Friday, March 26, 2010

RNA Secondary Structure Drawing

RNA Secondary Structure drawing can be a very time consuming task, and many times it ends on tediously annotating an existent map using photoshop. Fortunately the people who are involved in developing programs to solve such task are getting better and better, although, for the ribosome, they're not there yet.
To summarize these are the programs and groups which can do the task:

Assemble by Fabrice Jossinet
http://serialized-thoughts.blogspot.com/

VARNA by Kevin Darty, Alain Denise and Yann Ponty
http://varna.lri.fr/index.html

Pseudo-viewer by Y. Byun and K. Han
http://wilab.inha.ac.kr/pseudoviewer

RNAMovies by Uni. Bielefeld group, Robert Giegerich, Dirk J. Evers
http://bibiserv.techfak.uni-bielefeld.de/rnamovies

XRNA by Noller lab.
http://rna.ucsc.edu/rnacenter/xrna/xrna.html

RNAstructure by Mathews/Turner labs.
http://rna.urmc.rochester.edu/RNAstructure.html

Tuesday, March 23, 2010

What is a non-structured RNA?

Westhof reviews an article of Weinberg at Breaker's lab (@ Yale) in Genome Biology, 2010, 11, 108.


I can't help but to wonder what non-structured RNA's are, and where one can find them.
Westhof is surprised about the possible emergence of a "whole new" wealth of structured RNA's, but then this makes me wonder what can a non-structured RNA possibly be?, and where are they at?, which shows my need to have a biologist friend. It also makes me wonder about mRNA structure, and why it remains, unstructured, if such is the case, is it due to temperature? Is it due to environment?, I mean, after what temperature are bases not so fond of base-pairing or stacking or, under which environments, meaning, more or less hydrated, closer or not to proteins, etc.

Song Cao, David P. Giedroc and Shi-Jie Chen in RNA 2010 16 538-552.


They extend Flory-Olson, virtual bond idea for RNA, to a new virtual bond between the C4' atom in the sugar, and the N9(N1) atom in the base, to predict loop–helix tertiary structural contacts in RNA pseudoknots, they have a program called V-fold which instantiates the model.
The picture for the, perhaps new (don't know for sure), virtual bond, follows:



J Comput Chem. 2010 Mar 17. Novel graph distance matrix. Randić M, Pisanski T, Novič M, Plavšić D.


And to wrap up these post on new articles for the week, Randic is at it again. He has published a paper which reviews graph distance matrices and proposes a new one which, he claims, can be used to describe 3D graphs of molecules, not just 2D, and in a different way to the D/D matrix which he has previously proposed. The new distance matrix is called ND (Novel Distance), and it's just the Euclidean Distance matrix of the Adjacency matrix of a molecular graph. YES!, that simple.

Monday, March 1, 2010

Weekly Briefing on RNA

In Zurich they (Erata, Kovacs, Sigel) find that using some type of fancy NMR technique called "(2)J-[(1)H,(15)N]-HSQC (Heteronuclear Single Quantum Coherence) NMR", they can find easier and faster ion bindings to N7 of RNA's Adenine and Guanine, that is, their Hoogsten "face". They use a 27 nucleotide domain 6 of group II Intron to prove their technique.

- J. Am. Chem. Soc., 2010, 132 (11), pp 3668–3669
Jacobs, Resendiz and Greenberg at Johns Hopkins do a direct strand breaking by creating a Uracil radical which then abstracts the C2' hydrogen from the sugar creating a C2' sugar radical which then follows by breakage of the C5' to O5' bond in the backbone. The backbone breakage in aerobic conditions is 1/7 that of the anaerobic case.






Weiss, Zhai, Bhatia and Romaniuk at British Columbia Canada have made an RNA aptamer which binds preferentially to Zinc Fingers (A common protein motif).