Webserver WATlas v0.1: Atlas of DNA hydration

Methods

The watNA atlas is based on a data-mining study [1] of a large set of high-resolution crystal structures of naked DNA and protein/DNA complexes. For the analysis of DNA hydration, we used dinucleotide fragments classified according to their sequence and NtC conformation, as defined by our dinucleotide alphabet [2].

Figure 1

By Fourier-averaging the positions of water molecules extracted from a large set of structures, we derived 3D maps of water distribution around DNA dinucleotides, and identified hydration sites as the maxima in the probability density.

Applications

We propose that the watNA atlas can be used to predict water molecule positions around DNA for various applications, e.g. to validate water placement in electron density maps in crystallographic refinement, for the interpretation of cryo-EM maps, and to prepare and evaluate molecular dynamics simulations.

References

[1] Biedermannova et al.: Sequence- and structure-dependent DNA hydration. In preparation (2021).

[2] Cerny et al.: A unified dinucleotide alphabet describing both RNA and DNA structures. Nucleic Acids Research, 48(11), 6367 (2020).

Acknowledgements

The research was performed at the Laboratory of Biomolecular Recognition, Institute of Biotechnology, Czech Academy of Sciences, at the BIOCEV research infrastructure, and received support from the Elixir project.

The website was last updated on 2022-02-15

Contacts:

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Authors: Lada Biedermannová^a, Jiří Černý^b and Bohdan Schneider^a

^aLaboratory of Biomolecular Recognition, Institute of Biotechnology of the Czech Academy of Sciences, Průmyslová 595, 252 50 Vestec, Czech Republic

^bLaboratory of Structural Bioinformatics of Proteins, Institute of Biotechnology of the Czech Academy of Sciences, Průmyslová 595, 252 50 Vestec, Czech Republic

How to cite:

Lada Biedermannová^a*, Jiří Černý^b, Alžběta Šrůtková^a, Michaela Nekardová^a, and Bohdan Schneider^a*: Hydration of DNA is sequence- and structure-dependent. (manuscript in preparation)

^aLaboratory of Biomolecular Recognition, Institute of Biotechnology of the Czech Academy of Sciences, Průmyslová 595, 252 50 Vestec, Czech Republic

^bLaboratory of Structural Bioinformatics of Proteins, Institute of Biotechnology of the Czech Academy of Sciences, Průmyslová 595, 252 50 Vestec, Czech Republic

Correspondence: lada.biedermannova@ibt.cas.cz, bohdan.schneider@ibt.cas.cz

Download:

Hydration site positions and pseudo-occupancies for each NtC/sequence category in PDB file format.

3D maps of water distribution: to obtain the whole set of pseudo-electron density maps in CCP4 file format, please email the authors.