Homogenization of Chromosomes Revealed by Oligonucleotide-Stickiness

Ayumu SAITO and Koichi NISHIGAKI*

Department of Functional Materials Science, Saitama University
255 Shimo-okubo, Sakura-ku, Saitama, Saitama 338-8570, Japan

(Received: May 25, 2004; Accepted for publication: October 5, 2004; Published on Web: November 19, 2004)

Genomic DNA contains sequences that are relics of evolution together with functional protein sequences and regulatory operands. The mutual relationship of chromosomes that constitute the genome is of interest from the viewpoint of evolution as well as from that of systems biology. Chromosome origin, the frequency of chromosomal alteration, and the nature of these alterations can be addressed by analyzing oligostickiness, which is highly informative of the hidden properties of genome sequences. Oligostickiness analysis is an oligonucleotide-affinity test performed along the genome sequence. This analysis revealed that frequent recombination events occur during the course of evolution, which is a phenomenon inherent to chromosomes. This was further supported by the finding of chromosome homogeneity in the nucleus and by the assimilation of oligostickiness for pairs of complementary oligonucleotides. Genomes consisting of multiple chromosomes possess a common property where all chromosomes share the same tendency of oligostickiness for any kind of probe (oligonucleotide), indicating that these chromosomes all experienced random-mode frequent inter-/intra-recombinations. The phenomenon observed here, namely the homogeneity of chromosomes, was novel but it could be interpreted in terms of random-mode frequent recombination of chromosomes with a considerable contribution of repeated sequences. Therefore, oligostickiness is useful for analyzing the similarity of chromosomes.

Keywords: Genome sequence analysis, Nucleic acid thermodynamics, Chromosome evolution, Negentropy, Recombination

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