Mechanical properties of symmetric and asymmetric DNA A-tracts: implications for looping and nucleosome positioning

DNA A-tracts Are Not Curved in Solutions Containing High Concentrations of Monovalent Cations

(2013) Earle Stellwagen et al.   BIOCHEMISTRY

A sequence-dependent rigid-base model of DNA

(2013) O. Gonzalez et al.   JOURNAL OF CHEMICAL PHYSICS

Determinants of nucleosome positioning

(2013) Kevin Struhl et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Poly(dA:dT)-Rich DNAs Are Highly Flexible in the Context of DNA Looping

(2013) Stephanie Johnson et al.   PLoS One

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

Theoretical models of DNA flexibility

(2013) Tomáš Dršata et al.   Wiley Interdisciplinary Reviews-Computational Molecular Science

Impact of Methylation on the Physical Properties of DNA

(2012) Alberto Pérez et al.   BIOPHYSICAL JOURNAL

Structure, Stiffness and Substates of the Dickerson-Drew Dodecamer

(2012) Tomáš Dršata et al.   Journal of Chemical Theory and Computation

Molecular Dynamics Study of the Role of the Spine of Hydration in DNA A-Tracts in Determining Nucleosome Occupancy

(2012) Xiao Zhu et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Tuning gene expression with nucleosome-disfavoring sequences

(2012) Timothy Palpant et al.   NATURE GENETICS

Manipulating nucleosome disfavoring sequences allows fine-tune regulation of gene expression in yeast

(2012) Tali Raveh-Sadka et al.   NATURE GENETICS

The mechanics behind DNA sequence-dependent properties of the nucleosome

(2012) Eugene Y. D. Chua et al.   NUCLEIC ACIDS RESEARCH

Sequence dependence of transcription factor-mediated DNA looping

(2012) Stephanie Johnson et al.   NUCLEIC ACIDS RESEARCH

Definition of the persistence length in the coarse-grained models of DNA elasticity

(2012) A. Fathizadeh et al.   PHYSICAL REVIEW E

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

(2012) R. Vafabakhsh et al.   SCIENCE

Frontiers in Molecular Dynamics Simulations of DNA

(2011) Alberto Pérez et al.   ACCOUNTS OF CHEMICAL RESEARCH

Calculation of Configurational Entropy with a Boltzmann–Quasiharmonic Model: The Origin of High-Affinity Protein–Ligand Binding

(2011) Kyle W. Harpole et al.   JOURNAL OF PHYSICAL CHEMISTRY B

The Chirality of DNA: Elasticity Cross-Terms at Base-Pair Level Including A-Tracts and the Influence of Ionic Strength

(2010) Agnes Noy et al.   JOURNAL OF PHYSICAL CHEMISTRY B

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

(2010) Jan Lipfert et al.   NATURE METHODS

A measure of bending in nucleic acids structures applied to A-tract DNA

(2010) F. Lankaš et al.   NUCLEIC ACIDS RESEARCH

Single-base resolution mapping of H1-nucleosome interactions and 3D organization of the nucleosome

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

DNA curvature and flexibility in vitro and in vivo

(2010) Justin P. Peters et al.   QUARTERLY REVIEWS OF BIOPHYSICS

Sequence Dependencies of DNA Deformability and Hydration in the Minor Groove

(2009) Yoshiteru Yonetani et al.   BIOPHYSICAL JOURNAL

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

(2009) Sreekala Balasubramanian et al.   BIOPHYSICAL JOURNAL

Poly(dA:dT) tracts: major determinants of nucleosome organization

(2009) Eran Segal et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

A systematic molecular dynamics study of nearest-neighbor effects on base pair and base pair step conformations and fluctuations in B-DNA

(2009) Richard Lavery et al.   NUCLEIC ACIDS RESEARCH

Local and global effects of strong DNA bending induced during molecular dynamics simulations

(2009) Jeremy Curuksu et al.   NUCLEIC ACIDS RESEARCH

Conformational analysis of nucleic acids revisited: Curves+

(2009) R. Lavery et al.   NUCLEIC ACIDS RESEARCH

On the parameterization of rigid base and basepair models of DNA from molecular dynamics simulations

(2009) F. Lankaš et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

Measurement of the Torque on a Single Stretched and Twisted DNA Using Magnetic Tweezers

(2009) Francesco Mosconi et al.   PHYSICAL REVIEW LETTERS

The unique structure of A-tracts and intrinsic DNA bending

(2009) Tali E. Haran et al.   QUARTERLY REVIEWS OF BIOPHYSICS

DNA Nanomechanics in the Nucleosome

(2009) Nils B. Becker et al.   STRUCTURE

Geometry of the Nucleosomal DNA Superhelix

(2008) Thomas C. Bishop   BIOPHYSICAL JOURNAL

Magnitude and direction of DNA bending induced by screw-axis orientation: influence of sequence, mismatches and abasic sites

(2008) J. Curuksu et al.   NUCLEIC ACIDS RESEARCH

Towards a molecular dynamics consensus view of B-DNA flexibility

(2008) Alberto Pérez et al.   NUCLEIC ACIDS RESEARCH