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Compound Shape and Substituent Effects in DNA Minor Groove Interactions

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Shapely DNA attracts the right partner

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Sequence-specific transitions of the torsion angle gamma change the polar-hydrophobic profile of the DNA grooves: implication for indirect protein–DNA recognition

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Isolating Influential Regions of Electrostatic Focusing in Protein and DNA Structure

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Fluorescent Nucleic Acid Analogues in Research and Clinical Diagnostics

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Sequence Variation in the Response Element Determines Binding by the Transcription Factor p73

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The many faces of the unusual biofilm activator RemA

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A ChIP-exo screen of 887 PCRP transcription factor antibodies in human cellsPreprint

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Nucleosome topology and DNA sequence modulate the engagement of pioneer factors SOX2 and OCT4Preprint

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Molecular Interactions of the Pioneer Transcription Factor GATA3 With DNA

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Adaptation of DNA to Protein Binding Revealed by Spectroscopy and Molecular Simulation

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Structural Basis for the Stabilization of DNA Nanostructures in Serum with Metallointercalators

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A fluorescent probe under the microscope showing dual recognition of B-DNA and G-quadruplex DNA

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A 3D puzzle approach to building protein–DNA structures

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Chemical principles additive model aligns low consensus DNA targets of p53 tumor suppressor protein

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Guanidino-aryl derivatives: protonation and structure tuning for spectrophotometric recognition of ds-DNA and ds-RNA

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Computational Insights into the Role of External and Local Electric Fields in Macrocyclic Chemical and Biological Systems

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Sub-nanometer-sized carbon nanoparticle shows higher biocompatibility to DNA than nanometer-sized nanoparticles

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Entropy Drives the Formation of Salt Bridges in the Protein GB3

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Diphenyl-Furanones and Diphenyl-Oxopyrrole Derivatives: From Analytical Reagents for Amino Groups to New Fluorochromes for Cytochemical Staining of Chromatin DNA and Chromosomes: Proposal for Intercalative Binding and Fluorescence Mechanism

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Protein– DNA Interactions

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Co-SELECT reveals sequence non-specific contribution of DNA shape to transcription factor binding in vitroPreprint

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Plasmid partitioning protein TubR from Bacillus cereus

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Transcriptional re-wiring by mutation of the yeast Hsf1 oligomerization domainPreprint

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Deciphering the regulatory logic of a Drosophila enhancer through systematic sequence mutagenesis and quantitative image analysisPreprint

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Bayesian Markov models improve the prediction of binding motifs beyond first orderPreprint

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Learning probabilistic protein-DNA recognition codes from DNA-binding specificities using structural mappingsPreprint

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Real-Time Structural Biology of DNA and DNA-Protein Complexes on an Optical MicroscopePreprint

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Species-specific satellite DNA composition dictates PRC1-mediated pericentric heterochromatinPreprint

Lamelza, P., Parrado, M., & Lampson, M. A. (2024) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2024.10.11.617947 · Cited by 2

Integrating genetic variation with deep learning provides context for variants impacting transcription factor binding during embryogenesisPreprint

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Graph Attention Neural Networks Reveal TnsC Filament Assembly in a CRISPR-Associated TransposonPreprint

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Effect of Topology on the Collapse Transition and the Instantaneous Shape of a Model Heteropolymer

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Crosstalk between chromatin and Shavenbaby defines transcriptional output along the Drosophila intestinal stem cell lineage

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DrivR-Base: a feature extraction toolkit for variant effect prediction model construction

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Oligomerization of the IHF Protein in the Presence of Metal Cations

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Prebiotic RNA self-assembling and the origin of life: Mechanistic and molecular modeling rationale for explaining the prebiotic origin and replication of RNA

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FRET analysis of the unwrapping of nucleosomal DNA containing a sequence characteristic of the + 1 nucleosome

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Predicting rare DNA conformations via dynamical graphical models: a case study of the B→A transition

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Genes, DNA, and Protein–DNA Interactions

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Genetic variation of white spot syndrome virus (WSSV) envelope protein VP28 influences its adaptivity in shrimps

