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