Two reviews have just come out from the Mondragón group at Northwestern and from the Pyle group at Yale.
Emerging Structural Themes in Large RNA Molecules
Nicholas J. Reiter, Clarence W. Chan and Alfonso Mondragón
Current Opinion in Structural Biology 21, 319-326 (2011)
In line with their previous research (i.e. the RNase P X-Ray structure, PDB_ID:3Q1Q) the authors stick to reviewing what has been learned from intermediate size RNA molecules, that is, RNA molecules larger than a hundred nucleotides, but smaller than say a thousand nucleotides.
The main points argued in this review are:
- RNA's of this size are relatively flat due to tertiary interactions, namely, "extensive" coaxial stacking, loop-loop interactions, and not mentioned in the review side by side helical arrangements.
- The structures of the functional cores of intermediate size RNA's are conserved, not necessarily the sequences.
- The functional cores don't need large conformational arrangements, they are said to be preassembled and usually this happens around a metal ion.
- Molecular recognition of "targets" is accomplished by shape-complementarity and specific atomic interactions (base-pairing, base-stacking, base-sugar, base-backbone). This is a general principle in molecular recognition.
- Adenine's are statistically more abundant than any other base in tertiary interacting regions, they are also the most conserved in all RNase P's.
- Proteins extend the functionality of RNA's and can be essential as in the case of the ribosome and the spliceosome, or non-essential, as in the case of RNase P and Group I and II Introns.
They conclude that the best is yet to come concerning RNA's in line with the promise, highly encouraged by Breaker's Lab. research, that many more RNA structures are to come and then this few empirical facts we've come to know will expand or change accordingly.
For the Group II Intron one can have an image like the above one, showing the helical regions as blue cylinders and the phosphates colored grey connected with a string in red, to illustrate the "flatness" of intermediate sized RNA's.
The Molecular Interactions That Stabilize RNA Tertiary Structure: RNA Motifs, Patterns, and Networks
Samuel E. Butcher and Anna Marie Pyle
Accounts of Chemical Research X, xxx-xxx (2011)
Interestingly enough the previous paper (the one of Reiter) comes from a whole issue devoted to nucleic acids and edited by Anna Pyle.
In this review Butcher and Pyle take a look at the main interactions and structural elements found in RNA's today.
These seem to be split into:
- Coaxial Stacking of Helical Regions.
- Geometric Organization of Helical Junctions.
- Long-Range Interactions of Watson-Crick Base-Pairs.
* Kissing-Loops.
* Pseudoknots.
- Minor Groove Triples and A-Minor Motifs.
- Kink Turns and Other Turn Motifs.
- Tetraloop-Receptor Motifs.
- Intercalation Motifs (T-Loops).
- Triple-stranded RNA's (more like RNA triplets)
- RNA Quadruplexes.
The final remarks on the review concern the nature of the ribose, the 2'-OH interactions (e.g. Ribose Zippers), metal ions (the description of new crystallographic results in accordance to Draper's seminal paper reviewed in this here blog) and non-canonical base-pairs.
In Figure 2 of the article an image of a kissing-loop interaction is shown. The following image reproduces such image with helical regions identified by 3DNA represented as blue cylinders.
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