We analyzed the structural behavior of DNA complexed with regulatory proteins (mostly transcription factors) 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) described in [1] 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. The analysis is described in detail in [2].
This work was financially supported by the institutional funding to the Institute of Biotechnology (RVO 86652036), and by two ERDF and MEYS projects: BIOCEV (CZ.1.05/1.1.00/02.0109) and ELIXIR-CZ (CZ.02.1.01/0.0/0.0/16_013/0001777).