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List of works by Carlos Bustamante

4.22 Viral DNA Packaging Motors

A frameshifting stimulatory stem loop destabilizes the hybrid state and impedes ribosomal translocation

scientific article published on 31 March 2014

A two-state kinetic model for the unfolding of single molecules by mechanical force

scientific article

A very low current scanning tunneling microscope

article

A viral packaging motor varies its DNA rotation and step size to preserve subunit coordination as the capsid fills

scientific article published on April 2014

ATP-dependent force generation and membrane scission by ESCRT-III and Vps4

scientific article published on 01 December 2018

An analysis of circular intensity differential scattering measurements: Studies on the sperm cell ofeledone cirrhosa

scientific article published in 1986

Analysis of P element transposase protein-DNA interactions during the early stages of transposition

scientific article published on 19 July 2007

Atomic force microscopy of photosystem II and its unit cell clustering quantitatively delineate the mesoscale variability in Arabidopsis thylakoids

scientific article

Attaching molecules to surfaces for scanning probe microscopy

scientific article published on March 1993

Backtracking determines the force sensitivity of RNAP II in a factor-dependent manner

scientific article published on 14 March 2007

Bayesian estimates of free energies from nonequilibrium work data in the presence of instrument noise

scientific article

Bias and error in estimates of equilibrium free-energy differences from nonequilibrium measurements

scientific article published on 3 October 2003

Biochemical and structural applications of scanning force microscopy

Characterization of the mechanical unfolding of RNA pseudoknots

scientific article

Chemically tunable mucin chimeras assembled on living cells

scientific article published on 29 September 2015

Chirality sensing by Escherichia coli topoisomerase IV and the mechanism of type II topoisomerases

scientific article

Circular DNA molecules imaged in air by scanning force microscopy

scientific article published on January 14, 1992

Circular dichroism in samples which scatter light

Circular dichroism studies on single Chinese hamster cells

scientific article published in September 1985

ClpX(P) generates mechanical force to unfold and translocate its protein substrates

scientific article published on April 2011

Complete Unfolding of the Titin Molecule under External Force ⬇️

scientific article published on January 1, 1998

Complete dissection of transcription elongation reveals slow translocation of RNA polymerase II in a linear ratchet mechanism

scientific article published on 24 September 2013

Condensation transition in DNA-polyaminoamide dendrimer fibers studied using optical tweezers

scientific article published in Physical Review Letters

Conformational flexibility in the chromatin remodeler RSC observed by electron microscopy and the orthogonal tilt reconstruction method

scientific article

Conjugation of DNA to Silanized Colloidal Semiconductor Nanocrystalline Quantum Dots

Counting single photoactivatable fluorescent molecules by photoactivated localization microscopy (PALM).

scientific article

Coupling translocation with nucleic acid unwinding by NS3 helicase

scientific article published on 29 September 2010

DNA overwinds when stretched

scientific article

DNA translocation and loop formation mechanism of chromatin remodeling by SWI/SNF and RSC.

scientific article

Daunomycin inverts the long-range chirality of DNA condensed states

scientific article published on 01 June 1991

Deciphering the Molecular Mechanism of the Bacteriophage φ29 DNA Packaging Motor.

scientific article

Design and construction of a circular intensity differential scattering instrument

Determination of thermodynamics and kinetics of RNA reactions by force

scientific article

Differential Polarization Microscopy: A New Imaging Technique

article

Differential detection of dual traps improves the spatial resolution of optical tweezers

scientific article

Differential force microscope for long time-scale biophysical measurements

scientific article

Differential polarization imaging. I. Theory

scientific article

Differential polarization imaging. II. Symmetry properties and calculations

scientific article

Differential polarization imaging. III. Theory confirmation. Patterns of polymerization of hemoglobin S in red blood sickle cells

scientific article

Differential polarization imaging. III. Theory confirmation. Patterns of polymerization of hemoglobin S in red blood sickle cells

article by D A Beach et al published March 1988 in Biophysical Journal

Differential polarization imaging. IV. Images in higher Born approximations

scientific article

Differential polarization imaging. V. Numerical aperture effects and the contribution of preferential scattering and absorption to the circular dichroism images

scientific article

Differential polarization microscope using an image dissector camera and phase‐lock detection

