RNA tertiary structures

The folding of RNA into a compact 3D structure is stabilized by tertiary interactions, which depend both on the nucleotide sequence and on the secondary structure. Although these interactions are structurally very diverse, some common features have been defined. 

Triple-base pairs single-strand helix interactions) 

Triple-base pairs occur when single-stranded nucleotides make hydrogen bonds with a Watson-Crick base pair. The third base may interact either within the major or the minor groove of the Watson-Crick base pair. For example, the folding of tRNA is stabilized by triple-base pairs between the junction loop and bases in the major groove of stem D. Also, a triple-base pair (UAU), between a U in a bulge and the U-A in the adjacent helix, is essential for the conformation of the binding site for human HIV protein Tat on TAR. 

Pseudoknots single-strand single-strand interaction) 

Originally, the terms knot or pseudoknot were used for any tertiary interaction between unpaired nucleotides in the secondary structure. However, recently the term pseudoknot is used more specifically to describe Watson-Crick base pairing between bases in single-stranded loops and bases outside the loop (Fig. 1.1). The 

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Strobel, S. A., and Doudna, J. A. (1997). RNA seeing double Close-packing of helices in RNA tertiary structure. Trends Biochem. Sci. 22, 262—266. 

Grilley, D., Misra, V., et al. (2007). Importance of partially unfolded conformations for Mg (2+)-induced folding of RNA tertiary structure Structural models and free energies of Mg2+ interactions. Biochemistry 46(36), 10266—10278. 

Das, R., and Baker, D. (2007). Automated de novo prediction of native-like RNA tertiary structures. Proc. Natl. Acad. Sci. USA 104, 14664—14669. 

Figure 21.2 Monovalent salt dependences for the formation of RNA tertiary structures. For both RNAs shown, log(Kobs) was calculated at 20 °C from the melting temperature (7 ln) and enthalpy (AH ) of the tertiary folding transition observed in melting curves by the formula ln(lC0i,s) = — (H /R) (1 / 7, 1/T0), where R is the gas...

Bukhman, Y. V., and Draper, D. E. (1997). Affinities and selectivities of divalent cation binding sites within an RNA tertiary structure. J. Mol. Biol. 273, 1020—1031. 

Leipply, D., and Draper, D. E. (2009). The dependence of RNA tertiary structure stability on Mg(2+) concentration Interpretation of the Hill equation and coefficient (submitted). 

Metal ions bound site-specifically within the RNA tertiary structure could induce cleavage of the phosphodiester backbone near the binding sites. One group of metal ions, including... 

Sigurdsson ST, Tuschl T, Eckstein F. Probing RNA tertiary structure interhelical crosslinking of the hammerhead ribozyme. RNA 1995 1 575-583. 

Since the secondary structure is not uniform along the length of the RNA chain, more variety is allowed in RNA tertiary structure. Three types of RNA molecules have been identified with different cell functions. The three are messenger RNA (mRNA), transfer RNA (tRNA), and ribosomal RNA (rRNA). 

Kim NK, Bowman MK, DeRose VJ (2010) Precise mapping of RNA tertiary structure via nanometer distance measurements with double electron-electron resonance spectroscopy. J Am Chem Soc 132(26) 8882-8884. doi 10.1021/Jal01317g... 

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