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Genes 2017, 8(10), 278; doi:10.3390/genes8100278

A DNA Structural Alphabet Distinguishes Structural Features of DNA Bound to Regulatory Proteins and in the Nucleosome Core Particle

1
Institute of Biotechnology of the Czech Academy of Sciences, BIOCEV, Průmyslová 595, CZ-252 50 Vestec, Prague West, Czech Republic
2
Laboratory of Informatics and Chemistry, Faculty of Chemical Technology, University of Chemistry and Technology Prague, Technická 5, CZ-166 28 Prague, Czech Republic
*
Author to whom correspondence should be addressed.
Academic Editors: Linda Bloom and Jörg Bungert
Received: 3 August 2017 / Revised: 6 October 2017 / Accepted: 13 October 2017 / Published: 18 October 2017
(This article belongs to the Special Issue Protein-DNA Interactions)
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Abstract

We analyzed the structural behavior of DNA complexed with regulatory proteins and the nucleosome core particle (NCP). The three-dimensional structures of almost 25 thousand dinucleotide steps from more than 500 sequentially non-redundant crystal structures were classified by using DNA structural alphabet CANA (Conformational Alphabet of Nucleic Acids) and associations between ten CANA letters and sixteen dinucleotide sequences were investigated. The associations showed features discriminating between specific and non-specific binding of DNA to proteins. Important is the specific role of two DNA structural forms, A-DNA, and BII-DNA, represented by the CANA letters AAA and BB2: AAA structures are avoided in non-specific NCP complexes, where the wrapping of the DNA duplex is explained by the periodic occurrence of BB2 every 10.3 steps. In both regulatory and NCP complexes, the extent of bending of the DNA local helical axis does not influence proportional representation of the CANA alphabet letters, namely the relative incidences of AAA and BB2 remain constant in bent and straight duplexes. View Full-Text
Keywords: DNA; DNA-protein recognition; transcription factors; regulatory proteins; histone; nucleosome core particle; molecular structure DNA; DNA-protein recognition; transcription factors; regulatory proteins; histone; nucleosome core particle; molecular structure
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Schneider, B.; Božíková, P.; Čech, P.; Svozil, D.; Černý, J. A DNA Structural Alphabet Distinguishes Structural Features of DNA Bound to Regulatory Proteins and in the Nucleosome Core Particle. Genes 2017, 8, 278.

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