Original scientific paper

Spectral Densities and Frequencies in the Power Spectrum of Higher Order Repeat Alpha Satellite in Human DNA Molecule

Vladimir Paar ; Department of Physics, Faculty of Science, University of Zagreb, Zagreb, Croatia
Nenad Pavin ; Department of Physics, Faculty of Science, University of Zagreb, Zagreb, Croatia
Ivan Basar ; Department of Physics, Faculty of Science, University of Zagreb, Zagreb, Croatia
Marija Rosandić ; Department of Internal Medicine, University Hospital Rebro, Zagreb, Croatia
Ivica Luketin ; Department of Physics, Faculty of Science, University of Split, Split, Croatia
Sonja Durajlija Žinić ; Ru|er Bošković Institute, Zagreb, Croatia

Abstract

Fast Fourier transform was applied to the central segment of a fully sequenced genomic segment from the centromeric region in human chromosome 7 (GenBank/AC017075.8, 193277 bp), which is characterized by alpha satellite higher order repeats (HOR). Frequencies and spectral densities were computed for all prominent peaks in the Fourier spectrum. We have additionally introduced a peak to noise ratio as effective spectral density in order to account for frequency variations of the noise level. We have shown that a very good description of computed Fourier frequencies can be obtained by using the multiple formula with the fundamental frequency corresponding to the 2734-bp HOR sequence. The peak at f₁₆ corresponds to the 171-bp monomer. Above the frequency f₁₆, the most pronounced peaks are mostly at multiples of f₁₆ (monomer-multiples). The lowest sixteen monomer-multiples kf₁₆ are locally dominant in spectral densities. The first monomer-multiple that is not locally dominant in spectral density is at k = 17. Above k = 27, the maximum of spectral density is systematically shifted to several neighboring higher frequency multiples. On the basis of the Fourier spectrum, the 171-bp monomer unit was subdivided into three approximately 57-bp subrepeats, which were further subdivided into 12-bp, 14-bp and 17-bp basic subrepeats.

Keywords

human DNA; alpha satellite; higher order repeat; Fourier spectrum

Hrčak ID:

102648

URI

https://hrcak.srce.hr/102648

Publication date:

31.5.2004.

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