In intrinsic termination, the RNA transcript doubles back and base pairs with itself, creating an RNA stem-loop, or hairpin, structure. This structure is critical for the release of both the transcript and polymerase at the end of transcription. In living cells, the key components are the stable stem-loop itself, as well as the sequence of 6-8 uracil residues that follow it. The stem usually consists of 8-9 mostly guanine and cytosine (G-C) base pairs, and the loop consists of 4-8 residues. It is thought that the stem portion of the structure is essential for transcription termination, while the loop is not. This is suggested by the fact that termination can be achieved in non-native structures that do not include the loop.
The stem portion of the hairpin is usually rich in G-C base pairs. G-C base pairs have significant base-stacking interactions, and can form three hydrogen bonds with each other, which makes them very thermodynamically favorable. Conversely, while the uracil-rich sequence that follows the hairpin is not always necessary for termination, it is hypothesized that the uracil-rich sequence aids in intrinsic termination because the U-A bond is not as strong as G-C bonds. This inherent instability acts to kinetically favor the dissociation of the RNA transcript.