Cited by 1,096DNA and Nucleic Acid ChemistryDiffusion and Search DynamicsGenomics and Chromatin Dynamics

The DOI matches its Crossref record; 51 of the 51 references it cites were found in a registry or an index.

The role of DNA shape in protein–DNA recognition

Open access

Rohs, Remo, West, Sean M., Sosinsky, Alona, Liu, Peng, Mann, Richard S., Honig, Barry·2009·Nature

Open this paper in CoChat — free account

Abstract

The recognition of specific DNA sequences by proteins is thought to depend on two types of mechanism: one that involves the formation of hydrogen bonds with specific bases, primarily in the major groove, and one involving sequence-dependent deformations of the DNA helix. By comprehensively analysing the three-dimensional structures of protein-DNA complexes, here we show that the binding of arginine residues to narrow minor grooves is a widely used mode for protein-DNA recognition. This readout mechanism exploits the phenomenon that narrow minor grooves strongly enhance the negative electrostatic potential of the DNA. The nucleosome core particle offers a prominent example of this effect. Minor-groove narrowing is often associated with the presence of A-tracts, AT-rich sequences that exclude the flexible TpA step. These findings indicate that the ability to detect local variations in DNA shape and electrostatic potential is a general mechanism that enables proteins to use information in the minor groove, which otherwise offers few opportunities for the formation of base-specific hydrogen bonds, to achieve DNA-binding specificity.

The claims and statistics of this paper haven’t been checked yet.

Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.

Integrity signals

Registry

Crossref · 10.1038/nature08473

Cites

51 of 51 references verified0 citation errors · 0 not checkable

Statistics

Claims the paper makes

The claims and statistics of this paper haven’t been checked yet.

Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.

Claims other papers make about this one

Each is checked against this paper’s own text: does it say what the citing paper says it does?

Self-check

Percentages, sums and reported differences re-computed from the paper’s own numbers.

The self-check needs the paper’s full text.

A Second Generation Force Field for the Simulation of Proteins, Nucleic Acids, and Organic Molecules
Cornell, W. D., Cieplak, P., Bayly, C. I., Gould, I. R., Merz, K. M., Ferguson, D. M., Spellmeyer, D. C., Fox, T., Caldwell, J. W., & Kollman, P. A. (1995) · Journal of the American Chemical Society · doi:10.1021/ja00124a002 · Cited by 13,111
SCOP: A structural classification of proteins database for the investigation of sequences and structures
Murzin, A. G., Brenner, S. E., Hubbard, T., & Chothia, C. (1995) · Journal of Molecular Biology · doi:10.1016/s0022-2836(05)80134-2 · Cited by 6,435
Classical Electrostatics in Biology and Chemistry
Honig, B. H., & Nicholls, A. O. (1995) · Science · doi:10.1126/science.7761829 · Cited by 2,891
Self-citation
Satisfying Hydrogen Bonding Potential in Proteins
McDonald, I. K., & Thornton, J. M. (1994) · Journal of Molecular Biology · doi:10.1006/jmbi.1994.1334 · Cited by 2,136
A genomic code for nucleosome positioning
Segal, E., Fondufe‐Mittendorf, Y. N., Chen, L., Thåström, A., Field, Y., Moore, I. K., Wang, J.-P. Z., & Widom, J. (2006) · Nature · doi:10.1038/nature04979 · Cited by 1,492
Solvent Mediated Interactions in the Structure of the Nucleosome Core Particle at 1.9Å Resolution
Davey, C. A., Sargent, D. F., Luger, K., Mäder, A. W., & Richmond, T. J. (2002) · Journal of Molecular Biology · doi:10.1016/s0022-2836(02)00386-8 · Cited by 1,490
The structure of DNA in the nucleosome core
Richmond, T. J., & Davey, C. A. (2003) · Nature · doi:10.1038/nature01595 · Cited by 1,287
Sequence-specific recognition of double helical nucleic acids by proteins.
Seeman, N. C., Rosenberg, J. M., & Rich, A. (1976) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.73.3.804 · Cited by 1,125
Crystal structure of a yeast TBP/TATA-box complex
Kim, Y., Geiger, J. H., Hahn, S., & Sigler, P. B. (1993) · Nature · doi:10.1038/365512a0 · Cited by 1,085
Co-crystal structure of TBP recognizing the minor groove of a TATA element
Kim, J. L., Nikolov, D. B., & Burley, S. K. (1993) · Nature · doi:10.1038/365520a0 · Cited by 1,065

