- Article -
| In Silico Biology 1, 0017 (1999); ©1999, Bioinformation Systems e.V. |
Curved DNA in promoter sequences
Andrei E. Gabrielian, David Landsman*
and Alexander Bolshoy**
Computational Biology Branch, National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Building 38A, Room 8N805, Bethesda, MD 20894, USA.
E-mail: landsman@ncbi.nlm.nih.gov
* to whom all correspondence should be addressed
**present address: Institute of Evolution, University of Haifa, Haifa, 31905 ISRAEL
Edited by E. Wingender; received April 23, 1999; revised June 15, 1999; accepted June 15, 1999
Abstract
Sequence-dependent DNA curvature is known to play an important role in initiation of transcription of many genes. We compared the distribution of predicted intrinsic curvature of Escherichia coli and human promoter sequences with the distribution of curvature of randomly selected coding and non-coding fragments from these organisms. Different methods of curvature calculation were found to yield mostly similar overall tendencies of DNA curvature in all groups of sequences. According to all methods of calculation, E. coli promoters were found to be more curved than coding sequences from the same genome and random sequences with the same nucleotide composition. By contrast, the average curvature of human promoter sequences was only marginally greater than the average curvature of human coding sequences. Non-coding intron sequences were found to be the most curved of the human sequences examined. Based on these observations, we hypothesize about the role of DNA curvature in promoter sequences.
Key words: DNA curvature, bendability, sequence analysis