Monday, July 25, 2011

Weekly RNA News - Week XXIX - July 2011

RNA is back in the front page news of "The New York Times".
A note by some guy called Dennis Overbye is bringing back news on RNA to the front pages. Well, really the news are not so new, but it's good to see that folks are still interested in the origin of life, of course, this is not at all to be unexpected since the main "hot-shot" in the article is Gerald Joyce, and yes, if that name rings a bell it's because is intimately associated with that of the great Leslie Orgel.
Joyce might have been the favorite grad. student of Orgel, and, actually must consider himself quite lucky since Orgel liked to work alone and seldom gave the privilege of coauthorship. Now, what's interesting is that, even though the article is well written and well informed and gives good credit to people like Alex Rich, it also states:

"The first inhabitant of this Eden, chemists suspect, was RNA"

And doesn't even give a small paragraph to say, that chemists also suspect that it could have been a pre-RNA molecule.

Evidence for a thermodynamically distinct Mg2+ ion associated with formation of an RNA tertiary structure
Desirae Leipply and David E. Draper
JACS, XX, xx-xx(2011)
Nice article showing a technique to be able to distinguish two types of association of Mg2+ ions to RNA.
The main idea the article exposes is that Mg2+ ions can interact with RNA's in two ways. In most cases they can form an ion atmosphere (purple haze in image) around the RNA, and in other cases they can get stuck in confined regions (site-bound - brown dot in image) and as such are considered as chelators.

They propose experiments where the free energies of these different ways of binding can be determined.



In the next image the larger green sphere represents a Magnesium site-bound to RNA. The purple, larger sphere is potassium also site-bound, and the surface is the solvent accessible surface mapped with the color of the electrostatic potential. In the right the secondary structure corresponding to structure PDB_ID:1hc8



Effect of Locked Nucleic Acid Modification on Thermal Stability of Non-canonical DNA Structure
Bhattacharyya J, Maiti S, Muhuri S, Nakano SI, Miyoshi D, Sugimoto N
Biochemistry, XX, xx-xx(2011)

A fast look at this paper shows that there are no references whatsoever to the structural work either from modelling studies of Pande and Nilsson, or to the experimental one of Eichert, Forster and collaborators.
Perhaps since they've focused their attention in parallel instead of the more common antiparallel strands, then they didn't worry so much about LNA studies on antiparallel DNA strands.

Thursday, July 21, 2011

Weekly RNA News - Week XXVIII - July 2011

The Endless Subtleties of RNA-Protein Complexes
Eric Westhof and Valerie Fritsch
Structure, 19, 902-903 (2011)

As in other occasions the authors give a good idea of what is to come in the field of RNA, or at least, what would be nice to see coming. In this case they comment on the work done at Juli Feigon's lab at UCLA on the interaction of a protein which binds a double-stranded RNA region of around 14 base-pairs and which contains two G.U wobble base-pairs and is flanked by a tetraloop. Westhof and Fritsch mention two tricks by which proteins can recognize double-stranded RNA helical regions. One is that the helical region per-se is "altered" from a canonical Watson-Crick paired one through bulges in the helical stem or non-canonical pairings modulating it's major groove so that it looks more like a B-DNA conformation one, that is, one which is wider and not as narrow, allowing for sequence recognition. The second trick, and which is the one adopted by the dsRBD (double-stranded RNA Binding Domain) of the reviewed NMR structural work, is that of interacting with the single nucleotides of the loop region. The Feigon lab. work shows how a tetraloop with a different sequence than the "canonical" AGNN one, but which accomplishes a very similar three dimensional fold, can also be bound by the dsRBD showing that not all can be predicted through RNA sequence alone, but that structural data is essential for understanding the details of protein-RNA interactions.
The Structures under PDB_ID: 2LBS have not been released yet.