Flagged first, then by citations

Show all 51 references

Sorted by citations

Items 701–800 of 1,000

Polymorphism and Flexibility of DNA in Alcohols*
Zhang, N., Li, M.-R., Xu, H., & Feng-Shou, Z. (2020) · Chinese Physics Letters · doi:10.1088/0256-307x/37/8/088701 · Cited by 7
A framework for mutational signature analysis based on DNA shape parameters
Karolak, A. M., Levatić, J., & Supek, F. (2022) · PLoS ONE · doi:10.1371/journal.pone.0262495 · Cited by 7
Genome-wide analysis of DNA uptake across the outer membrane of naturally competent Haemophilus influenzae
Mora, M., Mell, J. C., Ehrlich, G. D., Ehrlich, R. L., & Redfield, R. J. (2020) · iScience · doi:10.1016/j.isci.2020.102007 · Cited by 7
Symphony of the DNA flexibility and sequence environment orchestrates p53 binding to its responsive elements
Vanaja, A., Mallick, S. P., Kulandaivelu, U., Kumar, A. A., & Yella, V. R. (2021) · Gene · doi:10.1016/j.gene.2021.145892 · Cited by 7
Enzyme-guided DNA Sewing Architecture
Song, I. H., Shin, S. W., Park, K. S., Lansac, Y., Jang, Y. H., & Um, S. H. (2015) · Scientific Reports · doi:10.1038/srep17722 · Cited by 7
Mechanisms for DNA Interplay in Eukaryotic Transcription Factors
Muñoz, V., Goluguri, R. R., Ghosh, C., Tanielian, B., & Sadqi, M. (2025) · Annual Review of Biophysics · doi:10.1146/annurev-biophys-071524-111008 · Cited by 8
Quantitative and Systematic NMR Measurements of Sequence-Dependent A–T Hoogsteen Dynamics in the DNA Double Helix
Manghrani, A., Rangadurai, A., Szekely, O., Liu, B., Guseva, S., & Al‐Hashimi, H. M. (2025) · Biochemistry · doi:10.1021/acs.biochem.4c00820 · Cited by 6
Deciphering the binding mechanism of tafamidis to calf thymus DNA: multimodal spectroscopic, thermodynamic, and computational perspectives
Alossaimi, M. A., Elmansi, H., Belal, F. F., & Magdy, G. (2025) · RSC Advances · doi:10.1039/d5ra04723d · Cited by 6
Structural basis of RNA-guided transcription by a dCas12f–σE–RNAP complex
Xiao, R., Hoffmann, F. T., Xie, D., Wiegand, T., Palmieri, A. I., Sternberg, S. H., & Chang, L. (2026) · Nature · doi:10.1038/s41586-026-10178-3 · Cited by 6
Measuring transcription factor binding and gene expression using barcoded self-reporting transposon calling cards and transcriptomes
Lalli, M. A., Yen, A., Thopte, U., Dong, F., Moudgil, A., Chen, X., Milbrandt, J., Dougherty, J. D., & Mitra, R. D. (2022) · NAR Genomics and Bioinformatics · doi:10.1093/nargab/lqac061 · Cited by 5
Effects of parental age and polymer composition on short tandem repeat de novo mutation rates
Goldberg, M. E., Noyes, M. D., Eichler, E. E., Quinlan, A. R., & Harris, K. (2024) · Genetics · doi:10.1093/genetics/iyae013 · Cited by 8
Comprehensive insights into the role of extracellular polymeric substances of Geobacter in the horizontal transfer of antibiotic resistance genes
Liu, S., Wang, X., Zhang, Z., Gu, P., Yang, K., & Miao, H. (2025) · Journal of environmental chemical engineering · doi:10.1016/j.jece.2024.115257 · Cited by 6
Histone H3 tail charge patterns govern nucleosome condensate formation and dynamics
Hammonds, E. F., Singh, A., Suresh, K. K., Yang, S., Zahorodny, S. S. M., Gupta, R., Potoyan, D. A., Banerjee, P. R., & Morrison, E. A. (2026) · Nucleic Acids Research · doi:10.1093/nar/gkag050 · Cited by 6
Hydrogen bonds in Zif268 proteins – a theoretical perspective
Palanivel, U., & Lakshmipathi, S. (2015) · Journal of Biomolecular Structure and Dynamics · doi:10.1080/07391102.2015.1085903 · Cited by 6
Ion effects of Sr2+, Cs+ and I− on DNA in aqueous solutions
Shen, X., Ding, K., & Feng-Shou, Z. (2013) · Chemical Physics Letters · doi:10.1016/j.cplett.2013.04.029 · Cited by 6
PerPlot & PerScan: tools for analysis of DNA curvature-related periodicity in genomic nucleotide sequences
Mrázek, J., Chaudhari, T. B., & Basu, A. (2011) · Microbial Informatics and Experimentation · doi:10.1186/2042-5783-1-13 · Cited by 6
Using systems and structure biology tools to dissect cellular phenotypes
Floratos, A., Honig, B. H., Pe’er, D., & Califano, A. (2011) · Journal of the American Medical Informatics Association · doi:10.1136/amiajnl-2011-000490 · Cited by 6
Self-citation
Quantitative characterization of conformational-specific protein–DNA binding using a dual-spectral interferometric imaging biosensor
