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MucR binds multiple target sites in the promoter of its own gene and is a heat‐stable protein: Is MucR a H‐ NS ‐like protein?

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Thermodynamic principles link in vitro transcription factor affinities to single-molecule chromatin states in cells

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DEPPDB — DNA ELECTROSTATIC POTENTIAL PROPERTIES DATABASE: ELECTROSTATIC PROPERTIES OF GENOME DNA ELEMENTS

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Indirect Readout of DNA Sequence by P22 Repressor: Roles of DNA and Protein Functional Groups in Modulating DNA Conformation

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Role of sequence encoded κB DNA geometry in gene regulation by Dorsal

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Molecular Location Sensing Approach by Anisotropic Magnetism of an Endohedral Metallofullerene

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Quantifying Protein Electrostatic Interactions in Cells by Nuclear Magnetic Resonance Spectroscopy

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Mechanisms of Cre recombinase synaptic complex assembly and activation illuminated by Cryo-EM

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Predicting accurate ab initio DNA electron densities with equivariant neural networks

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CNN-Pred: Prediction of single-stranded and double-stranded DNA-binding protein using convolutional neural networks

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Decoding dissociation of sequence-specific protein–DNA complexes with non-equilibrium simulations

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EGPDI: identifying protein–DNA binding sites based on multi-view graph embedding fusion

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Rotational and translational positions determine the structural and dynamic impact of a single ribonucleotide incorporated in the nucleosome

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Protamine Binding Site on DNA: Molecular Dynamics Simulations and Free Energy Calculations with Full Atomistic Details

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Testing mechanisms of DNA sliding by architectural DNA-binding proteins: dynamics of single wild-type and mutant protein molecules in vitro and in vivo

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Structural basis of Streptomyces transcription activation by zinc uptake regulator

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The specificity and structure of DNA cross-linking by the gut bacterial genotoxin colibactin

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Intron exon boundary junctions in human genome have in-built unique structural and energetic signals

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The Role of Charge Density Coupled DNA Bending in Transcription Factor Sequence Binding Specificity: A Generic Mechanism for Indirect Readout

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Human Cytomegalovirus IE2 Both Activates and Represses Initiation and Modulates Elongation in a Context-Dependent Manner

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Lysine acetylation regulates the AT-rich DNA possession ability of H-NS

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NMR Studies of DNA Support the Role of Pre-Existing Minor Groove Variations in Nucleosome Indirect Readout

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Modeling protein–DNA binding via high-throughput in vitro technologies

Orenstein, Y., & Ron Shamir, A. (2016) · Briefings in Functional Genomics · doi:10.1093/bfgp/elw030 · Cited by 19

Ml proteins from Mesorhizobium loti and MucR from Brucella abortus: an AT-rich core DNA-target site and oligomerization ability

Baglivo, I., Pirone, L., Pedone, E. M., Pitzer, J. E., Muscariello, L., Marino, M. M., Malgieri, G., Freschi, A., Chambery, A., Roop, R. M., et al. (2017) · Scientific Reports · doi:10.1038/s41598-017-16127-5 · Cited by 18

Analysis of Genetic Variation Indicates DNA Shape Involvement in Purifying Selection

Wang, X., Zhou, T., Wunderlich, Z., Maurano, M. T., DePace, A. H., Nuzhdin, S. V., & Rohs, R. (2018) · Molecular Biology and Evolution · doi:10.1093/molbev/msy099 · Cited by 18

Dynamical aspects of supercooled TIP3P–water in the grooves of DNA

dos Santos, M. A. F., Habitzreuter, M. A., Schwade, M. H., Borrasca, R., Antonacci, M., Gonzatti, G. K., Netz, P. A., & Barbosa, M. C. (2019) · The Journal of Chemical Physics · doi:10.1063/1.5100601 · Cited by 18

The path towards functional nanoparticle-DNA origami composites

Johnson, J. A., Dehankar, A., Robbins, A., Kabtiyal, P., Jergens, E., Lee, K. H., Johnston‐Halperin, E., Poirier, M. G., Castro, C. E., & Winter, J. O. (2019) · Materials Science and Engineering R Reports · doi:10.1016/j.mser.2019.06.003 · Cited by 18

Delving into Eukaryotic Origins of Replication Using DNA Structural Features

Yella, V. R., Vanaja, A., Kulandaivelu, U., & Kumar, A. A. (2020) · ACS Omega · doi:10.1021/acsomega.0c00441 · Cited by 18

The RNA Polymerase α Subunit Recognizes the DNA Shape of the Upstream Promoter Element

Lara‐González, S., Machado, A. C. D., Rao, S., Napoli, A., Birktoft, J. J., Felice, R. D., Rohs, R., & Lawson, C. L. (2020) · Biochemistry · doi:10.1021/acs.biochem.0c00571 · Cited by 18

Systematic comparison and prediction of the effects of missense mutations on protein-DNA and protein-RNA interactions

Jiang, Y., Liu, H., & Liu, R. (2021) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1008951 · Cited by 19

Kinetic origin of nucleosome invasion by pioneer transcription factors

Mondal, A. K., Mishra, S. K., & Bhattacherjee, A. (2021) · Biophysical Journal · doi:10.1016/j.bpj.2021.10.039 · Cited by 16

SENIES: DNA Shape Enhanced Two-Layer Deep Learning Predictor for the Identification of Enhancers and Their Strength

Li, Y., Kong, F., Cui, H., Wang, F., Li, C., & Ma, J. (2022) · IEEE Transactions on Computational Biology and Bioinformatics · doi:10.1109/tcbb.2022.3142019 · Cited by 18

The Fur homologue BosR requires Arg39 to activate rpoS transcription in Borrelia burgdorferi and thereby direct spirochaete infection in mice

Katona, L. I. (2015) · Microbiology · doi:10.1099/mic.0.000166 · Cited by 18

Functional interplay between the RK motif and linker segment dictates Oct4–DNA recognition

Kong, X., Liu, J., Li, L., Yue, L., Zhang, L., Jiang, H., Xie, X., & Luo, C. (2015) · Nucleic Acids Research · doi:10.1093/nar/gkv323 · Cited by 18

A high security double lock and key mechanism in HUH relaxases controls oriT-processing for plasmid conjugation

Carballeira, J. D., González-Pérez, B., Moncalián, G., & de la Cruz, F. (2014) · Nucleic Acids Research · doi:10.1093/nar/gku741 · Cited by 18

Importance of the Sequence-Directed DNA Shape for Specific Binding Site Recognition by the Estrogen-Related Receptor

Mohideen-Abdul, K., Tazibt, K., Bourguet, M., Hazemann, I., Lebars, I., Takács, M., Cianférani, S., Klaholz, B. P., Moras, D., & Billas, I. M. L. (2017) · Frontiers in Endocrinology · doi:10.3389/fendo.2017.00140 · Cited by 18

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