International Centre for Genetic Engineering and Biotechnology (ICGEB), Area Science Park, Padriciano 99, 34012 Trieste, Italy
The ability of DNA to bend is thought to play important roles in processes such as gene regulation, packaging and DNA replication and is thought to be a crucial factor influencing DNA topology. Here we show that DNA sequences can be classified into groups according to their local bendability characteristics using trinucleotide parameters derived from deoxyribonuclease I cleavage experiments [1]. A vector representation of DNA bendability is used to compute numeric indices for bendability and curvature. Clusters of bendable, stiff and curved DNA segments are observed in a number of genomic sequences including the Haemophilus influenzae, the Mycoplasma genitalium genomes as well as the S. cerevisiae genome, and many of these coincide with known functionally important sites [2,3]. The non protein-coding parts of the eukaryotic genomes contain a large number of segments with extreme bendability characteristics while prokaryotic genomes have a less pronounced but detectable difference between their coding and non- coding portions. Highly curved segments - similar to artificially designed curved oligonucleotides - are extremely rare in natural DNA. The possibility that DNA may contain localized conformational signals, in addition to the information stored in the base sequence, has been raised more than 15 years ago [4]. It appears that bendability characteristics meet the basic criteria of conservation and uniqueness expected from such conformational signals.
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dependent bending propensity of DNA as revealed by DNase I: parameters
for trinucleotides. EMBO J., 14, 1812-1818.
[2] Gabrielian,A, Simoncsits, A. and Pongor,S. (1996) Distribution
of bending propensity in DNA sequences, FEBS Letters, 393, 124-130
[3] Gabrielian,A. and Pongor,S. (1996) Correlation of intrinsic DNA
curvature with DNA property periodicity, FEBS Letters, 393, 65-68
[4] Trifonov, E.N. and Sussman, J.L. (1980) The pitch of chromatin
DNA is reflected in its nucleotide sequence. Proc. Natnl. Acad. Sci.
USA ,77, 3816-3820.