Bullied no more: when and how DNA shoves proteins around

Targeting G-quadruplexes in gene promoters: a novel anticancer strategy?

(2011) Shankar Balasubramanian et al.   NATURE REVIEWS DRUG DISCOVERY

The ancestral role of ATP hydrolysis in type II topoisomerases: prevention of DNA double-strand breaks

(2011) A. D. Bates et al.   NUCLEIC ACIDS RESEARCH

Second-Order Selection for Evolvability in a Large Escherichia coli Population

(2011) R. J. Woods et al.   SCIENCE

Origins of Specificity in Protein-DNA Recognition

(2010) Remo Rohs et al.   Annual Review of Biochemistry

Topoisomerases and site-specific recombinases: similarities in structure and mechanism

(2010) Wei Yang   CRITICAL REVIEWS IN BIOCHEMISTRY AND MOLECULAR BIOLOGY

The shape of the DNA minor groove directs binding by the DNA-bending protein Fis

(2010) S. Stella et al.   GENES & DEVELOPMENT

Action at Hooked or Twisted–Hooked DNA Juxtapositions Rationalizes Unlinking Preference of Type-2 Topoisomerases

(2010) Zhirong Liu et al.   JOURNAL OF MOLECULAR BIOLOGY

Parallel Genetic and Phenotypic Evolution of DNA Superhelicity in Experimental Populations of Escherichia coli

(2010) E. Crozat et al.   MOLECULAR BIOLOGY AND EVOLUTION

General organisational principles of the transcriptional regulation system: a tree or a circle?

(2010) Georgi Muskhelishvili et al.   Molecular BioSystems

Bacterial nucleoid-associated proteins, nucleoid structure and gene expression

(2010) Shane C. Dillon et al.   NATURE REVIEWS MICROBIOLOGY

Gene repression by minimal lac loops in vivo

(2010) Laura M. Bond et al.   NUCLEIC ACIDS RESEARCH

The genome of Streptococcus pneumoniae is organized in topology-reacting gene clusters

(2010) M.-J. Ferrandiz et al.   NUCLEIC ACIDS RESEARCH

Local site preference rationalizes disentangling by DNA topoisomerases

(2010) Zhirong Liu et al.   PHYSICAL REVIEW E

Double-stranded DNA homology produces a physical signature

(2010) Xing Wang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Topoisomerase IB-DNA Interactions: X Marks the Spot

(2010) Lynn Zechiedrich et al.   STRUCTURE

Crystal Structure of a Bacterial Topoisomerase IB in Complex with DNA Reveals a Secondary DNA Binding Site

(2010) Asmita Patel et al.   STRUCTURE

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

(2009) Sreekala Balasubramanian et al.   BIOPHYSICAL JOURNAL

Non-B DNA structure-induced genetic instability and evolution

(2009) Junhua Zhao et al.   CELLULAR AND MOLECULAR LIFE SCIENCES

The folding and unfolding of eukaryotic chromatin

(2009) Andrew Bassett et al.   CURRENT OPINION IN GENETICS & DEVELOPMENT

The Newer Fluoroquinolones

(2009) Maureen K. Bolon   INFECTIOUS DISEASE CLINICS OF NORTH AMERICA

The role of DNA shape in protein–DNA recognition

(2009) Remo Rohs et al.   NATURE

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

(2009) Davide Demurtas et al.   NUCLEIC ACIDS RESEARCH

In the absence of writhe, DNA relieves torsional stress with localized, sequence-dependent structural failure to preserve B-form

(2009) Graham L. Randall et al.   NUCLEIC ACIDS RESEARCH

The why and how of DNA unlinking

(2009) Zhirong Liu 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

Phylogenomics of DNA topoisomerases: their origin and putative roles in the emergence of modern organisms

(2009) P. Forterre et al.   NUCLEIC ACIDS RESEARCH

The homology recognition well as an innate property of DNA structure

(2009) A. A. Kornyshev et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Allosteric modulation of DNA by small molecules

(2009) D. M. Chenoweth et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Tetramer opening in LacI-mediated DNA looping

(2009) D. Rutkauskas 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

Mechanisms of chiral discrimination by topoisomerase IV

(2009) K. C. Neuman et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Local DNA Topography Correlates with Functional Noncoding Regions of the Human Genome

(2009) S. C. J. Parker et al.   SCIENCE

Increased fluoroquinolone resistance with time in Escherichia coli from >17,000 patients at a large county hospital as a function of culture site, age, sex, and location

(2008) Lauren Becnel Boyd et al.   BMC INFECTIOUS DISEASES

DNA Supercoiling-Dependent Gene Regulation in Chlamydia

(2008) E. Niehus et al.   JOURNAL OF BACTERIOLOGY

How Do Type II Topoisomerases Use ATP Hydrolysis to Simplify DNA Topology beyond Equilibrium? Investigating the Relaxation Reaction of Nonsupercoiling Type II Topoisomerases

(2008) Tanya Stuchinskaya et al.   JOURNAL OF MOLECULAR BIOLOGY

DNA Double Helices Recognize Mutual Sequence Homology in a Protein Free Environment

(2008) Geoff S. Baldwin et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Geometrical and Electronic Structure Variability of the Sugar−phosphate Backbone in Nucleic Acids

(2008) Daniel Svozil et al.   JOURNAL OF PHYSICAL CHEMISTRY B

The functional response of upstream DNA to dynamic supercoiling in vivo

(2008) Fedor Kouzine et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

3D visualization software to analyze topological outcomes of topoisomerase reactions

(2008) I. K. Darcy et al.   NUCLEIC ACIDS RESEARCH

Bacterial DNA topology and infectious disease

(2008) C. J. Dorman et al.   NUCLEIC ACIDS RESEARCH

Towards a molecular dynamics consensus view of B-DNA flexibility

(2008) Alberto Pérez et al.   NUCLEIC ACIDS RESEARCH

Helical coherence of DNA in crystals and solution

(2008) Aaron Wynveen et al.   NUCLEIC ACIDS RESEARCH

Supercoiling and Denaturation of DNA Loops

(2008) T. B. Liverpool et al.   PHYSICAL REVIEW LETTERS

Abrupt Buckling Transition Observed during the Plectoneme Formation of Individual DNA Molecules

(2008) Scott Forth et al.   PHYSICAL REVIEW LETTERS

How DNA coiling enhances target localization by proteins

(2008) B. van den Broek et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

DNA topoisomerases: harnessing and constraining energy to govern chromosome topology

(2008) Allyn J. Schoeffler et al.   QUARTERLY REVIEWS OF BIOPHYSICS

Transcription Factors Bind Thousands of Active and Inactive Regions in the Drosophila Blastoderm

(2008) Xiao-yong Li et al.   PLOS BIOLOGY