Tuesday, April 5, 2011

Weekly RNA News - Week XII - March 2011

A. Vazquez-Mayagoitia and S.R. Horton and B.G. Sumpter and J. Sponer and J.E. Sponer and M. Fuentes-Cabrera
Ab-initio modeling of a possible prebiotic reaction favors ribose over other possible sugars.
Astrobiology, 11, 115-121 (2011)
Many of us like to munch from time to time into the big question. That of the origin of life. Frankly, my guess is that anyone who works with RNA at any level is always tickled, to varying levels, by the big question. The authors of the referenced paper show a detailed quantum mechanical Ab-intio study on a so-called "silicate-mediated formose reaction" which, they show, by energetically favoring arguments, prefers ribose over other sugary options.

Robert V Brown; Laurence H Hurley @ Uni. Arizona
A Review of Cases where DNA might act like RNA
Biochemical Society Transactions, 39, 635-640 (2011)
A fun review mainly concerning the G-quadruplex and how this, and other DNA conformations with loops, for example, might behave in a similar fashion to RNA. It´s interesting to see their reproduced graph of the relation between G-quadruplexes and cancer.

Weekly RNA News - Week XI - March 2011

Jun Feng and Nils G. Walter and Charles L. Brooks, III @ University of Michigan
All-atom Go model study of preQ1 riboswitch aptamer domain folding.
Journal of the American Chemical Society, 133, 4196-4199 (2011)
Feng, Walter and Brooks present interesting results using a Go model for simulating the folding of an RNA sequence into a riboswitch aptamer in the presence of a metabolite called preQ1. The model used seems to favor a description of a funnel shaped free-energy landscape for the folding of this RNA riboswitch. It's interesting to see that what is described as a structure made of two helices called P1 and P2 could also be described as an "irregular" triple-helix:
Some very interesting thoughts come out from reading this article. The folding of this riboswitches must be pretty fast, pico, nano seconds? so, these are good cases for performing MD simulations. In general the folding of parts of mRNA into structured regions seem to be good targets for MD research. I also wonder if the methodology used can take into account the possibility of having a rugged RNA folding landscape and if such case would influence the sequential and cooperative folding mechanism results.
Other things which would be interesting to see are the electrostatics of the A-tract of the folded configuration, for example.

Martin Mann and Konstantin Klemm @ Freiburg & Leipzig
Efficient exploration of discrete energy landscapes
Physical Review E, 83, 1-7 (2011)
The authors use a so-called number partitioning problem, which is common in computer science, to be able to stochasically sample the free energy landscape of RNA secondary structures.