DNA Motifs and Sequence Periodicities

Article type: Research Article

Authors: Kumar, Lokesh | Futschik, Matthias | Herzel, Hanspeter

Affiliations: Institute for Theoretical Biology, Humboldt University, Invalidenstr. 43, 10115 Berlin, Germany

Note: [] Corresponding author. E-mail: h.herzel@biologie.hu-berlin.de

Abstract: Genomic DNA sequences contain a wealth of information about the bendability and curvature of the DNA molecule. For example, the well-known 10–11 bp periodicities within genomes can be attributed to supercoiled structures or wrapping around nucleosomes. Such periodic signals have previously been examined mainly based on mono- or dinucleotide correlations. In this study, we generalize this approach and analyze correlation functions of longer motifs such as tetramers or poly(A) sequences. Periodically placed motifs may indicate regular protein binding or curvature signals. We detected various periodic signals e.g. strong 10–11 bp oscillations of periodically placed poly(A), poly(T) or poly(W) stretches. These observations lead to a new view on the intensively studied 10–11 bp periodicities.

Keywords: Genomic DNA, periodicities, supercoiling, nucleosomes, motif, correlation, C. elegans, DNA bendability, poly(A) sequences

Journal: In Silico Biology, vol. 6, no. 1,2, pp. 71-78, 2006