Zhang, X., Daaboul, G. G., Spuhler, P. S., Dröge, P., & Ünlü, M. S. (2016) · Nanoscale · doi:10.1039/c5nr06785e · Cited by 6
Predicting Variation of DNA Shape Preferences in Protein-DNA Interaction in Cancer Cells with a New Biophysical Model
Batmanov, K., & Wang, J. (2017) · Genes · doi:10.3390/genes8090233 · Cited by 6
Unveiled electric profiles within hydrogen bonds suggest DNA base pairs with similar bond strengths
Ruiz‐Blanco, Y. B., Almeida, Y., Torres, C. M. S., & García, Y. (2017) · PLoS ONE · doi:10.1371/journal.pone.0185638 · Cited by 6
Transient Hoogsteen Base Pairs Observed in Unbiased Molecular Dynamics Simulations of DNA
Galindo‐Murillo, R., & Cheatham, T. E. (2022) · The Journal of Physical Chemistry Letters · doi:10.1021/acs.jpclett.2c01348 · Cited by 6
Understanding the Target Search by Multiple Transcription Factors on Nucleosomal DNA
Mishra, S. K., & Bhattacherjee, A. (2023) · ChemPhysChem · doi:10.1002/cphc.202200644 · Cited by 6
Structural insights into the DNA recognition mechanism by the bacterial transcription factor PdxR
Freda, I., Exertier, C., Barile, A., Chaves-Sanjuán, A., Vega, M. V., Isupov, M. N., Harmer, N. J., Gugole, E., Swuec, P., Bolognesi, M., et al. (2023) · Nucleic Acids Research · doi:10.1093/nar/gkad552 · Cited by 6
Molecular Characterization and Genome Mechanical Features of Two Newly Isolated Polyvalent Bacteriophages Infecting Pseudomonas syringae pv. garcae
Silva, E. C., Quinde, C. A., Cieza, B., Basu, A., Vila, M. M. D. C., & Balcão, V. M. (2024) · Genes · doi:10.3390/genes15010113 · Cited by 6
Nitroxide Sensing of a DNA Microenvironment: Mechanistic Insights from EPR Spectroscopy and Molecular Dynamics Simulations
Popova, A. M., Hatmal, M. M., Frushicheva, M. P., Price, E. A., Qin, P. Z., & Haworth, I. S. (2012) · The Journal of Physical Chemistry B · doi:10.1021/jp303303v · Cited by 6
On the Possibility of Facilitated Diffusion of Dendrimers Along DNA
Ficici, E., & Andricioaei, I. (2015) · The Journal of Physical Chemistry B · doi:10.1021/acs.jpcb.5b02090 · Cited by 6
Synthesis of azonia cyanine derivatives as NIR fluorescent probes for nucleic acid detection and cell imaging
Chen, Y., Wei, X.-R., Sun, R., Xu, Y.-J., & Ge, J. (2019) · Analytical Methods · doi:10.1039/c9ay00982e · Cited by 6
A New Method Combining DNA Shape Features to Improve the Prediction Accuracy of Transcription Factor Binding Sites
Wang, S., Shen, Z., He, Y., Zhang, Q., Yuan, C., Qin, X., Wu, H., & Zhao, X. (2020) · Lecture notes in computer science · doi:10.1007/978-3-030-60802-6_8 · Cited by 5
Polymorphisms within DIO2 and GADD45A genes increase the risk of liver disease progression in chronic hepatitis b carriers
Rybicka, M., Verrier, E. R., Baumert, T. F., & Bielawski, K. P. (2023) · Scientific Reports · doi:10.1038/s41598-023-32753-8 · Cited by 6
Molecular dynamics simulations of the glucocorticoid receptor DNA-binding domain suggest a role of the lever-arm mobility in transcriptional output
Álvarez, L. D., Presman, D. M., & Pecci, A. (2017) · PLoS ONE · doi:10.1371/journal.pone.0189588 · Cited by 6
Oxygen–aromatic contacts in intra-strand base pairs: Analysis of high-resolution DNA crystal structures and quantum chemical calculations
Jain, A. K., Deepak, R. N. V. K., & Sankararamakrishnan, R. (2014) · Journal of Structural Biology · doi:10.1016/j.jsb.2014.04.008 · Cited by 6
Gene Expression Divergence is Coupled to Evolution of DNA Structure in Coding Regions
Dai, Z., & Dai, X. (2011) · PLoS Comput. Biol. · doi:10.1371/journal.pcbi.1002275 · Cited by 4
Nucleosomes as Control Elements for Accessing the Genome
Dechassa, M. L., & Luger, K. (2011) · Wiley eBooks · doi:10.1002/9783527639991.ch3 · Cited by 6
Crystal structure of the HMGA AT-hook 1 domain bound to the minor groove of AT-rich DNA and inhibition by antikinetoplastid drugs
Nué-Martínez, J. J., Maturana, M., Lagartera, L., Rodríguez-Gutiérrez, J.-A., Boer, R., Campos, J. L., Saperas, N., & Dardonville, C. Y. (2024) · Scientific Reports · doi:10.1038/s41598-024-77522-3 · Cited by 5
START domains generate paralog-specific regulons from a single network architecture
