title: The distributions of nucleotides near bacterial transcription initiation and termination sites show distinct signals that may affect DNA geometry.
abstract: Compilation and analysis of all bacterial sequences which are aligned by their transcription initiation sites show a dramatic behavior of the four nucleotides. Large peaks of T and A are observed. This highly nonrandom distribution is likely to affect the DNA geometry in addition to affecting the strength of binding between the two DNA strands. Following this site, the G and C rise above their overall bacterial mean. Alignment by transcription termination sites indicates that this behavior continues till the mRNA 3' termini. At this site the concentrations of A and T rise again above the mean. Analysis of the distributions of the 256 quartets in the 1000 nucleotide regions surrounding both transcription initiation and termination sites has been carried out. Some A/T combination sequences may serve as signals to the bacterial transcription machinery, in addition to the well-established TTGACA and TATAAT at positions -35 and -10, respectively, and a run of Ts at the transcription termination site. The frequent occurrences of (dA)/(dT) runs in the vicinity of these sites may result in curved DNA structures, affecting recognition and the nature of the interaction between the RNA polymerase and the DNA.
mesh_terms: D001419:Bacteria / Q000235:genetics; D005075:Biological Evolution; D004269:DNA, Bacterial / Q000235:genetics*; D005796:Genes; D005798:Genes, Bacterial; D009690:Nucleic Acid Conformation; D012333:RNA, Messenger / Q000235:genetics; D014158:Transcription, Genetic
chemical_list: D004269:DNA, Bacterial; D012333:RNA, Messenger