Research techniques

Computer Simulation of Ribosome at LANL
exogenous nucleobase rescue of abasic substitutions
siRNA
SMaRT Spliceosome-Mediated RNA Trans-splicing
E-MAP Technique Offers New View of Dynamic Biological Landscape

Computer Simulation of Ribosome at LANL

Largest Computational Biology Simulation Mimics Life's Most Essential Nanomachine: "The ribosome is so fundamental to life that many portions of this molecular machine are identical in every organism ever genetically sequenced. In developing the project, the team identified a corridor inside the ribosome that the transfer RNA must pass through for the decoding to occur, and it appears to be constructed almost entirely of universal bases, implying that it is evolutionarily ancient."

exogenous nucleobase rescue of abasic substitutions

BIO.COM: Biotechnology & Pharmaceutical News, Jobs, Software, Reports, Books, Events: A research technique called 'exogenous nucleobase rescue of abasic substitutions' provides a method by which researchers are able to delete particular nucleobases from the active site of an RNA enzyme without disrupting its structure, and subsequently to restore activity by providing nucleobases in solution.

Exogenous nucleobase rescue involves substitution of RNA nucleotides of interest with abasic residues. These maintain the continuity of the RNA chain but have a single hydrogen atom in place of a critical nucleobase. The researchers insert small molecules to rescue the activity lost because of the missing nucleobase.

siRNA

siRNA Technology and Applications: "Small interfering RNA (siRNA) is a tool that is revolutionizing bioscience research. The increased use of siRNA in peer reviewed publications clearly demonstrates that it is an incredibly powerful means to specifically knock-down a gene's message, and subsequently the protein level of the targeted gene. In this manner, cellular-based assays can be conducted in the absence and presence of the targeted gene's protein.

The value of such an experiment has long been known as researchers the world over have employed genetic knock-out technologies, dominant negatives and chemical inhibitors of protein activities to perform such experiments. The use of siRNA is replacing all three of these methodologies."

SMaRT Spliceosome-Mediated RNA Trans-splicing

American Society of Gene Therapy News Release: "Current gene transfer methods rely on the efficient transfer of cDNAs to effect phenotypic change. A study presented at the American Society of Gene Therapy Annual Meeting demonstrated a new approach to gene therapy. The researchers developed in vivo data supporting a novel method for genetic repair based on the correction of mutant pre-mRNA.

Christopher Walsh, MD, and Hengjun Chao, MD, at the University of North Carolina at Chapel Hill and Gary Mansfield, MD, and collaborators at Intronn Inc, Rockville, MD, made use of a natural mechanism that splices out introns and joins together the protein-coding exons. The normal process is called 'cis-splicing.' The researchers developed a new technology, called 'Spliceosome-mediated RNA trans-splicing (SMaRT),' to correct the hemophilia phenotype in Factor VIII knock out mice. A gene therapy vector is made by inserting their 'trans-splicing cassette' into a viral vector.

The researchers found that when they injected their vector into the hemophiliac mice, a significant increase in functional Factor VIII was found in the bloodstream of the mice. This factor allowed the mice to survive the bleeding trauma, which is lethal to untreated hemophilia mice. They demonstrated that the mutant FVIII RNA was repaired and that 'RNA repair' occurred via trans-splicing.This novel RNA repair method can provide a new approach in gene therapy for many genetic diseases, which are difficult to deal with by current gene transfer methods."