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Posts Tagged ‘RNA’

Breakthrough in understanding folding of single stranded viral RNAs could lead to cure for the common cold

February 9, 2015 Leave a comment

Pretty cool stuff, not only is it the primary sequence, but all the secondary structural interacts are absolutely key for folding and assembly into the viral partciel.

Title overstates the case but excerpt from: Scientists have figured out how to stop the common cold in its tracks

“We have understood for decades that the RNA carries the genetic messages that create viral proteins, but we didn’t know that, hidden within the stream of letters we use to denote the genetic information, is a second code governing virus assembly,” one of the team, biophysicist Roman Tuma from the University of Leeds in the UK, told Laura Donnelly at The Telegraph. “It is like finding a secret message within an ordinary news report and then being able to crack the whole coding system behind it.”

Single-stranded RNA viruses are the most simple type of viruses known to science, and it’s thought that they were probably one of the first to evolve. And being around for a long time means they’re super-effective at what they do. Rhinovirus, which is the predominant cause of the common cold, is responsible for 1 billion infections per year – in the US alone.

Revealing the density of encoded functions in a viral RNA

We present direct experimental evidence that assembly of a single-stranded RNA virus occurs via a packaging signal-mediated mechanism. We show that the sequences of coat protein recognition motifs within multiple, dispersed, putative RNA packaging signals, as well as their relative spacing within a genomic fragment, act collectively to influence the fidelity and yield of capsid self-assembly in vitro. These experiments confirm that the selective advantages for viral yield and encapsidation specificity, predicted from previous modeling of packaging signal-mediated assembly, are found in Nature. Regions of the genome that act as packaging signals also function in translational and transcriptional enhancement, as well as directly coding for the coat protein, highlighting the density of encoded functions within the viral RNA. Assembly and gene expression are therefore direct molecular competitors for different functional folds of the same RNA sequence. The strongest packaging signal in the test fragment, encodes a region of the coat protein that undergoes a conformational change upon contact with packaging signals. A similar phenomenon occurs in other RNA viruses for which packaging signals are known. These contacts hint at an even deeper density of encoded functions in viral RNA, which if confirmed, would have profound consequences for the evolution of this class of pathogens.

Researchers at GIT show spontaneous assembly of “proto-RNAs” in water

February 21, 2013 Leave a comment

Really interesting work. Essentially shows that stacking interactions and hydrogen bonding of the nitrogenous bases is sufficient to form a “proto-RNA” filament. While far from being definitive proof of anything, this work certainly builds on and supports the RNA-world hypothesis for the origins of life. Very cool stuff, will update this post when more information becomes available.

Excerpt from “Molecules assemble in water, hint at origins of life” in e! Science News

 

Researchers at the Georgia Institute of Technology are exploring an alternate theory for the origin of RNA: they think the RNA bases may have evolved from a pair of molecules distinct from the bases we have today. This theory looks increasingly attractive, as the Georgia Tech group was able to achieve efficient, highly ordered self-assembly in water with small molecules that are similar to the bases of RNA. These “proto-RNA bases” spontaneously assemble into gene-length linear stacks, suggesting that the genes of life could have gotten started from these or similar molecules.

The discovery was made by a team of scientists led by Georgia Tech Professor Nicholas Hud, who has been trying for years to find simple molecules that will assemble in water and be capable of forming RNA or its ancestor. Hud’s group knew that they were on to something when they added a small chemical tail to a proto-RNA base and saw it spontaneously form linear assemblies with another proto-RNA base. In some cases, the results produced 18,000 nicely ordered, stacked molecules in one long structure.

Hud concedes that scientists may never be 100 percent sure what existed four billion years ago when a complex mixture of chemicals started to work together to start life. His next goal is to determine whether the proto-RNA bases can be linked by a backbone to form a polymer that could have functioned as a genetic material.

 

Special Seminar: RNA on Steroids 2 pm Friday, 5/25, LS1022.

May 24, 2012 Leave a comment

RNA on Steroids
2 pm Friday, 5/25, LS1022.
Dr Loren Williams, Director, NASA Center for Ribosomal Evolution and Adaptation, GA Tech, Atlanta

Dr Williams works on rewinding the “tape of life”: to shed light on the nature of protein synthesis prior to the last universal common ancestor of life. His center focuses on the characteristics of ancient macromolecules and their assemblies, specifically on aboriginal mechanisms of peptide synthesis by RNA – an attempt to uncover clues about key steps in the transition from the RNA world to the protein. In part, Dr Williams work carries the potential of discovering and characterizing the oldest traceable macromolecules and machines of life, and the earliest discernable connection between RNA and protein. The formation of the Peptidyl Transferase Center  marked the beginning of the translation machinery and the beginning of the end of the RNA world. Therefore, working on the resurrection and the structures of ancestral Peptidyl Transferase Centers allows Dr Williams to test ideas about primitive living systems, as well as the origin of protein.

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