Signals in DNA sequences and their potential properties

DNA and RNA molecules contain signals which are recognized by regulatory proteins or enzymes either directly, through their nucleotide sequences or indirectly, through induced structural changes on their neighboring sequences. To date, most signal searches have been focused on specific recurrences of nucleotide sequences. Much less attention has been directed towards the structure, flexibility and hydrogen-bonding patterns that recognition elements may possess. Here we review the various methods involved in such searches. In particular, however, we also address the searches for potential properties. In this regard it is of interest to inspect the asymmetry in the distributions of complementary oligomers near biological features. Upstream of transcription initiation the frequencies of G-rich oligomers are particularly high (Nussinov, 1987a; 1990). The frequencies of C-rich oligomers are lower. A-tracts are also very frequent in these regions. This may correlate with the recent finding that guanine, but not cytosine, tracts enhance A-tract directed bends (Milton et al., 1990). Presumably A-tracts near G-tracts on the same strand may induce a structural change in the G-tracts which may enhance the bend. G-tracts may have the potential for participating in a DNA bend due to their compression of the major groove. Thus, proteins may not always be necessary to induce DNA conformational changes. This example illustrates the importance of studies of the properties of DNA oligomers in regulatory regions, and of algorithms for their detection.