DNA mechanics and its biological impact

Molecular flexibility of DNA as a key determinant of RAD 51 recruitment

(2020) Federico Paoletti et al.   EMBO JOURNAL

Histone H2A Ubiquitination Reinforces Mechanical Stability and Asymmetry at the Single-Nucleosome Level

(2020) Xue Xiao et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Negative supercoil at gene boundaries modulates gene topology

(2020) Yathish Jagadheesh Achar et al.   NATURE

Chromatin fibers stabilize nucleosomes under torsional stress

(2020) Artur Kaczmarczyk et al.   Nature Communications

Understanding the paradoxical mechanical response of in-phase A-tracts at different force regimes

(2020) Alberto Marin-Gonzalez et al.   NUCLEIC ACIDS RESEARCH

Sub-nucleosomal Genome Structure Reveals Distinct Nucleosome Folding Motifs

(2019) Masae Ohno et al.   CELL

Epigenetic changes during aging and their reprogramming potential

(2019) Alice E. Kane et al.   CRITICAL REVIEWS IN BIOCHEMISTRY AND MOLECULAR BIOLOGY

Nucleosome Orientation Map Finds Two New Chromatin Folding Motifs

(2019) Viviana I. Risca   CELL

Base-Pair Mismatch Can Destabilize Small DNA Loops through Cooperative Kinking

(2019) Jiyoun Jeong et al.   PHYSICAL REVIEW LETTERS

How B-DNA Dynamics Decipher Sequence-Selective Protein Recognition

(2019) Federica Battistini et al.   JOURNAL OF MOLECULAR BIOLOGY

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

(2019) Zhijie Chen et al.   eLife

Submicrometer elasticity of double-stranded DNA revealed by precision force-extension measurements with magnetic tweezers

(2019) Min Ju Shon et al.   Science Advances

The diverse roles of DNA methylation in mammalian development and disease

(2019) Maxim V. C. Greenberg et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

The Texture of Chromatin

(2019) Fedor Kouzine et al.   CELL

Intrinsic elasticity of nucleosomes is encoded by histone variants and calibrated by their binding partners

(2019) Daniël P. Melters et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

DNA loop extrusion by human cohesin

(2019) Iain F. Davidson et al.   SCIENCE

Dynamic coupling between conformations and nucleotide states in DNA gyrase

(2018) Aakash Basu et al.   Nature Chemical Biology

Real-time imaging of DNA loop extrusion by condensin

(2018) Mahipal Ganji et al.   SCIENCE

Contribution of epigenetic variation to adaptation in Arabidopsis

(2018) Marc W. Schmid et al.   Nature Communications

DNA sequence encodes the position of DNA supercoils

(2018) Sung Hyun Kim et al.   eLife

Understanding nucleosome dynamics and their links to gene expression and DNA replication

(2017) William K. M. Lai et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Influence of DNA sequence on the structure of minicircles under torsional stress

(2017) Qian Wang et al.   NUCLEIC ACIDS RESEARCH

Sequence-dependent response of DNA to torsional stress: a potential biological regulation mechanism

(2017) Anna Reymer et al.   NUCLEIC ACIDS RESEARCH

Links between DNA methylation and nucleosome occupancy in the human genome

(2017) Clayton K. Collings et al.   Epigenetics & Chromatin

Mechanisms of ATP-Dependent Chromatin Remodeling Motors

(2016) Coral Y. Zhou et al.   Annual Review of Biophysics

Insights into Nucleosome Organization in Mouse Embryonic Stem Cells through Chemical Mapping

(2016) Lilien N. Voong et al.   CELL

Variable chromatin structure revealed by in situ spatially correlated DNA cleavage mapping

(2016) Viviana I. Risca et al.   NATURE

Categorical spectral analysis of periodicity in nucleosomal DNA

(2016) Hu Jin et al.   NUCLEIC ACIDS RESEARCH

H2A.Z controls the stability and mobility of nucleosomes to regulate expression of the LH genes

(2016) Sergei Rudnizky et al.   Nature Communications

Effects of cytosine modifications on DNA flexibility and nucleosome mechanical stability

(2016) Thuy T. M. Ngo et al.   Nature Communications

In vitro selection of DNAs with an increased propensity to form small circles

(2015) Gabriel Rosanio et al.   BIOPOLYMERS

Asymmetric Unwrapping of Nucleosomes under Tension Directed by DNA Local Flexibility

(2015) Thuy T.M. Ngo et al.   CELL

Dependence of DNA Persistence Length on Ionic Strength of Solutions with Monovalent and Divalent Salts: A Joint Theory–Experiment Study

(2015) Annaël Brunet et al.   MACROMOLECULES

DNA methylation in Arabidopsis has a genetic basis and shows evidence of local adaptation

