title: Sequence structure of Lowary/Widom clones forming strong nucleosomes.
abstract: Lowary and Widom selected from random sequences those which form exceptionally stable nucleosomes, including clone 601, the current champion of strong nucleosome (SN) sequences. This unique sequence database (LW sequences) carries sequence elements which confer stability on the nucleosomes formed on the sequences, and, thus, may serve as source of information on the structure of "ideal" or close to ideal nucleosome DNA sequence. An important clue is also provided by crystallographic study of Vasudevan and coauthors on clone 601 nucleosomes. It demonstrated that YR·YR dinucleotide stacks (primarily TA·TA) follow one another at distances 10 or 11 bases or multiples thereof, such that they all are located on the interface between DNA and histone octamer. Combining this important information with alignment of the YR-containing 10-mers and 11-mers from LW sequences, the bendability matrices of the stable nucleosome DNA are derived. The matrices suggest that the periodically repeated TA (YR), RR, and YY dinucleotides are the main sequence features of the SNs. This consensus coincides with the one for recently discovered SNs with visibly periodic DNA sequences. Thus, the experimentally observed stable LW nucleosomes and SNs derived computationally appear to represent the same entity - exceptionally stable SNs.
authors.affiliation: a Institute of Evolution , University of Haifa , Mount Carmel, 31905 Haifa , Israel.
authors.forename: Edward N
authors.initials: EN
authors.lastname: Trifonov
mesh_terms: D001483:Base Sequence; D016384:Consensus Sequence; D004247:DNA / Q000737:chemistry; D006657:Histones / Q000737:chemistry; D009707:Nucleosomes / Q000737:chemistry*; D059372:Nucleotide Motifs
chemical_list: D006657:Histones; D009707:Nucleosomes; D004247:DNA
keywords: TA-periodic nucleosomes; insulators; nucleosome DNA; nucleosome mapping; strong nucleosomes