Differential scattering of circularly polarized light by the helical sperm head from the octopus Eledone cirrhosa

scientific article published in Nature

Direct measurement of the mechanical work during translocation by the ribosome

scientific article

Direct observation of a force-induced switch in the anisotropic mechanical unfolding pathway of a protein

scientific article published on 4 September 2012

Direct observation of large chiral domains in chloroplast thylakoid membranes by differential polarization microscopy

scientific article

Direct observation of the three-state folding of a single protein molecule

scientific article

Dynamic SpoIIIE assembly mediates septal membrane fission during Bacillus subtilis sporulation

scientific article

Effect of Poly(ADP-ribosyl)ation and Mg2+Ions on Chromatin Structure Revealed by Scanning Force Microscopy†

scientific article published on 01 September 2001

Effect of force on mononucleosomal dynamics

scholarly article

Effect of protein structure on mitochondrial import.

scientific article

Electrodeposition procedure of E. coli RNA polymerase onto gold and deposition of E. coli RNA polymerase onto mica for observation with scanning force microscopy.

scientific article published in July 1992

Equilibrium information from nonequilibrium measurements in an experimental test of Jarzynski's equality

scientific article

Escherichia coli RNA polymerase activity observed using atomic force microscopy

scientific article published in January 1997

Exact solutions for kinetic models of macromolecular dynamics

scientific article published on 29 March 2008

Experimental test of connector rotation during DNA packaging into bacteriophage phi29 capsids

scientific article

Expressions for the interpretation of circular intensity differential scattering of chiral aggregates

scientific article published in August 1985

Extracting signal from noise: kinetic mechanisms from a Michaelis-Menten-like expression for enzymatic fluctuations

scientific article

Facilitated target location on DNA by individual Escherichia coli RNA polymerase molecules observed with the scanning force microscope operating in liquid.

scientific article

Finding a protein's Achilles heel

scientific article published in September 2003

Fluorescence Microscopy of the Dynamics of Supercoiling, Folding, and Condensation of Bacterial Chromosomes, Induced by Acridine Orange

article

Fluorescence measurements on the E.coli DNA polymerase clamp loader: implications for conformational changes during ATP and clamp binding

scientific article published in March 2004

Folding-unfolding transitions in single titin molecules characterized with laser tweezers.

scientific article published on May 1997

Following the assembly of RNA polymerase-DNA complexes in aqueous solutions with the scanning force microscope

scientific article

Following translation by single ribosomes one codon at a time.

scientific article published on 9 March 2008

Force unfolding kinetics of RNA using optical tweezers. I. Effects of experimental variables on measured results

scientific article

Force unfolding kinetics of RNA using optical tweezers. II. Modeling experiments.

scientific article

Full molecular trajectories of RNA polymerase at single base-pair resolution

scientific article published on 19 January 2018

Guanosine triphosphate acts as a cofactor to promote assembly of initial P-element transposase-DNA synaptic complexes

scientific article

High degree of coordination and division of labor among subunits in a homomeric ring ATPase

scientific article published on November 2012

High-resolution and high-accuracy topographic and transcriptional maps of the nucleosome barrier

scientific article published on 31 July 2019

High-resolution dual-trap optical tweezers with differential detection: alignment of instrument components

scientific article

High-resolution dual-trap optical tweezers with differential detection: an introduction

scientific article published on October 2009

High-resolution dual-trap optical tweezers with differential detection: data collection and instrument calibration

scientific article

High-resolution dual-trap optical tweezers with differential detection: instrument design

scientific article

High-resolution dual-trap optical tweezers with differential detection: managing environmental noise

High-resolution dual-trap optical tweezers with differential detection: minimizing the influence of measurement noise

Hydrophobic catalysis and a potential biological role of DNA unstacking induced by environment effects

scientific article published on 14 August 2019

Identification of oligonucleotide sequences that direct the movement of the Escherichia coli FtsK translocase

scientific article

Identification of the FtsK sequence-recognition domain

scientific article published on 15 October 2006

Identifying kinetic barriers to mechanical unfolding of the T. thermophila ribozyme

scientific article

In singulo biochemistry: when less is more

scientific article

Interaction of water-soluble porphyrins with single- and double-stranded polyribonucleotides

article

Intercalation of cationic dyes in the DNA double helix: Introductory theory

scientific article published in 1984

Intersubunit coordination in a homomeric ring ATPase

scientific article

Introduction to Single Molecule Imaging and Mechanics: Seeing and Touching Molecules One at a Time

scientific article published on 01 March 2014

Ionic effects on the elasticity of single DNA molecules

scientific article

Laminin and biomimetic extracellular elasticity enhance functional differentiation in mammary epithelia

scientific article published on 09 October 2008

Length control and sharpening of atomic force microscope carbon nanotube tips assisted by an electron beam