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Novel fold and wing structure of Forkhead transcription factor facilitate DNA binding

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Decoding the mechanisms of cooperative DNA binding by the Paired-like homeodomain family

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From simulation to immunization: efficient non-viral delivery of HIV-1 Nefmut-Tat DNA construct using CM18-TAT11 cell penetrating peptide

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Tuning Polyacrylate Composition to Recognize and Modulate Fluorescent Proteins

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iEnhancer-Flow: Integrating Transformer-Based Sequence Learning with DNA Shape Insights for Robust Enhancer Prediction

Huan, L., Luo, H., Luo, L., & Ding, P. (2025) · Interdisciplinary Sciences Computational Life Sciences · doi:10.1007/s12539-025-00787-3 · Cited by 1

Sequence Effect on the Bending Elasticity of Double-Stranded DNA

Dong, H., Zheng, C.-C., & Yu, T. (2026) · The Journal of Physical Chemistry B · doi:10.1021/acs.jpcb.5c08507 · Cited by 1

Programmable Deformation of DNA Nanostructures: Mastering Size and Topology for Tailored Mechanics

Xu, Y., Yan, Z.-S., Ma, Y., & Ding, H. (2026) · Langmuir · doi:10.1021/acs.langmuir.6c00135 · Cited by 1

Recognition of diverse GATA motifs necessitates multimodal GATA3-DNA binding

Gharui, S., Puntambekar, S. S., Sarkar, R. R., Narlikar, L., & Sengupta, D. (2026) · Biochemical and Biophysical Research Communications · doi:10.1016/j.bbrc.2026.153718 · Cited by 1

5-Formylcytosine functions as a chemical regulator of nucleosome positioning

Furuhata, T., Lin, Y., Hino, G., & Okamoto, A. (2026) · Nature Communications · doi:10.1038/s41467-026-73755-0 · Cited by 1

Explicit dynamic cross-strand interactions for DNA sequence language modelling

Yang, C., Liu, Y., Ling, L., Liu, Y., Li, F. H., Chen, C., Wang, L., Yu, F., Qiao, L., Zeng, X., et al. (2026) · Nature Machine Intelligence · doi:10.1038/s42256-026-01249-1 · Cited by 3

Harnessing DNA minor groove binding for cancer therapy: An overview

Fageeri, M. F., Ramadan, W. S., Kawaf, R. R., Alqedra, S., Msallam, Y. A., Alniss, H. Y., & El‐Awady, R. (2026) · European Journal of Medicinal Chemistry · doi:10.1016/j.ejmech.2026.119089 · Cited by 1

Caveat emptor: predicting and modeling protein–DNA recognition and binding via machine-learning computational approaches

Esler, M. A., Werther, R. A., Doyle, L., Ubilla‐Rodriguez, N. C., Schwensen, J. S., Hallinan, J. P., Lambert, A. R., Young, J. C., Silverstein, M., & Stoddard, B. L. (2026) · Nucleic Acids Research · doi:10.1093/nar/gkag608 · Cited by 1

Effects of dna shape and sequence of protein-dna recognition

West, S. M. (2011)

DNA binding shapes up

Tullius, T. D. (2009) · Nature · doi:10.1038/4611225a · Cited by 10

The role of DNA minor groove deformation in specific recognition of DNA by proteins

Faltejsková, K. (2020) · Digital Repository (National Repository of Grey Literature)

68 Deconvoluting the recognition of DNA shape from DNA sequence

Abe, N., Slattery, M. G., Dror, I., Rohs, R., Honig, B. H., & Mann, R. S. (2013) · Journal of Biomolecular Structure and Dynamics · doi:10.1080/07391102.2013.786502 · Cited by 1

Electrostatic Interactions between Arginines and the Minor Groove in the Nucleosome

West, S. M., Rohs, R., Mann, R. S., & Honig, B. H. (2010) · Journal of Biomolecular Structure and Dynamics · doi:10.1080/07391102.2010.10508587 · Cited by 83