Correlation between the rate of productive transcription initiation and the strand-melting property of Escherichia coli promoters.
"Opening potential"s of DNA segments of about ten base pairs in length were calculated for eleven promoters of Escherichia coli using the thermodynamic parameter values [Gotoh and Tagashira (1981) Biopolymers 20, 1043-1058] for the stabilities of ten kinds of nearest neighbor base pair doublets in a melting reaction. They were compared with the strength of each promoter determined experimentally with a "mixed transcription" system [Kajitani and Ishihama (1983) Nucleic Acids Res. 11, 3873-3888]. A positive correlation was found between the calculated opening potential in the -9 to +3 region (+1 denotes the nucleotide position at which the transcription starts) and the rate of open complex formation.
Tachibana
H
H
Ishihama
A
A
D001483:Base Sequence; D004269:DNA, Bacterial / Q000235:genetics*; D004926:Escherichia coli / Q000235:genetics*; D006860:Hydrogen Bonding; D009691:Nucleic Acid Denaturation; D011401:Promoter Regions, Genetic; D012329:RNA, Bacterial / Q000096:biosynthesis; D013329:Structure-Activity Relationship; D013816:Thermodynamics; D014158:Transcription, Genetic
D004269:DNA, Bacterial; D012329:RNA, Bacterial