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The role of DNA shape in protein–DNA recognition

Author

Listed:
  • Remo Rohs

    (Howard Hughes Medical Institute, Center for Computational Biology and Bioinformatics, Columbia University, 1130 Saint Nicholas Avenue, New York, New York 10032, USA)

  • Sean M. West

    (Howard Hughes Medical Institute, Center for Computational Biology and Bioinformatics, Columbia University, 1130 Saint Nicholas Avenue, New York, New York 10032, USA)

  • Alona Sosinsky

    (Howard Hughes Medical Institute, Center for Computational Biology and Bioinformatics, Columbia University, 1130 Saint Nicholas Avenue, New York, New York 10032, USA
    Present address: Institute of Structural and Molecular Biology, School of Crystallography, Birkbeck College, Malet Street, London WC1E 7HX, UK.)

  • Peng Liu

    (Howard Hughes Medical Institute, Center for Computational Biology and Bioinformatics, Columbia University, 1130 Saint Nicholas Avenue, New York, New York 10032, USA)

  • Richard S. Mann

    (Columbia University, 701 West 168th Street, HHSC 1104, New York, New York 10032, USA)

  • Barry Honig

    (Howard Hughes Medical Institute, Center for Computational Biology and Bioinformatics, Columbia University, 1130 Saint Nicholas Avenue, New York, New York 10032, USA)

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.

Suggested Citation

  • Remo Rohs & Sean M. West & Alona Sosinsky & Peng Liu & Richard S. Mann & Barry Honig, 2009. "The role of DNA shape in protein–DNA recognition," Nature, Nature, vol. 461(7268), pages 1248-1253, October.
    • Handle: RePEc:nat:nature:v:461:y:2009:i:7268:d:10.1038_nature08473
    DOI: 10.1038/nature08473
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    Cited by:

    1. Nikolai Schleussner & Pierre Cauchy & Vedran Franke & Maciej Giefing & Oriol Fornes & Naveen Vankadari & Salam A. Assi & Mariantonia Costanza & Marc A. Weniger & Altuna Akalin & Ioannis Anagnostopoulo, 2023. "Transcriptional reprogramming by mutated IRF4 in lymphoma," Nature Communications, Nature, vol. 14(1), pages 1-18, December.
    2. Jie Li & Haonan Zhang & Dongyu Li & Ya-Jun Liu & Edward A. Bayer & Qiu Cui & Yingang Feng & Ping Zhu, 2023. "Structure of the transcription open complex of distinct σI factors," Nature Communications, Nature, vol. 14(1), pages 1-12, December.
    3. Janik Sielemann & Donat Wulf & Romy Schmidt & Andrea Bräutigam, 2021. "Local DNA shape is a general principle of transcription factor binding specificity in Arabidopsis thaliana," Nature Communications, Nature, vol. 12(1), pages 1-8, December.
    4. Jinsen Li & Tsu-Pei Chiu & Remo Rohs, 2024. "Predicting DNA structure using a deep learning method," Nature Communications, Nature, vol. 15(1), pages 1-12, December.

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