3-, 10.5-, 200- and 400-base periodicities in genome sequences

E.N. Trifonov

Physica A: Statistical Mechanics and its Applications, 1998, vol. 249, issue 1, 511-516

Abstract: The above periodicities are the main hidden oscillating patterns detected so far in the genomic sequences. The 3-base periodicity is characteristic for the protein-coding sequences only. The source of the approximately 10.5-base sequence period is twofold. On the one hand, the sequences coding for alpha-helical coiled-coil regions in proteins have the hidden 3.5 aminoacid repeat which appears as 10.5-base periodicity in the nucleotide sequences. On the other hand, deformability of DNA important for its folding in chromatin is facilitated by periodical positioning of certain dinucleotides along the sequences, with the period close to 10.5 bases. There are some sequence features which are repeated at approximately 400-base distances, nearly periodically. This is due to the general segmented organization of the genomes, which appear to have evolved by fusion of genome segments of nearly standard sizes, close to typical 350 bases for eukaryotes and 440 bases for prokaryotes. Respective half-units (about 200 bases) are also frequently observed.

Keywords: Coding; DNA curvature; Nucleosome; Genome units; Beat effects (search for similar items in EconPapers)
Date: 1998
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Citations: View citations in EconPapers (1)

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Persistent link: https://EconPapers.repec.org/RePEc:eee:phsmap:v:249:y:1998:i:1:p:511-516

DOI: 10.1016/S0378-4371(97)00510-4

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