Sequence-dependent deformational anisotropy of chromatin DNA

Abstract

As found in previous work (E.N. Trifonov and J.L. Sussman, Proc. Natl. Acad. Sci. USA, in press) some dinucleotides of the chromatin DNA sequences have a clear tendency to be repeated along the sequences with a period of about 10.5 bases. A special iteration procedure is developed to find if there are phase relationships between different periodically repeating dinucleotides of chromatin DNA. A very specific symmetrical pattern of preferences of different dinucleotides to certain positions within a repeating 10.5 base frame is indeed found. This is interpreted as a manifestation of sequence-dependent deformational anisotropy of the chromatin DNA which facilitates its smooth folding in chromatin. The pattern found can be used for locating unidirectionally curved portions of the DNA molecules, possibly corresponding to nucleosomal DNA. This implies that the DNA is bound to the nucleosomes by one specific side which corresponds to the direction of the sequence-dependent curving of the DNA axis. The 10.5 base periodicity found can be considered as the second message present in chromatin DNA sequences together with 3 base frame coding message.