Protoc (2009) 0.81