Oritatami

Oritatami (折りたたみ, "folding") is a mathematical model describing cotranscriptional RNA folding.

Cotranscriptional RNA Folding

RNA is generated by the following process:

1. The enzyme RNAP (RNA polymerase) unzips a double-stranded DNA helix.

2. RNAP attaches to one of the unzipped strands at a promoting sequence of nucleotides.

3. RNAP travels linearly along the DNA strand from the promoter sequence, reading the DNA's nucleotides. As it does so, it adds the complementary ribonucleotides to the RNA strand growing out of it.

4. RNAP releases the grown RNA strand upon reading a terminating sequence of nucleotides.

Cotranscriptional folding occurs as the RNA strand is elongated. In other words, hydrogen bonds form between ribonucleotides in the strand as new ones are added to it, not afterword. Hence, the form of the strand at the time of its release is not simply that which has the minimum energy. Rather, it is the one which has "stepwise" minimum energy. At any point in time only the last few ribonucleotides in the sequence may rearrange themselves; the rest must preserve their existing bonds.