Monday, November 21, 2011

Weekly RNA News - Week XLIV - November 2011

Meni Wanunu, Swati Bhattacharya, Yun Xie, Yitzhak Tor, Aleksei Aksimentiev, and Marija Drndic
Northeastern, Uni. Illinois and UCSD
Nanopore Analysis of Individual RNA/Antibiotic Complexes.

Nanopores in thin solid-state membranes are used to rapidly analyze individual RNA/drug complexes. The interactions of a truncated A-site RNA model of the prokaryotic ribosome with aminoglycoside antibiotics are characterized by passing individual molecules through a 3–3.5 nm diameter pore fabricated in a 8–10 nm thick silicon nitride membrane. Complexes of the A-site RNA with aminoglycosides can be distinguished from unbound A-site based on the ion current signatures produced as they pass through the nanopores. Counting the fraction of free and drug-bound molecules affords label-free drug–RNA binding isotherms consistent with literature reports and with data generated using independent fluorescence-based assays. Our measurements are supported by molecular dynamics simulations, which illustrate the relationship between the ionic current and complexation of the A-site RNA with paramomycin, a prototypical aminoglycoside antibiotic.

http://dx.doi.org/10.1021/nn203764j

Tuesday, November 15, 2011

Weekly RNA News - Week XLIII - November 2011

Lately I have been late on my weekly posts, so, for now I will only put some brief news until I find the time to write better posts.

- According to experiments carried out by Victoria Jeanne DeRose , Alethia A. Hostetter , and Maire F. Osborn from the University of Oregon, there is more cisplatin acumulation in total RNA in yeast than in total DNA in yeast.
http://pubs.acs.org/doi/abs/10.1021/cb200279p


- Researchers Jeremy E. Wilusz, Joseph M. Whipple, Eric M. Phizicky and Phillip A. Sharp, from the MIT and Uni-Rochester have found that tRNAs marked with CCACCA are targeted for degradation.
http://www.sciencemag.org/content/334/6057/817.abstract


- Antony M Jose, Giancarlo A Garcia and Craig P Hunter.
Harvard and U.Maryland.
Two classes of silencing RNAs move between Caenorhabditis elegans tissues
http://www.nature.com/nsmb/journal/v18/n11/full/nsmb.2134.html


- H. James Tripp, Ian Hewson, Sam Boyarsky, Joshua M. Stuart and Jonathan P. Zehr
UCSC and Cornell
Misannotations of rRNA can now generate 90% false positive protein matches in metatranscriptomic studies.
http://nar.oxfordjournals.org/content/39/20/8792.short?rss=1


-Lipfert J, Kerssemakers JJ, Rojer M, Dekker NH.
Delft Uni. Netherlands
A method to track rotational motion for use in single-molecule biophysics
http://www.ncbi.nlm.nih.gov/pubmed/22047303