Analysis of DNA curvature distribution in mycobacterial promoters using theoretical models.
In this paper, 125 different mycobacterial promoters are analyzed for their DNA curvature distribution using several di- and tri-nucleotide dependent models of DNA curvature. Different models give similar behavior and therefore qualitative validation of the results. Mycobacterial promoters resembling the E. coli sigma(70) type have almost 81% (85%) sequences having medium and high curvature profiles using dinucleotide-dependent models. Non-E. coli sigma(70) type mycobacterial promoters have comparatively higher percent of low curvature profiles. Very few extended -10 promoters have low curvature profiles. Mycobacterial promoters having A(n)T(m) (n+m > or =3) tract in the upstream region of -35 box and repeated in phase with each other have high curvature profiles. M. smegmatis promoters have high curvature profiles compared to M. tuberculosis promoters.
Kalate
Rupali N
RN
Chemical Engineering Division, National Chemical Laboratory, Pune 411 008, India.
Kulkarni
B D
BD
Nagaraja
V
V
D001483:Base Sequence; D004247:DNA / Q000737:chemistry* / Q000235:genetics; D008957:Models, Genetic; D008969:Molecular Sequence Data; D009161:Mycobacterium / Q000235:genetics*; D009690:Nucleic Acid Conformation; D009841:Oligonucleotides; D011401:Promoter Regions, Genetic; D016415:Sequence Alignment
D009841:Oligonucleotides; D004247:DNA