Letting the cat out of the bag: a personal journey in Biophysics

scientific article published on 08 October 2014

Light-powering Escherichia coli with proteorhodopsin

scientific article

Limitations of constant-force-feedback experiments

scientific article

Linker DNA accessibility in chromatin fibers of different conformations: a reevaluation

scientific article

Measurement of the effect of monovalent cations on RNA hairpin stability

scientific article

Mechanical operation and intersubunit coordination of ring-shaped molecular motors: insights from single-molecule studies

scientific article

Mechanical processes in biochemistry

scientific article

Mechanical, electrical, and chemical manipulation of single DNA molecules

Mechanics and structure of titin oligomers explored with atomic force microscopy.

scientific article published in June 2003

Mechanism of force generation of a viral DNA packaging motor

scientific article

Mechanisms of cellular proteostasis: insights from single-molecule approaches

scientific article

Mechanistic constraints from the substrate concentration dependence of enzymatic fluctuations

scientific article

Mechanochemical analysis of DNA gyrase using rotor bead tracking

scientific article

Mechanochemical coupling and bi-phasic force-velocity dependence in the ultra-fast ring ATPase SpoIIIE.

scientific article published on 5 March 2018

Mechanochemistry of a viral DNA packaging motor

scientific article published on 7 May 2010

Methods in statistical kinetics

scientific article published in January 2010

Model and computer simulations of the motion of DNA molecules during pulse field gel electrophoresis

article

Model computations on the differential scattering of circularly polarized light (CIDS) by dense macromolecular particles

article

Molecular handles for the mechanical manipulation of single-membrane proteins in living cells

scientific article published in December 2005

Molecular machines one molecule at a time

scientific article published in July 2017

Molecular mechanisms of transcription through single-molecule experiments

scientific article published on 06 February 2014

Molecular switch-like regulation enables global subunit coordination in a viral ring ATPase

article published in the Proceedings of the National Academy of Sciences of the United States of America

Multiple modes of Escherichia coli DNA gyrase activity revealed by force and torque

scientific article published on 4 March 2007

NS3 helicase actively separates RNA strands and senses sequence barriers ahead of the opening fork

scientific article

Nascent RNA structure modulates the transcriptional dynamics of RNA polymerases

scientific article

New insights into the regulatory mechanisms of ppGpp and DksA on Escherichia coli RNA polymerase-promoter complex.

scientific article published on 27 April 2015

Nicholas R. Cozzarelli (1938–2006)

Nucleic acids — controlling biology and controlled by biophysics

Nucleosomal elements that control the topography of the barrier to transcription

scientific article published on November 2012

Nucleosomal fluctuations govern the transcription dynamics of RNA polymerase II.

scientific article published on July 2009

Nucleotide and Partner-Protein Control of Bacterial Replicative Helicase Structure and Function

scientific article

ORGANIZATION OF PIGMENT-PROTEIN COMPLEXES INTO MACRODOMAINS IN THE THYLAKOID MEMBRANES OF WILD-TYPE and CHLOROPHYLL fo-LESS MUTANT OF BARLEY AS REVEALED BY CIRCULAR DICHROISM

article by G. Garab et al published August 1991 in Photochemistry and Photobiology

Of torques, forces, and protein machines

scientific article published in November 2004

Optical-trap force transducer that operates by direct measurement of light momentum

scientific article

Optimized two-color super resolution imaging of Drp1 during mitochondrial fission with a slow-switching Dronpa variant

scientific article

Pause sequences facilitate entry into long-lived paused states by reducing RNA polymerase transcription rates

scientific article published in Nature Communications

Peptide nucleic acids as tools for single-molecule sequence detection and manipulation

scientific article published on November 2010

Physical Parameters That Control the Imaging of Purple Membranes with the Scanning Tunneling Microscope

