DNA mismatches reveal conformational penalties in protein–DNA recognition

Infrared Spectroscopic Observation of a G-C+ Hoogsteen Base Pair in the DNA:TATA-Box Binding Protein Complex Under Solution Conditions

(2019) Allison L. Stelling et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

How B-DNA Dynamics Decipher Sequence-Selective Protein Recognition

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

Unexpected implications of STAT3 acetylation revealed by genetic encoding of acetyl-lysine

(2019) Yael Belo et al.   BIOCHIMICA ET BIOPHYSICA ACTA-GENERAL SUBJECTS

High-Throughput Investigation of Diverse Junction Elements in RNA Tertiary Folding

(2018) Sarah Knight Denny et al.   CELL

Atomic structures of excited state A–T Hoogsteen base pairs in duplex DNA by combining NMR relaxation dispersion, mutagenesis, and chemical shift calculations

(2018) Honglue Shi et al.   JOURNAL OF BIOMOLECULAR NMR

Experimental maps of DNA structure at nucleotide resolution distinguish intrinsic from protein-induced DNA deformations

(2018) Robert N Azad et al.   NUCLEIC ACIDS RESEARCH

Divergence in DNA Specificity among Paralogous Transcription Factors Contributes to Their Differential In Vivo Binding

(2018) Ning Shen et al.   Cell Systems

New Insights into the Role of DNA Shape on Its Recognition by p53 Proteins

(2018) Dmitrij Golovenko et al.   STRUCTURE

The first crystal structure of a DNA-free nuclear receptor DNA binding domain sheds light on DNA-driven allostery in the glucocorticoid receptor

(2018) Filipp Frank et al.   Scientific Reports

Intrinsic DNA Shape Accounts for Affinity Differences between Hox-Cofactor Binding Sites

(2018) Tim Zeiske et al.   Cell Reports

Somatic and Germline Mutation Periodicity Follow the Orientation of the DNA Minor Groove around Nucleosomes

(2018) Oriol Pich et al.   CELL

SelexGLM differentiates androgen and glucocorticoid receptor DNA-binding preference over an extended binding site

(2017) Liyang Zhang et al.   GENOME RESEARCH

Insights into Watson–Crick/Hoogsteen breathing dynamics and damage repair from the solution structure and dynamic ensemble of DNA duplexes containing m1A

(2017) Bharathwaj Sathyamoorthy et al.   NUCLEIC ACIDS RESEARCH

Diverse p53/DNA binding modes expand the repertoire of p53 response elements

(2017) Pratik Vyas et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Computational investigation of proton transfer, pKa shifts and pH-optimum of protein-DNA and protein-RNA complexes

(2017) Yunhui Peng et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Thermodynamic Additivity for Impacts of Base-Pair Substitutions on Association of the Egr-1 Zinc-Finger Protein with DNA

(2016) Abhijnan Chattopadhyay et al.   BIOCHEMISTRY

Nucleotide excision repair is impaired by binding of transcription factors to DNA

(2016) Radhakrishnan Sabarinathan et al.   NATURE

Pharmacologic efficacy of PU.1 inhibition by heterocyclic dications: a mechanistic analysis

(2016) Dominique C. Stephens et al.   NUCLEIC ACIDS RESEARCH

Differential sensitivity to methylated DNA by ETS-family transcription factors is intrinsically encoded in their DNA-binding domains

(2016) Dominique C. Stephens et al.   NUCLEIC ACIDS RESEARCH

Eukaryotic Mismatch Repair in Relation to DNA Replication

(2015) Thomas A. Kunkel et al.   Annual Review of Genetics

ff14SB: Improving the Accuracy of Protein Side Chain and Backbone Parameters from ff99SB

(2015) James A. Maier et al.   Journal of Chemical Theory and Computation

Lagging-strand replication shapes the mutational landscape of the genome

(2015) Martin A. M. Reijns et al.   NATURE

The structural impact of DNA mismatches

(2015) Giulia Rossetti et al.   NUCLEIC ACIDS RESEARCH

Gene target specificity of the Super Elongation Complex (SEC) family: how HIV-1 Tat employs selected SEC members to activate viral transcription

