BioPortfolio Cancer: BioPortfolio News Dicer an... The ubiquitous hammerhead ribozyme + Author Affiliations + Author Notes ↵5 Present address: Ribogenetics@Biochemistry Laboratory, Jacobs University Bremen, 28759 Bremen, Germany. Abstract The hammerhead ribozyme is a small catalytic RNA motif capable of endonucleolytic (self-) cleavage. It is composed of a catalytic core of conserved nucleotides flanked by three helices, two of which form essential tertiary interactions for fast self-scission under physiological conditions. Copyright © 2012 RNA Society Natural Sciences Bibliography | 350,000 References and More Down-regulation of JAK1 by RNA interference inhibits growth of the lung cancer cell line A549 and interferes with the PI3K/mTOR pathway - Life Sciences Social Network
3D RNA modeling opens scientific doors Monday, April 16, 2012 RNA hairpin Credit: Vossman/CC3.0 In a paper published today in the journal Nature Methods, a team from the University of North Carolina at Chapel Hill demonstrates a simple, cost-effective technique for three-dimensional RNA structure prediction that will help scientists understand the structures, and ultimately the functions, of the RNA molecules that dictate almost every aspect of human cell behavior. Over the past five decades, scientists have described more than 80,000 protein structures, most of which are now publicly available and provide important information to medical researchers searching for targets for drug therapy. "To effectively target these molecules, researchers often need a three-dimensional picture of what they look like," says Nikolay Dokholyan, PhD, professor in the department of biochemistry and biophysics, and the project's co-leader. "With Dr. University of North Carolina School of Medicine:
Current Opinion in Structural Biology - Squaring theory with practice in RNA design Volume 22, Issue 4, August 2012, Pages 457–466 Engineering and design / Membranes Edited By Jane Clarke, William Schief, Tamir Gonen and Gabriel Waksman Ribonucleic acid (RNA) design offers unique opportunities for engineering genetic networks and nanostructures that self-assemble within living cells. Recent years have seen the creation of increasingly complex RNA devices, including proof-of-concept applications for in vivo three-dimensional scaffolding, imaging, computing, and control of biological behaviors. Expert intuition and simple design rules — the stability of double helices, the modularity of noncanonical RNA motifs, and geometric closure — have enabled these successful applications. Highlights Copyright © 2012 Elsevier Ltd.
Seq faces a tough road to the cancer clinic Despite the development of molecular classifications, and prognostic and predictive gene-expression signatures, microarray-based studies have not yielded definitive answers to many of the questions that remain germane for the successful implementation of personalized medicine. Similar challenges are likely to be encountered in translating next-generation sequencing data into clinically useful information. Needs Challenges Weigelt B, Pusztai L, Ashworth A, Reis-Filho JS. Challenges translating breast cancer gene signatures into the clinic. In vitro Transcription and Capping of Gaussia Luciferase mRNA Followed by HeLa Cell Transfection This method describes high yield in vitro synthesis of both capped and uncapped mRNA from a linearized plasmid containing the Gaussia luciferase (GLuc) gene. The RNA is purified and a fraction of the uncapped RNA is enzymatically capped using the Vaccinia virus capping enzyme. In the final step, the mRNA is transfected into HeLa cells and cell culture supernatants are assayed for luciferase activity. Date Published: 3/26/2012, Issue 61; doi: 10.3791/3702 Keywords: Genetics, Issue 61, In vitro transcription, Vaccinia capping enzyme, transfection, T7 RNA Polymerase, RNA synthesis Jani, B., Fuchs, R. In vitro transcription is the synthesis of RNA transcripts by RNA polymerase from a linear DNA template containing the corresponding promoter sequence (T7, T3, SP6) and the gene to be transcribed (Figure 1A). Large amounts of high quality RNA are often required for a variety of applications. Addition of a 5' end cap structure to the RNA is an important process in eukaryotes. 1. 2. 3. 4. 5. 6.
LincRNA-p21 Suppresses Target mRNA Translation. [Mol Cell. 2012 MicroRNA-296 is enriched in cancer cells and downregulates p21WAF1 mRNA expression via interaction with its 3′ untranslated region + Author Affiliations *To whom correspondence should be addressed. Tel: +81 29 861 9464; Fax: +81 29 861 2900; Email: renu-wadhwa@aist.go.jp Correspondence may also be addressed to Chae-Ok Yun. MicroRNAs (miRNAs) are a class of noncoding small RNAs that act as negative regulators of gene expression. Chromatin Isolation by RNA Purification (ChIRP) ChIRP is a novel and rapid technique to map genomic binding sites of long noncoding RNAs (lncRNAs). The method takes advantage of the specificity of anti-sense tiling oligonucleotides to allow the enumeration of lncRNA-bound genomic sites. Date Published: 3/25/2012, Issue 61; doi: 10.3791/3912 Keywords: Genetics, Issue 61, long noncoding RNA (lncRNA), genomics, chromatin binding, high-throughput sequencing, ChIRP Cite this Article Chu, C., Quinn, J., Chang, H. Long noncoding RNAs are key regulators of chromatin states for important biological processes such as dosage compensation, imprinting, and developmental gene expression 1,2,3,4,5,6,7. Prior studies mapping RNA occupancy at chromatin have revealed substantial insights 15,16, but only at a single gene locus at a time. 1. Design anti-sense DNA tiling probes for selective retrieval of RNA target by ChIRP. Design anti-sense oligo probes using the online probe designer at singlemoleculefish.com 18. 2. 3. 4. 5. 6. 7. 8. 10. Figure 1.