Holub, A. S., Choudury, S. G., Andrianova, E. P., Dresden, C. E., Camacho, R. A. U., Zhulin, I. B., & Husbands, A. Y. (2024) · Nature Communications · doi:10.1038/s41467-024-54269-z · Cited by 6
MutPNI: A Unified Model Architecture for Accurately Predicting the Effects of Mutations on Protein-Nucleic Acid Interactions
Yan, Z., Ge, F., Zhang, Y., He, Y., Liu, Y., Zhu, Y., Song, J., & Yu, D. (2025) · Journal of Chemical Information and Modeling · doi:10.1021/acs.jcim.5c00756 · Cited by 5
Post-translational modifications of the nucleoid protein H-NS: sites, mechanisms, and regulatory cues
Liu, Y., & Wang, X. (2025) · FEMS Microbiology Reviews · doi:10.1093/femsre/fuaf045 · Cited by 5
Solid-phase engineering of molecularly imprinted nanoparticles (NanoMIPs): how template and solid-phase drive polymer composition and binding performance
Bosch-Tamayo, T., Iakimova, T. M., Shen, A. Q., & Sullivan, M. V. (2025) · Journal of Materials Chemistry B · doi:10.1039/d5tb01580d · Cited by 5
Potential of a newly isolated lytic bacteriophage to control Pseudomonas coronafaciens pv. garcae in coffee plants: Molecular characterization with in vitro and ex vivo experiments
MOTA, L. C., Silva, E. C., Quinde, C. A., Cieza, B., Basu, A., Rodrigues, L. M. R., Vila, M. M. D. C., & Balcão, V. M. (2024) · Enzyme and Microbial Technology · doi:10.1016/j.enzmictec.2024.110573 · Cited by 5
Molecular dynamics study of DNA binding by INT‐DBD under a polarized force field
Yao, X. X., Ji, C., Xie, D. Q., & Zhang, J. Z. H. (2013) · Journal of Computational Chemistry · doi:10.1002/jcc.23244 · Cited by 5
Molecular dynamics simulation reveals DNA-specific recognition mechanism via c-Myb in pseudo-palindromic consensus of mim-1 promoter
Weng, J., Yang, S., Shen, J., Liu, H., Xu, Y., Hao, D., & Wang, S. (2023) · Journal of Zhejiang University SCIENCE B · doi:10.1631/jzus.b2200634 · Cited by 5
Understanding base and backbone contributions of phosphorothioate DNA for molecular recognition with SBD proteins
Li, J., Luo, S., Ouyang, X., Wu, G., Deng, Z., He, X., & Zhao, Y. (2023) · Physical Chemistry Chemical Physics · doi:10.1039/d3cp02820h · Cited by 5
A box-in-box supramolecular assembly for the highly selective recognition of natural, epigenetically and chemically modified cytosines in water
Qin, S.-Q., Xu, W., Wang, Q., Chen, R.-Y., Yang, D., Yang, L., Ye, W., & Jiang, R. (2023) · Organic Chemistry Frontiers · doi:10.1039/d3qo01649h · Cited by 5
The role of nucleotide opening dynamics in facilitated target search by DNA-repair proteins
Mishra, S. K., Sangeeta, Heermann, D. W., & Bhattacherjee, A. (2024) · Biochimica et Biophysica Acta (BBA) - Gene Regulatory Mechanisms · doi:10.1016/j.bbagrm.2024.195026 · Cited by 5
DNA Electric Charge Oscillations Govern Protein–DNA Recognition
Štěpánek, J., Kopecký, V., Turpin, P., Li, Z., Alpert, B., & Zentz, C. (2015) · PLoS ONE · doi:10.1371/journal.pone.0124444 · Cited by 5
Investigation of Interactions between DNA and Nuclear Receptors: A Review of the Most Used Methods
Fattori, J., Indolfo, N. D. C., Campos, J. C. L. D. O., Videira, N. B., Bridi, A. V., Doratioto, T. R., de Assis, M. A., & Figueira, A. C. M. (2014) · Nuclear Receptor Research · doi:10.11131/2014/101090 · Cited by 5
Protein Nano-Object Integrator (ProNOI) for generating atomic style objects for molecular modeling
Smith, N., Campbell, B., Li, L., Li, C., & Alexov, E. G. (2012) · BMC Structural Biology · doi:10.1186/1472-6807-12-31 · Cited by 5
103 Probing DNA shape and methylation state on a genomic scale with DNase I
Lazarovici, A., Zhou, T., Shafer, A., Machado, A. C. D., Sandstrom, R. S., Sabo, P. J., Lü, Y., Rohs, R., Stamatoyannopoulos, J. A., & Bussemaker, H. J. (2013) · Journal of Biomolecular Structure and Dynamics · doi:10.1080/07391102.2013.786345 · Cited by 5
Self-citation
Conformational selection underpins recognition of multiple DNA sequences by proteins and consequent functional actions
Naiya, G., Raha, P., Mondal, M., Pal, U., Saha, R., Chaudhuri, S., Batabyal, S., Pal, S. K., Bhattacharyya, D., Maiti, N. C., et al. (2016) · Physical Chemistry Chemical Physics · doi:10.1039/c6cp03278h · Cited by 6
Structural dynamics of wild type and mutated forms of human L1 endonuclease and insights into its sequence specific nucleic acid binding mechanism: A molecular dynamics study