(2015) Huasong Lu et al.   NUCLEIC ACIDS RESEARCH

New insights into Hoogsteen base pairs in DNA duplexes from a structure-based survey

(2015) Huiqing Zhou et al.   NUCLEIC ACIDS RESEARCH

The Mechanism by which TATA-Box Polymorphisms Associated with Human Hereditary Diseases Influence Interactions with the TATA-Binding Protein

(2014) Irina Drachkova et al.   HUMAN MUTATION

Contribution of phenylalanine side chain intercalation to the TATA-box binding protein–DNA interaction: molecular dynamics and dispersion-corrected density functional theory studies

(2014) Manas Mondal et al.   JOURNAL OF MOLECULAR MODELING

Recent development and application of constant pH molecular dynamics

(2014) Wei Chen et al.   MOLECULAR SIMULATION

Incorporation of protein flexibility and conformational energy penalties in docking screens to improve ligand discovery

(2014) Marcus Fischer et al.   Nature Chemistry

Measuring similarity between dynamic ensembles of biomolecules

(2014) Shan Yang et al.   NATURE METHODS

Widespread transient Hoogsteen base pairs in canonical duplex DNA with variable energetics

(2014) Heidi S. Alvey et al.   Nature Communications

Routine Microsecond Molecular Dynamics Simulations with AMBER on GPUs. 2. Explicit Solvent Particle Mesh Ewald

(2013) Romelia Salomon-Ferrer et al.   Journal of Chemical Theory and Computation

Protein-DNA binding: complexities and multi-protein codes

(2013) T. Siggers et al.   NUCLEIC ACIDS RESEARCH

Genomic Regions Flanking E-Box Binding Sites Influence DNA Binding Specificity of bHLH Transcription Factors through DNA Shape

(2013) Raluca Gordân et al.   Cell Reports

Massively parallel measurements of molecular interaction kinetics on a microfluidic platform

(2012) M. Geertz et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Non-DNA-binding cofactors enhance DNA-binding specificity of a transcriptional regulatory complex

(2011) T. Siggers et al.   Molecular Systems Biology

Transient Hoogsteen base pairs in canonical duplex DNA

(2011) Evgenia N. Nikolova et al.   NATURE

Principles of dimer-specific gene regulation revealed by a comprehensive characterization of NF-κB family DNA binding

(2011) Trevor Siggers et al.   NATURE IMMUNOLOGY

3D maps of RNA interhelical junctions

(2011) Maximillian H Bailor et al.   Nature Protocols

Mismatch Repair, But Not Heteroduplex Rejection, Is Temporally Coupled to DNA Replication

(2011) H. Hombauer et al.   SCIENCE

PHENIX: a comprehensive Python-based system for macromolecular structure solution

(2010) Paul D. Adams et al.   ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY

Origins of Specificity in Protein-DNA Recognition

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

NMR Studies of Translocation of the Zif268 Protein between Its Target DNA Sites

(2010) Yuki Takayama et al.   BIOCHEMISTRY

Multiplexed massively parallel SELEX for characterization of human transcription factor binding specificities

(2010) A. Jolma et al.   GENOME RESEARCH

Diversity in DNA recognition by p53 revealed by crystal structures with Hoogsteen base pairs

(2010) Malka Kitayner et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Sequence-dependent cooperative binding of p53 to DNA targets and its relationship to the structural properties of the DNA targets

(2010) Itai Beno et al.   NUCLEIC ACIDS RESEARCH

Topology Links RNA Secondary Structure with Global Conformation, Dynamics, and Adaptation

(2010) M. H. Bailor et al.   SCIENCE

MolProbity: all-atom structure validation for macromolecular crystallography

(2009) Vincent B. Chen et al.   ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY

Hidden alternative structures of proline isomerase essential for catalysis

(2009) James S. Fraser et al.   NATURE

The role of DNA shape in protein–DNA recognition

(2009) Remo Rohs et al.   NATURE

Algorithm for prediction of tumour suppressor p53 affinity for binding sites in DNA

(2008) Dmitry B. Veprintsev et al.   NUCLEIC ACIDS RESEARCH