Search for DNA conformational features for functional sites. Investigation of the TATA box.
A method for search of DNA conformational features significant for functional sites is developed. The method uses helical angles averaged for known X-ray structures. Nucleotide sequences are assigned mean angles in a given region. Choice of the significant angles is based on their capabilities to discriminate functional sites from random sequences. The yeast, invertebrate and vertebrate TATA boxes are analyzed using this method. Regions neighboring the TATA boxes are found to have smaller helical twist and roll angles. The results agree with the experimental data on Dickerson-Drew dodecamers. There is a significant decrease in the length of a small roll angle region with increasing complexity of taxon organization.
Ponomarenko
M P
MP
Institute of Cytology and Genetics, Novosibirsk, Russia.
Ponomarenko
J V
JV
Kel
A E
AE
Kolchanov
N A
NA
D000818:Animals; D001483:Base Sequence; D018360:Crystallography, X-Ray; D004247:DNA / Q000737:chemistry* / Q000235:genetics*; D004271:DNA, Fungal / Q000737:chemistry / Q000235:genetics; D015226:Dinucleoside Phosphates / Q000737:chemistry*; D004926:Escherichia coli; D019143:Evolution, Molecular; D007448:Invertebrates; D009690:Nucleic Acid Conformation; D011401:Promoter Regions, Genetic; D012441:Saccharomyces cerevisiae; D014714:Vertebrates
D004271:DNA, Fungal; D015226:Dinucleoside Phosphates; D004247:DNA