Rajagopalan, M., Balasubramanian, S., & Ramaswamy, A. (2017) · Journal of Molecular Graphics and Modelling · doi:10.1016/j.jmgm.2017.07.002 · Cited by 5
Coop-Seq Analysis Demonstrates that Sox2 Evokes Latent Specificities in the DNA Recognition by Pax6
Hu, C., Malik, V., Chang, Y. K., Veerapandian, V., Srivastava, Y., Huang, Y.-H., Hou, L., Cojocaru, V., Stormo, G. D., & Jauch, R. (2017) · Journal of Molecular Biology · doi:10.1016/j.jmb.2017.10.013 · Cited by 5
Parallelized DNA tethered bead measurements to scrutinize DNA mechanical structure
Allemand, J., Tardin, C., & Salomé, L. (2019) · Methods · doi:10.1016/j.ymeth.2019.07.020 · Cited by 5
Streptomyces IHF uses multiple interfaces to bind DNA
Nanji, T., Gehrke, E. J., Shen, Y., Gloyd, M., Zhang, X., Firby, C. D., Huynh, A., Razi, A., Ortega, J., Elliot, M. A., et al. (2019) · Biochimica et Biophysica Acta (BBA) - General Subjects · doi:10.1016/j.bbagen.2019.07.014 · Cited by 5
Progress on the Physiological Function of Mitochondrial DNA and Its Specific Detection and Therapy
Zhang, C., Xue, Y., Wang, L., Wu, Q., Fang, B., Sheng, Y., Bai, H., Peng, B., Yang, N., & Li, L. (2021) · ChemBioChem · doi:10.1002/cbic.202100474 · Cited by 5
Inferring primase-DNA specific recognition using a data driven approach
Soffer, A., Eisdorfer, S. A., Ifrach, M., Ilic, S., Afek, A., Schussheim, H., Vilenchik, D., & Akabayov, B. (2021) · Nucleic Acids Research · doi:10.1093/nar/gkab956 · Cited by 5
Histone H4 Tails in Nucleosomes: a Fuzzy Interaction with DNA
Rabdano, S. O., Shannon, M. D., Izmailov, S. A., Salguero, N. G., Zandian, M., Purusottam, R. N., Poirier, M. G., Skrynnikov, N. R., & Jaroniec, C. P. (2021) · Angewandte Chemie · doi:10.1002/ange.202012046 · Cited by 5
Deep learning for de-convolution of Smad2 versus Smad3 binding sites
Ng, J. W. K., Ong, E. H., Tucker‐Kellogg, L., & Tucker‐Kellogg, G. (2022) · BMC Genomics · doi:10.1186/s12864-022-08565-x · Cited by 5
Interaction preferences between protein side chains and key epigenetic modifications 5-methylcytosine, 5-hydroxymethycytosine and N6-methyladenine
Hajnić, M., Alonso‐Gil, S., Polyansky, A. A., de Ruiter, A., & Žagrović, B. (2022) · Scientific Reports · doi:10.1038/s41598-022-23585-z · Cited by 5
DNA structural properties of DNA binding sites for 21 transcription factors in the mycobacterial genome
Dey, U., Olymon, K., Banik, A., Abbas, E., Yella, V. R., & Kumar, A. A. (2023) · Frontiers in Cellular and Infection Microbiology · doi:10.3389/fcimb.2023.1147544 · Cited by 5
A short GC‐rich palindrome of human mannose receptor gene coding region displays a conformational switch
Bansal, A., Prasad, M., Roy, K., & Kukreti, S. (2012) · Biopolymers · doi:10.1002/bip.22111 · Cited by 5
Dynamic and Structural Changes in the Minimally Restructuring EcoRI Bound to a Minimally Mutated DNA Chain
Ramakrishnan, V., Jagannathan, S., Shaikh, A. R., & Rajagopalan, R. (2012) · Journal of Biomolecular Structure and Dynamics · doi:10.1080/073911012010525020 · Cited by 5
Small Sequence‐Sensitive Compounds for Specific Recognition of the G⋅C Base Pair in DNA Minor Groove
Farahat, A. A., Guo, P., Shoeib, H., Paul, A., Boykin, D. W., & Wilson, W. D. (2019) · Chemistry - A European Journal · doi:10.1002/chem.201904396 · Cited by 5
The complex structure of hsRosR-S5 (VNG0258H/RosR-S5)
Shaanan, B., & Kutnowski, N. (2019) · Worldwide Protein Data Bank · doi:10.2210/pdb6qh0/pdb · Cited by 5
Single-fiber nucleosome density shapes the regulatory output of a mammalian chromatin remodeling enzymePreprint
Abdulhay, N. J., Hsieh, L. J., McNally, C. P., Ketavarapu, M., Kasinathan, S., Nanda, A. S., Ostrowski, M. S., Wu, K., Moore, C. M., Goodarzi, H., et al. (2021) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2021.12.10.472156 · Cited by 5
Genome-wide promoter assembly in E. coli measured at single-base resolutionPreprint
John, J. D., Jabbar, J., Badjatia, N., Rossi, M. J., Lai, W., & Pugh, B. F. (2022) · Genome Research · doi:10.1101/gr.276544.121 · Cited by 5
Structural basis of directionality control in large serine integrasesPreprint
