- For transcription initiation the DNA template must be
brought into the polymerase active site and held stably in a helical
conformation and that the initiating ribo-nucleotide be brought into the active
site and held stably on the template while the next NTP is presented with
correct geometry for the chemistry of polymerization to occur.
- This is particularly difficult because RNA polymerase starts
most transcripts with an A, and that ribonucleotide binds the template
nucleotide (T) with only two hydrogen bonds (as opposed to the three between C
and G).
- Thus, the enzyme has to make specific interactions with one
or all of the DNA template strand, the initiating ribonucleotide, and the second
ribonucleotide- holding one (or all) rigidly in the correct orientation to
allow chemical attack on the incoming NTP.
- The requirement for such specific interactions
between the enzyme and the initiating nucleotide probably explains why most
transcripts start with the same nucleotid
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