SEQUENCE PERIODICITY IN COMPLETE GENOMES OF ARCHAEA SUGGESTS POSITIVESUPERCOILING

The topological state of genomic DNA is of importance for its replicat ion, recombination and transcription. The wrapping of the DNA around n ucleosomes is associated with sequence periodicities (Trifonov and Sus sman, Proc. Natl. Acad. Sci. USA, 77, pp. 3816-20). Recently also the negative supercoiling of eubacterial DNA was related to I I base pair (bp) periodicity (Herzel et al. Physica A, 249, pp. 449-59). Archaeal plasmids and a virus-like particle from Sulfolobus are positively supe rcoiled, but the superhelical conformation of archaeal genomic DNA is still uncertain. The problem of superhelicity can now be addressed via a comparative statistical analysis of the available complete genomes. For this purpose one has to look for periodicities which are in phase with the helical repeat of 10-11 bp. Similar periodicities are induce d, however, by the amphipatic character of alpha-helices of encoded pr oteins (Zhurkin, Nucl. Acids Res., 9, pp. 1963-71). We show that these protein-induced periodicities are extended over a few periods only. T he periods of additional long-ranging oscillations deviate significant ly from the value for free DNA. A period of 11 bp in Eubacteria reflec ts negative supercoiling, whereas the significantly different period o f thermophilic Archaea close to 10 bp suggests positive Supercoiling o f archaeal genomes.