Shin, H., Pigli, Y. Z., Reyes, T. P., Bello, A. J., Fuller, J. R., Olorunniji, F. J., & Rice, P. A. (2025) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2025.01.03.631226 · Cited by 5
Generative design of sequence specific DNA binding proteinsPreprint
Sehgal, E., Politanska, Y., Mitra, R., Kim, P. T., González-Rodríguez, N., Warrier, T., Kubaney, A., Morishita, A., Quijano, R. N., Butcher, J., et al. (2026) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.64898/2026.04.27.720408 · Cited by 6
CERENKOV
Yao, Y., Liu, Z., Singh, S. H., Wei, Q., & Ramsey, S. A. (2017) · ACM International Conference on Bioinformatics, Computational Biology, and Health Informatics (ACM-BCB) · doi:10.1145/3107411.3107414 · Cited by 4
Probing the hierarchical dynamics of DNA-sperm nuclear transition protein complexes through fuzzy interaction and mesoscale condensation
Xie, S., Yue, C., Ye, S., & Li, Z. (2024) · Physical Chemistry Chemical Physics · doi:10.1039/d3cp05957j · Cited by 5
Intrinsically Disordered Compositional Bias in Proteins: Sequence Traits, Region Clustering, and Generation of Hypothetical Functional Associations
Harrison, P. M. (2024) · Bioinformatics and Biology Insights · doi:10.1177/11779322241287485 · Cited by 5
Alternative Approach to Sequence-Specific Recognition of DNA: Cooperative Stacking of Dication Dimers─Sensitivity to Compound Curvature, Aromatic Structure, and DNA Sequence
Paul, A., Terrell, J. R., Farahat, A. A., Ogbonna, E. N., Kumar, A., Boykin, D. W., Neidle, S., & Wilson, W. D. (2025) · ACS Chemical Biology · doi:10.1021/acschembio.4c00800 · Cited by 4
Symmetry, gauge freedoms, and the interpretability of sequence-function relationships
Posfai, A., McCandlish, D. M., & Kinney, J. B. (2025) · Physical Review Research · doi:10.1103/physrevresearch.7.023005 · Cited by 4
TRAFICA: an open chromatin language model to improve transcription factor binding affinity prediction
Xu, Y. G., Wang, C., Xu, K., Ding, Y., Lü, A., & Zhang, L. (2025) · Bioinformatics · doi:10.1093/bioinformatics/btaf469 · Cited by 4
Does the nucleosome break its own rules?
Davey, C. A. (2013) · Current Opinion in Structural Biology · doi:10.1016/j.sbi.2013.01.011 · Cited by 4
Identification of basepairs within Tn5 termini that are critical sfor H-NS binding to the transpososome and regulation of Tn5 transposition
Whitfield, C. R., Shilton, B. H., & Haniford, D. B. (2012) · Mobile DNA · doi:10.1186/1759-8753-3-7 · Cited by 4
Computational analysis suggests a highly bendable, fragile structure for nucleosomal DNA
Nozaki, T., Yachie, N., Ogawa, R., Saito, R., & Tomita, M. (2011) · Gene · doi:10.1016/j.gene.2011.02.004 · Cited by 4
DNA Structure Helps Predict Protein Binding
Stormo, G. D., & Roy, B. (2016) · Cell Systems · doi:10.1016/j.cels.2016.09.004 · Cited by 4
New Insights into the Interactions of a DNA Oligonucleotide with mPEGylated-PAMAM by Circular Dichroism and Solution NMR
Dou, X., Meints, G. A., & Sedaghat‐Herati, R. (2018) · The Journal of Physical Chemistry B · doi:10.1021/acs.jpcb.8b08517 · Cited by 4
Intrinsic DNA topology as a prioritization metric in genomic fine-mapping studies
Ainsworth, H. C., Howard, T. D., & Langefeld, C. D. (2020) · Nucleic Acids Research · doi:10.1093/nar/gkaa877 · Cited by 3
DNA– Drug Interactions
Jayaram, B., Singh, T., & Fenley, M. O. (2011) · CRC Press eBooks · doi:10.1201/b11691-17 · Cited by 4
emDNA – A Tool for Modeling Protein-decorated DNA Loops and Minicircles at the Base-pair Step Level
Young, R. T., Clauvelin, N., & Olson, W. K. (2022) · Journal of Molecular Biology · doi:10.1016/j.jmb.2022.167558 · Cited by 4
Heterogeneity in winged helix‐turn‐helix and substrate DNA interactions: Insights from theory and experiments
Boral, A., & Mitra, D. (2023) · Journal of Cellular Biochemistry · doi:10.1002/jcb.30369 · Cited by 4
NMP4, an Arbiter of Bone Cell Secretory Capacity and Regulator of Skeletal Response to PTH Therapy
Korff, C., Atkinson, E. G., Adaway, M., Klunk, A. J., Wek, R. C., Vashishth, D., Wallace, J. M., Anderson‐Baucum, E. K., Evans‐Molina, C., Robling, A. G., et al. (2023) · Calcified Tissue International · doi:10.1007/s00223-023-01088-x · Cited by 4
MucR from Sinorhizobium meliloti: New Insights into Its DNA Targets and Its Ability to Oligomerize
