Holliday Junction Thermodynamics and Structure: Coarse-Grained Simulations and Experiments

Coarse-Grained Ions for Nucleic Acid Modeling

(2015) Daniel M. Hinckley et al.   Journal of Chemical Theory and Computation

Martini Coarse-Grained Force Field: Extension to DNA

(2015) Jaakko J. Uusitalo et al.   Journal of Chemical Theory and Computation

How do metal ions direct ribozyme folding?

(2015) Natalia A. Denesyuk et al.   Nature Chemistry

Programmable materials and the nature of the DNA bond

(2015) M. R. Jones et al.   SCIENCE

Short Inverted Repeats Are Hotspots for Genetic Instability: Relevance to Cancer Genomes

(2015) Steve Lu et al.   Cell Reports

A nucleotide-level coarse-grained model of RNA

(2014) Petr Šulc et al.   JOURNAL OF CHEMICAL PHYSICS

An experimentally-informed coarse-grained 3-site-per-nucleotide model of DNA: Structure, thermodynamics, and dynamics of hybridization

(2013) Daniel M. Hinckley et al.   JOURNAL OF CHEMICAL PHYSICS

RNA 3D Structure Prediction by Using a Coarse-Grained Model and Experimental Data

(2013) Zhen Xia et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Coarse-Grained Model for Predicting RNA Folding Thermodynamics

(2013) Natalia A. Denesyuk et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Molecular Dynamics of a DNA Holliday Junction: The Inverted Repeat Sequence d(CCGGTACCGG)4

(2012) Elizabeth G. Wheatley et al.   BIOPHYSICAL JOURNAL

Sequence-dependent thermodynamics of a coarse-grained DNA model

(2012) Petr Šulc et al.   JOURNAL OF CHEMICAL PHYSICS

Hidden complexity in the isomerization dynamics of Holliday junctions

(2012) Changbong Hyeon et al.   Nature Chemistry

Coarse-Grained Simulations of Macromolecules: From DNA to Nanocomposites

(2011) Juan J. de Pablo   Annual Review of Physical Chemistry

HU Binding to a DNA Four-Way Junction Probed by Förster Resonance Energy Transfer

(2011) Codruta Iulia Vitoc et al.   BIOCHEMISTRY

Cruciform structures are a common DNA feature important for regulating biological processes

(2011) Václav Brázda et al.   BMC MOLECULAR BIOLOGY

Optimization of the CHARMM Additive Force Field for DNA: Improved Treatment of the BI/BII Conformational Equilibrium

(2011) Katarina Hart et al.   Journal of Chemical Theory and Computation

Capturing the essence of folding and functions of biomolecules using coarse-grained models

(2011) Changbong Hyeon et al.   Nature Communications

Coarse-Grained Model for Simulation of RNA Three-Dimensional Structures

(2010) Zhen Xia et al.   JOURNAL OF PHYSICAL CHEMISTRY B

A Coarse-Grained Model of DNA with Explicit Solvation by Water and Ions

(2010) Robert C. DeMille et al.   JOURNAL OF PHYSICAL CHEMISTRY B

DNA Nanotweezers Studied with a Coarse-Grained Model of DNA

(2010) Thomas E. Ouldridge et al.   PHYSICAL REVIEW LETTERS

Molecular pathways in DNA-DNA hybridization of surface-bound oligonucleotides

(2010) Moritz Julian Hoefert et al.   Soft Matter

A Rare Nucleotide Base Tautomer in the Structure of an Asymmetric DNA Junction

(2009) Patricia Khuu et al.   BIOCHEMISTRY

A Mesoscale Model of DNA and Its Renaturation

(2009) E.J. Sambriski et al.   BIOPHYSICAL JOURNAL

Coarse-grained modeling of large RNA molecules with knowledge-based potentials and structural filters

(2009) M. A. Jonikas et al.   RNA

Structure, Dynamics, and Branch Migration of a DNA Holliday Junction: A Single-Molecule Fluorescence and Modeling Study

(2008) Mikhail A. Karymov et al.   BIOPHYSICAL JOURNAL

Determination of Alkali and Halide Monovalent Ion Parameters for Use in Explicitly Solvated Biomolecular Simulations

(2008) In Suk Joung et al.   JOURNAL OF PHYSICAL CHEMISTRY B

AFM for analysis of structure and dynamics of DNA and protein–DNA complexes

(2008) Yuri L. Lyubchenko et al.   METHODS

Hierarchies of networked phases induced by multiple liquid-liquid critical points

(2008) C. W. Hsu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

New insight into the recognition of branched DNA structure by junction-resolving enzymes

(2007) Anne-Cécile Déclais et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY