Slippery sequence explained

A slippery sequence is a small section of codon nucleotide sequences (usually UUUAAAC) 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 (−1) after it has paired with its anticodon, changing the reading frame.^{[1] [2] [3] [4] [5]} A −1 frameshift triggered by such a sequence 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.^[6] Tension on the mRNA molecule also plays a role. A list of slippery sequences found in animal viruses is available from Huang et al.^[7]

Slippery sequences that cause a 2-base slip (−2 frameshift) have been constructed out of the HIV UUUUUUA sequence.^[8]

See also

• Nucleic acid tertiary structure
• Open reading frame
• Ribosomal frameshifting
• Translational frameshift
• Transposable element

External links

• Pseudobase
• Recode
  • Wise2 - aligns a protein against a DNA sequence allowing frameshifts and introns
• FastY - compare a DNA sequence to a protein sequence database, allowing gaps and frameshifts
• Path - tool that compares two frameshift proteins (back-translation principle)
• Recode2 - Database of recoded genes, including those that require programmed Translational frameshift.

Notes and References

1. Green L, Kim CH, Bustamante C, Tinoco I . Characterization of the mechanical unfolding of RNA pseudoknots . Journal of Molecular Biology . 375 . 2 . 511–28 . January 2008 . 18021801 . 10.1016/j.jmb.2007.05.058 . 7094456 .
2. Yu CH, Noteborn MH, Olsthoorn RC . Stimulation of ribosomal frameshifting by antisense LNA . Nucleic Acids Research . 38 . 22 . 8277–83 . December 2010 . 20693527 . 3001050 . 10.1093/nar/gkq650 .
3. Web site: Dr Ian Brierley Research description . Department of Pathology, University of Cambridge . 2013-07-28 . dead . https://web.archive.org/web/20131002121121/http://www.path.cam.ac.uk/research/investigators/brierley/research.html . 2013-10-02 .
4. Web site: Molecular Biology: Frameshifting occurs at slippery sequences . Molecularstudy.blogspot.com . 2012-10-16. 2013-07-28.
5. Farabaugh PJ, Björk GR . How translational accuracy influences reading frame maintenance . The EMBO Journal . 18 . 6 . 1427–34 . March 1999 . 10075915 . 1171232 . 10.1093/emboj/18.6.1427 .
6. Cao S, Chen SJ . Predicting ribosomal frameshifting efficiency . Physical Biology . 5 . 1 . 016002 . March 2008 . 18367782 . 2442619 . 10.1088/1478-3975/5/1/016002 . 2008PhBio...5a6002C .
7. Huang X, Cheng Q, Du Z . A genome-wide analysis of RNA pseudoknots that stimulate efficient -1 ribosomal frameshifting or readthrough in animal viruses . BioMed Research International . 2013 . 984028 . 2013 . 24298557 . 3835772 . 10.1155/2013/984028 . free .
8. Lin Z, Gilbert RJ, Brierley I . Spacer-length dependence of programmed -1 or -2 ribosomal frameshifting on a U6A heptamer supports a role for messenger RNA (mRNA) tension in frameshifting . Nucleic Acids Research . 40 . 17 . 8674–89 . September 2012 . 22743270 . 3458567 . 10.1093/nar/gks629 . free .