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