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

0484505 - BTÚ 2018 RIV CH eng J - Journal Article
Schneider, Bohdan - Božíková, Paulina - Čech, P. - Svozil, D. - Černý, Jiří
A DNA Structural Alphabet Distinguishes Structural Features of DNA Bound to Regulatory Proteins and in the Nucleosome Core Particle.
Genes. Roč. 8, č. 10 (2017), č. článku 278. E-ISSN 2073-4425
R&D Projects: GA MŠMT(CZ) ED1.1.00/02.0109
Grant - others:GA MŠk(CZ) EF16_013/0001777
Program: EF - Operační program výzkum, vývoj, vzdělávání (2014 - 2020)
Institutional support: RVO:86652036
Keywords : DNA * DNA-protein recognition * transcription factors
OECD category: Computer sciences, information science, bioinformathics (hardware development to be 2.2, social aspect to be 5.8)
Impact factor: 3.191, year: 2017

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.
Permanent Link: http://hdl.handle.net/11104/0281849