Polymer chain statistics and conformational analysis of DNA molecules with bends or sections of different flexibility

article

Polymerization and mechanical properties of single RecA-DNA filaments

scientific article published on August 1999

Porphyrin assemblies on DNA as studied by a resonance light-scattering technique

article

Positive torsional strain causes the formation of a four-way junction at replication forks

scientific article published on 30 October 2000

Probing the mechanical folding kinetics of TAR RNA by hopping, force-jump, and force-ramp methods

scientific article

Production and characterization of a highly pure RNA polymerase holoenzyme from Mycobacterium tuberculosis

scientific article

Programming PAM antennae for efficient CRISPR-Cas9 DNA editing

scientific article published on 08 May 2020

Programming chain-growth copolymerization of DNA hairpin tiles for in-vitro hierarchical supramolecular organization

scientific article published on 01 March 2019

Proofreading dynamics of a processive DNA polymerase

scientific article published on 06 August 2009

Protein-DNA chimeras for single molecule mechanical folding studies with the optical tweezers

scientific article published on 9 January 2008

Pulling a single chromatin fiber reveals the forces that maintain its higher-order structure

scientific article

Pulling chromatin fibers: computer simulations of direct physical micromanipulations

RECENT ADVANCES IN POLARIZATION SPECTROSCOPY: PERSPECTIVES OF THE EXTENSION TO THE SOFT X-RAY REGION

scientific article published on 01 September 1986

RNA translocation and unwinding mechanism of HCV NS3 helicase and its coordination by ATP

scientific article (publication date: 5 January 2006)

Rapid spontaneous accessibility of nucleosomal DNA.

scientific article

Real-time control of the energy landscape by force directs the folding of RNA molecules

scholarly article

Real-time imaging of single DNA molecules with fluorescence microscopy

scientific article

Recent advances in optical tweezers

scientific article published on January 2008

Replication of mitochondrial DNA occurs by strand displacement with alternative light-strand origins, not via a strand-coupled mechanism

scientific article

Retracted: The bacterial condensin MukBEF compacts DNA into a repetitive, stable structure

retracted paper

Reversible unfolding of single RNA molecules by mechanical force

scientific article published in April 2001

Revisiting the Central Dogma One Molecule at a Time

article published in 2011

Revisiting the central dogma one molecule at a time

scientific article

Ribosomal protein S1 unwinds double-stranded RNA in multiple steps

scientific article

Ribosome excursions during mRNA translocation mediate broad branching of frameshift pathways

scientific article

Ribosome. Mechanical force releases nascent chain-mediated ribosome arrest in vitro and in vivo

scientific article published on 23 April 2015

Scanning Force Microscopy in Biology

Scanning force microscopy of DNA deposited onto mica: equilibration versus kinetic trapping studied by statistical polymer chain analysis.

scientific article published on December 1996

Scanning force microscopy of nucleic acids and nucleoprotein assemblies

Scanning force microscopy under aqueous solutions.

scientific article published on October 1997

Scanning tunneling microscopy images of metal‐coated bacteriophages and uncoated, double‐stranded DNA

scholarly article by Rebecca W. Keller et al published January 1990 in Journal of Vacuum Science & Technology A

Scanning tunneling microscopy. I. Theoretical framework and coherence effects

scientific article published on 01 April 1995

Scanning tunneling microscopy. II. Calculation of images of atomic and molecular adsorbates

scientific article published on 01 April 1995

Sequence-dependent upstream DNA-RNA polymerase interactions in the open complex with lambdaPR and lambdaPRM promoters and implications for the mechanism of promoter interference

scientific article

Sequence-directed DNA export guides chromosome translocation during sporulation in Bacillus subtilis.

scientific article

Sequence-directed DNA translocation by purified FtsK.

scientific article

Sequence-specific recognition of cytosine C5 and adenine N6 DNA methyltransferases requires different deformations of DNA.

scientific article published on July 1996

Single molecule conformational memory extraction: p5ab RNA hairpin

scientific article published on 5 June 2014

Single molecule transcription elongation

scientific article

Single-base pair unwinding and asynchronous RNA release by the hepatitis C virus NS3 helicase

scientific article

Single-molecule derivation of salt dependent base-pair free energies in DNA

scientific article

Single-molecule diffusometry reveals no catalysis-induced diffusion enhancement of alkaline phosphatase as proposed by FCS experiments

scientific article published on 18 August 2020

Single-molecule in vivo imaging of bacterial respiratory complexes indicates delocalized oxidative phosphorylation.

scientific article published on 7 February 2014

Single-molecule studies of the effect of template tension on T7 DNA polymerase activity.