(2015) Manu J Dubin et al.   eLife

Reversing DNA Methylation: Mechanisms, Genomics, and Biological Functions

(2014) Hao Wu et al.   CELL

Gold rotor bead tracking for high-speed measurements of DNA twist, torque and extension

(2014) Paul Lebel et al.   NATURE METHODS

Probing the elastic limit of DNA bending

(2014) Tung T. Le et al.   NUCLEIC ACIDS RESEARCH

DNA Bending Propensity in the Presence of Base Mismatches: Implications for DNA Repair

(2013) Monika Sharma et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position

(2013) Jason D Buenrostro et al.   NATURE METHODS

Transcription forms and remodels supercoiling domains unfolding large-scale chromatin structures

(2013) Catherine Naughton et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Transcription-generated torsional stress destabilizes nucleosomes

(2013) Sheila S Teves et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Transcription-dependent dynamic supercoiling is a short-range genomic force

(2013) Fedor Kouzine et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Effects of DNA methylation on nucleosome stability

(2013) Clayton K. Collings et al.   NUCLEIC ACIDS RESEARCH

Chemical map of Schizosaccharomyces pombe reveals species-specific features in nucleosome positioning

(2013) G. Moyle-Heyrman et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Transcription Under Torsion

(2013) J. Ma et al.   SCIENCE

Torque modulates nucleosome stability and facilitates H2A/H2B dimer loss

(2013) Maxim Y. Sheinin et al.   Nature Communications

Impact of Methylation on the Physical Properties of DNA

(2012) Alberto Pérez et al.   BIOPHYSICAL JOURNAL

The ABCs of molecular dynamics simulations on B-DNA, circa 2012

(2012) David L Beveridge et al.   JOURNAL OF BIOSCIENCES

Histone H1 compacts DNA under force and during chromatin assembly

(2012) Botao Xiao et al.   MOLECULAR BIOLOGY OF THE CELL

A map of nucleosome positions in yeast at base-pair resolution

(2012) Kristin Brogaard et al.   NATURE

Comprehensive molecular characterization of human colon and rectal cancer

(2012)   NATURE

The accessible chromatin landscape of the human genome

(2012) Robert E. Thurman et al.   NATURE

ATP binding controls distinct structural transitions of Escherichia coli DNA gyrase in complex with DNA

(2012) Aakash Basu et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Histone H2A variants in nucleosomes and chromatin: more or less stable?

(2012) C. Bonisch et al.   NUCLEIC ACIDS RESEARCH

Extreme Bendability of DNA Less than 100 Base Pairs Long Revealed by Single-Molecule Cyclization

(2012) R. Vafabakhsh et al.   SCIENCE

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

(2011) Lacramioara Bintu et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Cooperative kinking at distant sites in mechanically stressed DNA

(2011) Troy A. Lionberger et al.   NUCLEIC ACIDS RESEARCH

Cytosine methylation alters DNA mechanical properties

(2011) Philip M. D. Severin et al.   NUCLEIC ACIDS RESEARCH

Freely orbiting magnetic tweezers to directly monitor changes in the twist of nucleic acids

(2011) Jan Lipfert et al.   Nature Communications

Magnetic torque tweezers: measuring torsional stiffness in DNA and RecA-DNA filaments

(2010) Jan Lipfert et al.   NATURE METHODS

Sequence dependence of DNA bending rigidity

(2010) S. Geggier et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

DNA Sequence-Directed Organization of Chromatin: Structure-Based Computational Analysis of Nucleosome-Binding Sequences

(2009) Sreekala Balasubramanian et al.   BIOPHYSICAL JOURNAL

Nucleosome Assembly Depends on the Torsion in the DNA Molecule: A Magnetic Tweezers Study

(2009) Pooja Gupta et al.   BIOPHYSICAL JOURNAL

High-resolution dynamic mapping of histone-DNA interactions in a nucleosome

(2009) Michael A Hall et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

IHF-binding sites inhibit DNA loop formation and transcription initiation

(2009) Yi-Xin Huo et al.   NUCLEIC ACIDS RESEARCH

Bending modes of DNA directly addressed by cryo-electron microscopy of DNA minicircles

(2009) Davide Demurtas et al.   NUCLEIC ACIDS RESEARCH

Unraveling the structure of DNA during overstretching by using multicolor, single-molecule fluorescence imaging

(2009) J. van Mameren et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Oscillations in supercoiling drive circadian gene expression in cyanobacteria

(2009) Vikram Vijayan et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A compiled and systematic reference map of nucleosome positions across the Saccharomyces cerevisiae genome

(2009) Cizhong Jiang et al.   GENOME BIOLOGY

A practical guide to single-molecule FRET

(2008) Rahul Roy et al.   NATURE METHODS

Single-molecule force spectroscopy: optical tweezers, magnetic tweezers and atomic force microscopy

(2008) Keir C Neuman et al.   NATURE METHODS

H2A.Z: View from the Top

(2008) Jordanka Zlatanova et al.   STRUCTURE