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

Schneider, Bohdan; Božíková, Paulina; Čech, P.; Svozil, D.; Černý, Jiří

doi:https://dx.doi.org/10.3390/genes8100278

Number of the records: 1

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

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SYSNO ASEP	0484505
Document Type	J - Journal Article
R&D Document Type	Journal Article
Subsidiary J	Článek ve WOS
Title	A DNA Structural Alphabet Distinguishes Structural Features of DNA Bound to Regulatory Proteins and in the Nucleosome Core Particle
Author(s)	Schneider, Bohdan (BTO-N)_{RID, ORCID} Božíková, Paulina (BTO-N) Čech, P. (CZ) Svozil, D. (CZ) Černý, Jiří (BTO-N)_{RID, ORCID}
Number of authors	5
Article number	278
Source Title	Genes. - : MDPI Roč. 8, č. 10 (2017)
Number of pages	15 s.
Language	eng - English
Country	CH - Switzerland
Keywords	DNA ; DNA-protein recognition ; transcription factors
Subject RIV	EB - Genetics ; Molecular Biology
OECD category	Computer sciences, information science, bioinformathics (hardware development to be 2.2, social aspect to be 5.8)
R&D Projects	ED1.1.00/02.0109 GA MŠMT - Ministry of Education, Youth and Sports (MEYS)
Institutional support	BTO-N - RVO:86652036
UT WOS	000414862300043
EID SCOPUS	85032005464
DOI	10.3390/genes8100278
Annotation	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.
Workplace	Institute of Biotechnology
Contact	Monika Kopřivová, Monika.Koprivova@ibt.cas.cz, Tel.: 325 873 700
Year of Publishing	2018

Number of the records: 1