FLEXIBILITY OF DNA
Kristian Vlahovicek and Sandor Pongor
International Centre for Genetic Engineering and
Biotechnology (ICGEB), Area Science Park, Padriciano 99, 34012
Trieste, Italy,
E-mail: pongor@icgeb.trieste.it
The dynamic ability of DNA to bend is thought to be a crucial factor influencing DNA topology in processes such as gene regulation, packaging and DNA replication. 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 can be used to compute numeric indices for bendability and curvature propensity [2]. Clusters of bendable, stiff and curved DNA segments are observed in a number of genomic sequences including the H. influenzae, the M. genitalium, the M. jannaschii, the S. cerevisiae genome, as well as a number of mitochondrial and viral genomes. Many of these coincide with known functionally important sites. Bendability parameters can be used to construct realistic anisotropic elastic models of DNA [3] which account for the DNA-binding affinity of Cro protein [4] as well as for metal-induced kinking of DNA[7]. Binding site selection for artificial DNA-binding proteins also shows that bendability characteristics are important in regions not directly contacted by the protein [5] Both the bendability characteristics [2], and the calculated static curvature of DNA show particular distributions within the various genomes. The possibility that DNA may contain localized conformational signals, in addition to the information stored in the base sequence, was first raised in theory more than 15 years ago [6]. The dynamic bendability/static curvature characteristics of DNA meet the basic criteria of conservation and uniqueness expected from such conformational signals [7].