Facts & News

Jesse Stombaugh, Craig L. Zirbel, Eric Westhof and Neocles Leontis, NAR, 2009, 37, 2294-2312

The questions remains as to the ability of FR3D to go past rnaview in identification of base-pairs with the Leontis-Westhof annotation. That is, is it the case now that no N.A. base-pairs appear in the output? Hopefully it is.

Jin-Der Wen, Laura Lancaster, Courtney Hodges, Ana-Carolina Zeri, Shige H. Yoshimura, Harry F. Noller, Carlos Bustamante, Ignacio Tinoco, Nature, 452, 598-603, 3 April 2008
DOI: 10.1038/nature06716

Using single molecule spectroscopy Tinoco and collaborators have followed the translation in a single ribosome of and mRNA made up of a 60 bp-hairpin, a GUAA and GUUU tetraloop, and a 49 nucleotide 5' ss region. They have also used a larger mRNA composed of 274 b-p.

Naoko Abe, Hiroshi Abe and Yoshihiro Ito. JACS, 15 November 2007.
DOI: 10.1021/ja0754453

Ito el al. have synthesized dumbbell RNA's just as had been done before for DNA's by Breslauer et al. (Biochemistry, 1989, 28, 268-273). The utility of this dumbbell RNA's is in RNA interference, they are proven to be more stable to enzymatic degradation and at the same time offer longer RNAi acitivity since the shape does not offer loose ends for enzyme degradation. They have synthesized and compared four different sized dumbbells, that is, Db-15, Db-19, Db-23, Db-27, where the number refers to the size of the double stranded A-type region, the hairloops at the ends of the dumbells are of 9nt size.

David R. Corey and Bethany Janowski, Nat. Chem. Biol. 2007

Taken from C&EN February 5, 2007
Short pieces of double-stranded RNA may be able to activate gene expression. They target DNA instead of targeting mRNA as it happens in RNAi.

Gottesman et al. Science, 26 January 2007

Taken from C&EN January 22, 2007
Gottesman et al. have found that silent genes are no longer silent. They believe that the resulting proteins will differ in shape due to the different dynamics of their folding. The "silent" genes will act as delayers, and so the final configurational state that proteins with the same aminoacid sequence will fold to, when different synonymous genes are coding for the same aminoacid, will be different.

J. Chem. Theory Comput. 2006, 2, 1444-1452

The influence of stacking on the HB donating potential was shown to be dominated by the stacking geometry and not by the nature of the stacking partner. The present findings suggest that the pi-pi interaction on itself does not have an overall strengthening on H bonding in DNA.

Moore and Steitz, Tr. in Bioch. Sci. June 2005

There is still no atomic-resolution structure for a 70S ribosome in any of its states. Consequently, we have no idea why the peptydil-transferase activity of the 70S ribosome is ~10^4 times that of its isolated 50S subunit.

Onoa and Tinoco, Curr. Op. Str. Bio. 2003

The ultimate application of a better understanding of RNA folding is to predict the folded, partially folded and unfolded states of any RNA in physiological environment.

Chen and Dill, PNAS, 2002

The principle that emerges, for which there is growing experimental support, is that although protein folding tends to involve highly cooperative two-state thermodynamic transitions, without detectable intermediates, the folding of RNA secondary structures may involve rugged landscapes, often with more complex intermediate states.

Tianbing Xia, David H. Mathews and Douglas H. Turner, RNA, Pergamon Press 2001, Thermodynamics of RNA Secondary Structure Formation

Sequences with identical composition but different permutations of base pairs may have different free energy changes for duplex formation. For example, the duplexes (5'GUUCGAAC3')2 and (5'UUGGCCAA3')2 both have four AU and four GC base pairs, but have free energy changes of duplex formation at 37 C of -8.8 and -11.0 kcal mol-1, respectively. This difference of 2.2 kcal mol-1 translates into a 35-fold difference in equilibrium constants for duplex formation at 37 C. Thus, stability depends on more than the number of hydrogen bonds formed. Presumably, vertical stacking interactions between neighboring base pairs are the sequence-dependent variable.