Monday, December 19, 2011

Weekly RNA News - Week LI - December 2011

Top News of the Year.
According to Chemical and Engineering News

- Spliceosome Assembly Tracking by New Fluorescent Microscopy Technique
Melissa J. Moore at U. Mass. Medical, Jeff Gelles at Brandeis, Virginia Cornish at Columbia.
http://dx.doi.org/10.1126/science.1198830

These researchers use a new spectroscopic technique called Colocalization Single-Molecule Spectroscopy (CoSMOs) to track the dynamics of formation of the spliceosome. They corroborate what has been proposed before where the order of association of the spliceosome on the pre-mRNA is U1 -> U2 -> tri-snRNP (U4/U6.U5) -> NTC (multiprotein Prp 19-complex)
To summarize nothing better than their own mechanistic picture with estimated first order reaction constants.

So. I have been looking for the molecular weight of the Spliceosome for a while now and can't find it. I find that parts of it are around 200kDa, but I don't even know how much the so-called tri-snRNP assembly weighs. If you find it I would appreciate your feedback very much. The prokaryotic ribosome weighs about 2600 kDa.

- Modified Citosine
Guo-Liang Xu from Academy of Science of China and Chuan He from Chicago U.
http://dx.doi.org/10.1126/science.1210944

Evidence for Tighter Wrapping of DNA upon Methylation.
According to Chemical and Engineering News

On the science and technology concentrates from this week on C&EN, work on changes on DNA wrapping around the nucleosome are reported. The work comes from researchers Ju Yeon Lee and Tae-Hee Lee at Penn. State. In the article titled "Effects of DNA Methylation on the Structure of Nucleosome" http://dx.doi.org/10.1021/ja210273w published in the Journal of the American Chemical Society

Monday, December 12, 2011

Weekly RNA News - Week L - December 2011

Is Arsenic-DNA Possible?
A Controversy is Born.

For better or worse Felisa Wolfe-Simon, a research fellow at NASA's Astrobiology unit became a scientific celebrity a year ago. In an express paper to the highest ranked North-American journal, that is, Science,  Dr. Wolfe-Simon (who received her PhD from Rutgers in Oceanography) reported, along with her collaborators that:

"A Bacterium Can Grow by Using Arsenic Instead of Phosphorus"

The bacterium was taken from Mono Lake, California, a  "hypersaline and alkaline environment", as reported in the Science paper http://dx.doi.org/10.1126/science.1197258.
In the time since the express publication a number of papers have been written for, against, and in a neutral tone regarding the reported observations.

I find it interesting that before December 2010, that is, the date of the express report, Dr. Wolfe-Simon was already reporting along with Paul C. W. Davies (why is this name familiar?... ohhh, is the same guy of Superforce, the best-seller layman book on unification theory, a kind of Isaac Asimov guy!) on the Arsenic conjecture in a paper with the very suggestive title "Did Nature Also Choose Arsenic?" in the International Journal of Astrobiology, 2009, 8, 69-74.

Another one of the past collaborators of Dr. Wolfe-Simon and also a researcher at NASA's Astrobiology, but not a coauthor on the Science paper, that is, Steven A. Benner (not to be confused with Steven Brenner @ U.C. Berkeley) wrote a nice commentary  (http://dx.doi.org/10.1126/science.1201304) about the published paper. He highlights how the main problem with an arsenate-diester would be its estimated half-life in water, which, by back-of-the-envelope calculations, leads to a half-life which is too short (About 1 minute) compared to that of the phospho-diester backbone in DNA (About 30 million year). He also proposes and experiment which I'm sure a lot of researchers thought of when eyeing for the first time the Arsenic life report, that is, to use an Arsenic isotope.

One of many papers (http://dx.doi.org/10.4161/adna.2.1.15509) with some criticism is that of Frank-Kamenetskii of B.U published in a new journal named Artificial DNA, whose chief editor is PNA (Peptide Nucleic Acids) main-man Peter E. Nielsen, here it is:

"After all, recent history has taught the scientific community to be very skeptical to any unusual claim, especially appearing in such high-profile journals like Nature and Science. It suffices to  mention the most recent embarrassment with publication in  Science, with loud fanfares, of an article about “arsenic life”.
Once someone reads carefully the article and supporting data, it becomes clear that the data by no means support the claim that arsenic substitutes phosphorus in DNA of a bacterial strain obtained by the authors."

On the other hand theoreticians and modelers have not been shy on jumping right into the problem, two examples are the publications by  Liz Denning at Alex Mackerell group in Maryland (http://pubs.acs.org/doi/abs/10.1021/ja201213b) and Jiri Sponer's group at Brno, Czech Republic (http://dx.doi.org/10.1021/jz200015n).

In conclusion, this story just gets more interesting as it ages. On a personal note I would have to say that on my first read of the paper my thoughts were very close to those of the wise Maxim, but now I'm not so sure and see a window of possibility on this most interesting result. Only time and hopefully Felisa Wolfe-Simon will be able to wrap-up this story on whether she's found a very interesting extremophile, or an alien living among us.


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An update on my last comment is that there seems to be no results from Wolfe-Simon proving the much publicized article and it's critics are getting some interesting results in the sort of un-asked-for peer-review, as can be see in an article posted to arxiv called "Absence of arsenate in DNA from arsenate-grown GFAJ-1 cells". There is also an iteresting posting of some of the reviewers opinions at Redfield's website.