background: rna interference (rnai) is a phenomenon uses double-stranded rna (dsrna) to specifically inhibit gene expression. the non-specific silencing caused by interferon response to dsrna in mammalian cells limits the potential of utilizing rnai to study gene function. duplexes of 21-nucleotide short interfering dsrna (sirna) inhibit gene expression by rnai. in some organisms, sirna can als...

Because RNA lacks strong intrinsic fluorescence, it has proven challenging to track RNA molecules in real time. To address this problem and to allow the purification of fluorescently tagged RNA complexes, we have selected a high affinity RNA aptamer called RNA Mango. This aptamer binds a series of thiazole orange (fluorophore) derivatives with nanomolar affinity, while increasing fluorophore fl...

Splicing of mammalian precursor transfer RNA (tRNA) molecules involves two enzymatic steps. First, intron removal by the tRNA splicing endonuclease generates separate 5' and 3' exons. In animals, the second step predominantly entails direct exon ligation by an elusive RNA ligase. Using activity-guided purification of tRNA ligase from HeLa cell extracts, we identified HSPC117, a member of the UP...

Herein, we demonstrated a simple, rapid and automated RNA purification system based on a centrifugal force using three passive capillary valves and a silica sol-gel matrix. We designed three reservoirs (sample, washing solution, elution buffer) which were connected with different dimensional microfluidic channels. By controlling RPM, we could dispense the RNA sample, washing solution, and eluti...

Intermolecular RNA-RNA interactions are used by many noncoding RNAs (ncRNAs) to achieve their diverse functions. To identify these contacts, we developed a method based on RNA antisense purification to systematically map RNA-RNA interactions (RAP-RNA) and applied it to investigate two ncRNAs implicated in RNA processing: U1 small nuclear RNA, a component of the spliceosome, and Malat1, a large ...

The RNA-dependent RNA polymerase (1E Pol ) is involved in replication of grapevine fanleaf virus (GFLV, Nepovirus , Secoviridae and causes vein clearing symptoms Nicotiana benthamiana . Information on protein 1E interaction with other viral host proteins scarce. To study biology, three GFLV infectious clones, i.e. GHu (a symptomatic wild-type strain), GHu-1E K802G (an asymptomatic mutant) F13 w...

Bacteriophage T7 is the prototype of a group of bacterial viruses that each encode a single subunit DNA-dependent RNA polymerase (RNAP). Other members of this class include the coliphages T3 and BA14, the Salmonella phage SP6, the Pseudomonas phage gh1 and the Klebsiella phage K11 (9,16). The phage RNA polymerases have proven to be useful in a variety of applications, including large-scale RNA ...

A renewed interest in non-coding RNA (ncRNA) has led to the discovery of novel RNA species and post-transcriptional ribonucleoside modifications, and an emerging appreciation for the role of ncRNA in RNA epigenetics. Although much can be learned by amplification-based analysis of ncRNA sequence and quantity, there is a significant need for direct analysis of RNA, which has led to numerous metho...

RNA isolation is performed everyday by molecular biologists for a wide range of applications. No matter what protocol is used and how meticulous the user is, a risk to degrade RNA during the process or to carry over contaminants always exists which may affect the reliability of the subsequent analytical techniques. The parameters that are usually checked for quality control include the concentr...

RNA editing within the mitochondria of kinetoplastid protozoa is performed by a multicomponent -macromolecular machine known as the editosome. Editosomes are high molecular mass protein assemblies that consist of about 15-25 individual polypeptides. They bind pre-edited transcripts and convert them into translation-competent mRNAs through a biochemical reaction cycle of enzyme-catalyzed steps. ...