Double helical DNA became an emblematic symbol of fast-growing field of molecular biology soon after formulation of its architecture. The antiparallel double helix with the ladder of hydrogen-bonded bases four of which are able to code for all living creatures on Earth is not only esthetically appealing and intellectually satisfying but also conceptually very simple. Deceivingly simple, as has become evident in the later years when several new and unexpected conformations of DNA emerged. An important stimulus for renewed interest in detailed investigation of DNA conformations can be expected in connection with the need to understand fine-tuning of storing and decoding of genetic information, sequence preferences for packing into histones, conformational behavior of regions with repetitive sequences, and structural implications of DNA modifications such as cytosine or adenine methylation crucial in epigenetics.
In our effort to understand structural details of double helical architecture, we have taken advantage of vast volume of information accumulated by crystallographers. Based on the available crystal data, we classified conformations of dinucleotide steps into about twenty classes (Svozil et al. Nucleic Acids Research 36, 3690 (2008)), developed technique of automatic assignment of these step conformational classes to any DNA structure (Čech et al. BMC Bioinformatics 14, 205 (2013)), and recently improved both these steps significantly (Černý et al. to be published (2015)). In the talk, we present our latest results, in which we correlate conformation classes of two dinucleotides forming the base-paired counterparts of the DNA duplex. We analyze separately the correlations for dinucleotides joined in the duplex by Watson-Crick pairing of both pairs and dinucleotides in which one or both pairs are non-canonical. The crystal data provided enough information to analyze sequence dependencies for the Watson-Crick paired steps; the non-canonical parts of duplexes can be discussed only qualitatively. Some of the more interesting results will be discussed in the talk. Even the preliminary results demonstrate that the classes of dinucleotide steps represent a powerful tool to describe details of the double helical architecture. The main conclusion of our research is that combination of correlations between the dinucleotide classes and base pair types provides sufficient structural characterization of the related step.
This study was supported by BIOCEV CZ.1.05/1.1.00/02.0109 from the ERDF and by institutional grant RVO 86 652 036.