Slapakova, M., Sgambati, D., Pirone, L., Russo, V., D’Abrosca, G., Valletta, M., Russo, R., Chambery, A., Malgieri, G., Pedone, E. M., et al. (2023) · International Journal of Molecular Sciences · doi:10.3390/ijms241914702 · Cited by 4
Stability and dynamics of extradenticle modulates its function
Singh, A., Acharya, B., Mukherjee, B., Boorla, V. S., Boral, S., Maiti, S., & De, S. (2024) · Current Research in Structural Biology · doi:10.1016/j.crstbi.2024.100150 · Cited by 4
MulTFBS: A Spatial-Temporal Network with Multichannels for Predicting Transcription Factor Binding Sites
Zhuang, J., Huang, X., Liu, S., Gao, W., Su, R., & Feng, K. (2024) · Journal of Chemical Information and Modeling · doi:10.1021/acs.jcim.3c02088 · Cited by 4
DeepCTF: transcription factor binding specificity prediction using DNA sequence plus shape in an attention-based deep learning model
Tariq, S., & Amin, A. (2024) · Signal Image and Video Processing · doi:10.1007/s11760-024-03229-7 · Cited by 5
Specific and highly efficient condensation of GC and IC DNA by polyaza pyridinophane derivatives
Stojković, M. R., González‐García, J., Šupljika, F., Galiana‐Roselló, C., Guijarro, L., Gazze, S. A., Francis, L. W., Piantanida, I., & García‐España, E. (2017) · International Journal of Biological Macromolecules · doi:10.1016/j.ijbiomac.2017.11.156 · Cited by 4
Genetic Complexity of Mitral Valve Prolapse Revealed by Clinical and Genetic Evaluation of a Large Family.
Haskell, G., Jensen, B. C., Skrzynia, C., Pulikkotil, T., Tilley, C. R., Lu, Y., Marchuk, D. S., Samsa, L. A., Wilhelmsen, K. C., Lange, E. M., et al. (2017) · PubMed · Cited by 4
Mechanism of cognate sequence discrimination by the ETS-family transcription factor ETS-1
Huang, K., Xhani, S., Albrecht, A. V., Ha, V. L., Esaki, S., & Poon, G. M. K. (2019) · Journal of Biological Chemistry · doi:10.1074/jbc.ra119.007866 · Cited by 4
DNA sequence-dependent positioning of the linker histone in a nucleosome: A single-pair FRET study
De, M., Öztürk, M. A., Isbaner, S., Tóth, K., & Wade, R. C. (2021) · Biophysical Journal · doi:10.1016/j.bpj.2021.07.012 · Cited by 4
Anomalous DNA binding by E2 regulatory protein driven by spacer sequence TATA
Xi, Z., Zhang, Y., Hegde, R. S., Shakked, Z., & Crothers, D. M. (2010) · Nucleic Acids Research · doi:10.1093/nar/gkq114 · Cited by 4
Minor groove recognition is important for the transcription factor PhoB: a surface plasmon resonance study
Ritzefeld, M., Wollschläger, K., Niemann, G., Anselmetti, D., & Sewald, N. (2011) · Molecular BioSystems · doi:10.1039/c1mb05281k · Cited by 4
Structural study to analyze the DNA-binding properties of DsrC protein from the dsr operon of sulfur-oxidizing bacterium Allochromatium vinosum
Ghosh, S., & Bagchi, A. (2019) · Journal of Molecular Modeling · doi:10.1007/s00894-019-3945-3 · Cited by 4
Probing transcription factor combinatorics in different promoter classes and in enhancersPreprint
Vandel, J., Cassan, O., Lèbre, S., Lecellier, C., & Bréhélin, L. (2017) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/197418 · Cited by 4
Transcription factors operate on a limited vocabulary of binding motifs in Arabidopsis thalianaPreprint
Zenker, S., Wulf, D., Meierhenrich, A., Becker, S., Eisenhut, M., Stracke, R., Weißhaar, B., & Bräutigam, A. (2023) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2023.08.28.555073 · Cited by 4
Overlapping binding sites underlie TF genomic occupancyPreprint
Khetan, S., & Bulyk, M. L. (2024) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2024.03.05.583629 · Cited by 4
The ALX4 dimer structure provides insight into how disease alleles impact function
Cain, B., Yuan, Z., Thoman, E., Kovall, R. A., & Gebelein, B. A. (2025) · Nature Communications · doi:10.1038/s41467-025-59728-9 · Cited by 3
Expanding the quorum sensing toolbox: Promoter libraries and hybrid promoter for dynamic genetic circuits
Baets, J. D., Parmentier, I., Paepe, B. D., & Mey, M. D. (2025) · New Biotechnology · doi:10.1016/j.nbt.2025.09.004 · Cited by 3
Combining Physics-Based Protein–DNA Energetics with Machine Learning to Predict Interpretable Transcription Factor-DNA Binding
Masri, C. A., & Yu, J. H. (2025) · Journal of Chemical Information and Modeling · doi:10.1021/acs.jcim.5c01143 · Cited by 3

