Slippery sequence


A slippery sequence is a small section of codon nucleotide sequences that controls the rate and chance of ribosomal frameshifting. A slippery sequence causes a faster ribosomal transfer which in turn can cause the reading ribosome to "slip." This allows a tRNA to shift by 1 base after it has paired with its anticodon, changing the reading frame. A −1 frameshift triggered by a sequence like such is a Programmed −1 Ribosomal Frameshift. It is followed by a spacer region, and an RNA secondary structure. Such sequences are common in virus polyproteins.
The frameshift occurs due to wobble pairing. The Gibbs free energy of secondary structures downstream give a hint at how often frameshift happens. Tension on the mRNA molecule also plays a role. A list of slippery sequences found in animal viruses is available from Huang et al.
Slippery sequences that cause a 2-base slip have been constructed out of the HIV UUUUUUA sequence.