scientific article

Solid-state synthesis and mechanical unfolding of polymers of T4 lysozyme

scientific article

SpoIIIE strips proteins off the DNA during chromosome translocation.

scientific article published on July 2008

Stochastic approach to the molecular counting problem in superresolution microscopy

scientific article

Structural transitions and elasticity from torque measurements on DNA.

scientific article published on July 2003

Substrate interactions and promiscuity in a viral DNA packaging motor

scientific article published on October 2009

Substrate preparation for reliable imaging of DNA molecules with the scanning force microscope.

scientific article

Substrate-translocating loops regulate mechanochemical coupling and power production in AAA+ protease ClpXP

scientific article published on 26 September 2016

Temperature control methods in a laser tweezers system

scientific article published on 27 May 2005

Ten years of tension: single-molecule DNA mechanics

scientific article

Tension induces a base-paired overstretched DNA conformation

scientific article

Tension-dependent structural deformation alters single-molecule transition kinetics

scientific article

The ClpXP protease unfolds substrates using a constant rate of pulling but different gears.

scientific article published on 24 October 2013

The bacteriophage straight phi29 portal motor can package DNA against a large internal force

scientific article (publication date: 18 October 2001)

The development of single molecule force spectroscopy: from polymer biophysics to molecular machines

scientific article published in 2022

The effect of force on thermodynamics and kinetics of single molecule reactions

scientific article

The elongation rate of RNA polymerase determines the fate of transcribed nucleosomes.

scientific article published on 13 November 2011

The folding cooperativity of a protein is controlled by its chain topology

scientific article published on 23 May 2010

The heat released during catalytic turnover enhances the diffusion of an enzyme.

scientific article

The molten globule state is unusually deformable under mechanical force.

scientific article published on 21 February 2012

The ribosome modulates nascent protein folding

scientific article

The ribosome uses two active mechanisms to unwind messenger RNA during translation

scientific article

Thermal probing of E. coli RNA polymerase off-pathway mechanisms

scientific article published on 03 July 2008

Three-dimensional architecture of the bacteriophage φ29 packaged genome and elucidation of its packaging process

scholarly article by Luis R. Comolli et al published February 2008 in Virology

Three-dimensional structure of extended chromatin fibers as revealed by tapping-mode scanning force microscopy

scientific article published in November 1994

Towards a molecular description of pulsed-field gel electrophoresis.

scientific article published on January 1993

Transcription factors IIS and IIF enhance transcription efficiency by differentially modifying RNA polymerase pausing dynamics

scientific article published on 18 February 2014

Transcriptional activation via DNA-looping: visualization of intermediates in the activation pathway of E. coli RNA polymerase x sigma 54 holoenzyme by scanning force microscopy.

scientific article published in July 1997

Trapping of megabase-sized DNA molecules during agarose gel electrophoresis

scientific article

Trigger loop folding determines transcription rate of Escherichia coli's RNA polymerase

scientific article

Triplex structures in an RNA pseudoknot enhance mechanical stability and increase efficiency of -1 ribosomal frameshifting

scientific article published on 23 July 2009

Unfolding single RNA molecules: bridging the gap between equilibrium and non-equilibrium statistical thermodynamics

scientific article published on November 2005

Unraveling the Thousand Word Picture: An Introduction to Super-Resolution Data Analysis

scientific article

Unusual mechanical stability of a minimal RNA kissing complex

scholarly article

Unusual oligomerization required for activity of NtrC, a bacterial enhancer-binding protein

scientific article

Use of circularly polarized light to study biological macromolecules

scholarly article by I. Tinoco et al published 1 January 1984 in Pure and Applied Chemistry

Using a system's equilibrium behavior to reduce its energy dissipation in nonequilibrium processes

scientific article published on 13 March 2019

Using mechanical force to probe the mechanism of pausing and arrest during continuous elongation by Escherichia coli RNA polymerase

scientific article

Verification of the Crooks fluctuation theorem and recovery of RNA folding free energies

scientific article

Visualization and analysis of chromatin by scanning force microscopy.

scientific article published on May 1997

Visualization and functional dissection of coaxial paired SpoIIIE channels across the sporulation septum

scientific article published on 7 May 2015

Visualizing RNA extrusion and DNA wrapping in transcription elongation complexes of bacterial and eukaryotic RNA polymerases

scientific article

Wrapping of DNA around the E.coli RNA polymerase open promoter complex

scientific article published on August 1999

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