Selected article for: "frameshift pseudoknot and shift site"

Author: Atkins, John F.; Loughran, Gary; Bhatt, Pramod R.; Firth, Andrew E.; Baranov, Pavel V.
Title: Ribosomal frameshifting and transcriptional slippage: From genetic steganography and cryptography to adventitious use
  • Document date: 2016_9_6
  • ID: 0s8huajd_186
    Snippet: Studies of HIV recoding signal conformational changes were introduced at the start of this section because of the evidence for relevance of sequence both 5 and 3 of the shift site. Distinct from the techniques employed in its analysis, optical trapping has been used to reveal a dynamic ensemble of conformations of the mRNA encoding CCR5, a coreceptor for HIV-1, but their relevance to frameshifting requires further work (563) . However, it joins o.....
    Document: Studies of HIV recoding signal conformational changes were introduced at the start of this section because of the evidence for relevance of sequence both 5 and 3 of the shift site. Distinct from the techniques employed in its analysis, optical trapping has been used to reveal a dynamic ensemble of conformations of the mRNA encoding CCR5, a coreceptor for HIV-1, but their relevance to frameshifting requires further work (563) . However, it joins optical tweezers and others in the arsenal of techniques available. In contrast to several earlier proposals, optical tweezers experiments have strongly pointed to conformational dynamics (plasticity) being of prime relevance to frameshifting efficiency rather than the degree of pseudoknot resistance to mechanical unfolding (564) . Consistent with this, not all stable pseudoknots stimulate frameshifting and both structural (88, 565, 566) and mutational analysis of those that do, and do not, promote frameshifting has been insightful. There are many analyses of both categories but one of the mutational analyses is of the compact stimulatory pseudoknots of beet western yellows virus and potato leafroll virus where evidence has been obtained for certain bases being functionally significant but lacking substantial stability effects (567) . Studies with two pseudoknot stimulators show that frameshift efficiency is sensitive to the reading phase in which the translating ribosome encounters the pseudoknot but is not simply correlated with the extent of the associated translational pause (107) .

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