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pubmed:abstractText |
The transcription bubble formed in the binding complex of T7A1 promoter upon Escherichia coli RNA polymerase was analyzed by chemical probes, namely by single-strand specific reagents, to map the unpaired bases in the bubble, and by FeEDTA, to analyze the accessibility of the DNA backbone. The latter probe could also be used as a local hydroxyl radical probe placed close to the Mg2+-binding site in the active center. The data show that the transcription bubble consists of two parts, an Mg2+-dependent part and an Mg2+-independent part, both having individual transition temperatures. The data further suggest that formation of a transcription active open complex is preceded by a transition state complex having enhanced affinity for those Mg2+ ions presumably participating in the formation of the catalytic site. Our data also suggests that the three catalytically active Mg2+ ions in RNA polymerase are functionally not equivalent. One/two of the three Mg2+ ions are responsible for the polymerization, the other two/one for enlargement of the transcription bubble.
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