- Article -
| In Silico Biology 6, 0008 (2006); ©2006, Bioinformation Systems e.V. |
Workshop "GEOMETRY OF GENOME"
DNA motifs and sequence periodicities
Lokesh Kumar, Matthias Futschik and Hanspeter Herzel*
Institute for Theoretical Biology, Humboldt University, Invalidenstr. 43, 10115 Berlin, Germany
* Corresponding author
Email: h.herzel@biologie.hu-berlin.de
Edited by E. Wingender; received October 30, 2005; revised January 26, 2006; accepted January 29, 2006; published February 11, 2006
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