Base-pair resolution analysis of the effect of supercoiling on DNA flexibility and major groove recognition by triplex-forming oligonucleotides

TopoStats – A program for automated tracing of biomolecules from AFM images

(2021) Joseph G. Beton et al.   METHODS

Coarse-Grained Modeling of DNA Plectoneme Formation in the Presence of Base-Pair Mismatches

(2020) Parth Rakesh Desai et al.   BIOPHYSICAL JOURNAL

The Effect of DNA Topology on Observed Rates of R-Loop Formation and DNA Strand Cleavage by CRISPR Cas12a

(2019) Kara van Aelst et al.   Genes

Small extrachromosomal circular DNAs, microDNA, produce short regulatory RNAs that suppress gene expression independent of canonical promoters

(2019) Teressa Paulsen et al.   NUCLEIC ACIDS RESEARCH

Closing the DNA replication cycle: from simple circular molecules to supercoiled and knotted DNA catenanes

(2019) Jorge B Schvartzman et al.   NUCLEIC ACIDS RESEARCH

Substrate conformational dynamics facilitate structure-specific recognition of gapped DNA by DNA polymerase

(2019) Timothy D Craggs et al.   NUCLEIC ACIDS RESEARCH

Circular ecDNA promotes accessible chromatin and high oncogene expression

(2019) Sihan Wu et al.   NATURE

On the Stability of DNA Origami Nanostructures in Low-Magnesium Buffers

(2018) Charlotte Kielar et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

High-speed photothermal off-resonance atomic force microscopy reveals assembly routes of centriolar scaffold protein SAS-6

(2018) Adrian P. Nievergelt et al.   Nature Nanotechnology

Circular DNA elements of chromosomal origin are common in healthy human somatic tissue

(2018) Henrik Devitt Møller et al.   Nature Communications

Free Energy Landscape and Dynamics of Supercoiled DNA by High-Speed Atomic Force Microscopy

(2018) Tine Brouns et al.   ACS Nano

DNA sequence encodes the position of DNA supercoils

(2018) Sung Hyun Kim et al.   eLife

Transcription-coupled DNA supercoiling dictates the chromosomal arrangement of bacterial genes

(2016) Patrick Sobetzko   NUCLEIC ACIDS RESEARCH

Comparison of Molecular Contours for Measuring Writhe in Atomistic Supercoiled DNA

(2015) Thana Sutthibutpong et al.   Journal of Chemical Theory and Computation

Tuning the translational freedom of DNA for high speed AFM

(2015) Andrew J. Lee et al.   Nano Research

Parmbsc1: a refined force field for DNA simulations

(2015) Ivan Ivani et al.   NATURE METHODS

Detecting cancers through tumor-activatable minicircles that lead to a detectable blood biomarker

(2015) John A. Ronald et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Structural diversity of supercoiled DNA

(2015) Rossitza N. Irobalieva et al.   Nature Communications

Plectoneme tip bubbles: Coupled denaturation and writhing in supercoiled DNA

(2015) Christian Matek et al.   Scientific Reports

Single-Molecule Reconstruction of Oligonucleotide Secondary Structure by Atomic Force Microscopy

(2014) Alice Pyne et al.   Small

Beyond the Helix Pitch: Direct Visualization of Native DNA in Aqueous Solution

(2013) Shinichiro Ido et al.   ACS Nano

Toward Improved Description of DNA Backbone: Revisiting Epsilon and Zeta Torsion Force Field Parameters

(2013) Marie Zgarbová et al.   Journal of Chemical Theory and Computation

PTRAJ and CPPTRAJ: Software for Processing and Analysis of Molecular Dynamics Trajectory Data

(2013) Daniel R. Roe et al.   Journal of Chemical Theory and Computation

Cellular MYCro Economics: Balancing MYC Function with MYC Expression

(2013) D. Levens   Cold Spring Harbor Perspectives in Medicine

Reference Simulations of Noncanonical Nucleic Acids with Different χ Variants of the AMBER Force Field: Quadruplex DNA, Quadruplex RNA, and Z-DNA

(2012) Miroslav Krepl et al.   Journal of Chemical Theory and Computation

MMPBSA.py: An Efficient Program for End-State Free Energy Calculations

(2012) Bill R. Miller et al.   Journal of Chemical Theory and Computation

Atomic Force Microscopy with Nanoscale Cantilevers Resolves Different Structural Conformations of the DNA Double Helix

(2012) Carl Leung et al.   NANO LETTERS

Length Scale Dependence of DNA Mechanical Properties

(2012) Agnes Noy et al.   PHYSICAL REVIEW LETTERS

Torque measurements reveal sequence-specific cooperative transitions in supercoiled DNA

(2012) F. C. Oberstrass et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Bullied no more: when and how DNA shoves proteins around

(2012) Jonathan M. Fogg et al.   QUARTERLY REVIEWS OF BIOPHYSICS

Theoretical Analysis of Competing Conformational Transitions in Superhelical DNA

(2012) Dina Zhabinskaya et al.   PLoS Computational Biology

The NumPy Array: A Structure for Efficient Numerical Computation

(2011) Stéfan van der Walt et al.   COMPUTING IN SCIENCE & ENGINEERING

Cooperative kinking at distant sites in mechanically stressed DNA

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

Atomistic simulations reveal bubbles, kinks and wrinkles in supercoiled DNA

(2011) J. S. Mitchell et al.   NUCLEIC ACIDS RESEARCH

Cellular Strategies for Regulating DNA Supercoiling: A Single-Molecule Perspective

(2010) Daniel A. Koster et al.   CELL

Transfection of shRNA-encoding Minivector DNA of a few hundred base pairs to regulate gene expression in lymphoma cells

(2010) N Zhao et al.   GENE THERAPY

Theoretical Analysis of Disruptions in DNA Minicircles

(2009) Xiaozhong Zheng et al.   BIOPHYSICAL JOURNAL

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

(2009) Davide Demurtas 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

Unmasking Imaging Forces on Soft Biological Samples in Liquids When Using Dynamic Atomic Force Microscopy: A Case Study on Viral Capsids

(2008) Xin Xu et al.   BIOPHYSICAL JOURNAL

GROMACS 4:  Algorithms for Highly Efficient, Load-Balanced, and Scalable Molecular Simulation

(2008) Berk Hess et al.   Journal of Chemical Theory and Computation