Authors: Rohs, R., West, S. M., Sosinsky, A., Liu, P., Mann, R. S., & Honig, B.
Affiliations: Howard Hughes Medical Institute (US)
Columbia University (US)
Corresponding author: Mann, Richard S.
Honig, Barry
ORCID: Rohs, Remo
West, Sean M.
Sosinsky, Alona
Liu, Peng
Mann, Richard S.
Honig, Barry
Venue: Nature
Publisher: Springer Science and Business Media LLC
Published: 2009-10
Volume: 461
Issue: 7268
Pages: 1248-1253
ISSN: 0028-0836 (ISSN-L)
1476-4687
DOI: 10.1038/nature08473
PMC: PMC2793086
OpenAlex: W2012627860
Cited by: 1,096
References: 51
Citations by year: 2026: 51 · 2025: 68 · 2024: 73 · 2023: 66 · 2022: 77 · 2021: 76 · 2020: 58 · 2019: 57 · 2018: 55 · 2017: 65 · 2016: 52 · 2015: 76 · 2014: 72 · 2013: 74 · 2012: 64
FWCI: 23.46
Type: journal article
Language: en
Open access: green
www.ncbi.nlm.nih.gov
Licence: www.springer.com/tdm (tdm)
Locations: Nature (publishedVersion)
PubMed (publishedVersion)
PubMed Central (acceptedVersion)
RePEc: Research Papers in Economics (submittedVersion)
BIROn (Birkbeck, University of London) (submittedVersion)
Funders: Howard Hughes Medical Institute
National Cancer Institute (U54CA121852)
National Institute of General Medical Sciences (GM54510, R01GM030518, R01GM054510)
Topics: Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › DNA and Nucleic Acid Chemistry
Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Diffusion and Search Dynamics
Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Chromatin Dynamics
Keywords: protein-DNA recognition, DNA shape, minor groove, major groove, arginine binding, nucleosome core particle, A-tracts, sequence-specific DNA-binding proteins, DNA binding specificity, protein-DNA complex, hydrogen bonding
MeSH terms: Animals, Arginine, Base Sequence, DNA, DNA-Binding Proteins, Hydrogen Bonding, Lysine, Nucleic Acid Conformation, Nucleosomes, Protein Binding, Saccharomyces cerevisiae, Databases, Factual, AT Rich Sequence, Static Electricity

About these checks

Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.

Statistics and arithmetic are recomputed, not judged.

Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.

What counts as a claim ›How we measure confidence ›How we check this ›

Are you an author, or do you see a problem with this page? Request a review

The role of DNA shape in protein–DNA recognition

Abstract

Overview

Integrity signals

Verification

Claims the paper makes

Claims other papers make about this one

Self-check

Citations

Cites

Cited by

Related

Metadata

Record

About these checks