Structure Motifs of RNA

RNA motifs refer to the small, finite and natmaUy occurring structmal elements of RNAs that are present abundantly as non-canonical bps in hairpins/loops (loop motifs) and sequences involved in tertiary interactions (tertiary motifs). The most important secondary structural element in RNA is the A-form double helix (A-helix). However, motifs. 

1 Terminal loop motifs. A terminal loop is any sequence where RNA folds back on itself so that a stem can form and highly abundant in terminal loops. They are  

U-Turn The U-tum is common at the apices of the anticodon loops of tRNAs and an invariant feature of their T / loops. The consensus sequence for U-tum is unpaired UNRN (N for any bases and R for any purines). In T / loops, U is replaced by pseudouridine. The turns which are stabilized by hydrogen bonds between imino proton of U(l) and a phosphate oxygen of R(3), and between 2 -OH of U(l) and N of R(3), introduce an abmpt 180° change in the backbone direction of larger loops. 

2 Internal loop motifs. An internal loop is a sequence of bases within an A- 

Cross-strand purine stacks The cross-strand (rather than same-strand) stacking formed by the six-member ring of an A or G in one strand stacks on the six-manber of an A or G in the other (either A s stack on A s or G s stack on G s). The consensns sequence for cross-strand A-stack motifs is 5 (G/C)(G/A)A 3 (C/G)A(U/A). The initial (G C) pair is Watson-Crick type. The next pair is usually side-by-side (A G) or (A A via AN — N3 A) and the following pair can be either reversed Hoogsteen (A U vis UN3— Ny, UO2— N6A) or side-by-side AA. Additional nonhelical sequence must follow before an internal loop containing a cross-strand A-stack can be terminated and A-helix resumes. 

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A pseudoknot is a double-hairpin structure with an extended quasi-continuous double-helical stem region (Fig. 1.15). It is formed when bases outside a hairpin structure pair with bases within the hairpin or internal loop (111,112). The pseudoknot is a potentially important tertiary structural motif of RNA and it has been identified in 16S rRNA, U2 snRNA, and some plant viral RNAs with tRNA-... 

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