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.
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