Small hairpin RNA - Factbites

Small hairpin RNA - Factbites
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Topic: Small hairpin RNA

Note: these results are not from the primary (high quality) database.

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	LYNX Small RNA MPSS
		Micro RNAs (miRNA) are the result of the cleavage of longer precursors possessing a hairpin structure whereas small interfering RNAs (siRNA) and repeat associated small interfering RNAs (rasiRNA) are derived from double stranded RNA structures.
		A large number of the small RNA molecules map back to the regions of the genome containing transposons or repeats, indicating that these regions are actively silenced by this mechanism.
		Among these, regulatory RNAs of small sizes have been shown to be involved in pre- and post- transcriptional control of gene expression.
	www.lynxgen.com /wt/tert.php3?page_name=small_rna_mpss (765 words)

	World J Gastroenterol
		RNA interference by expression of short-interfering RNAs and hairpin RNAs in
		AIM: To synthesize three small-interference RNAs (siRNAs) by T7 RNA polymerase-catalyzed reaction, and to investigate their efficacy on modulating the expression of serine/threonine kinase Pim-2 in human colon cancer cell line.
		Transfection of the RNA oligonucleotides was performed using Lipofectamine 2000 (Invitrogen) as directed by the manufacturer to result in a final RNA concentration of 50 nmol/L. After transfection (incubation for 6 h at 37 °C), cells were washed with PBS and incubated in fresh culture medium until additional analyses.
	www.wjgnet.com /1007-9327/10/2657.asp (2823 words)

	Probing the MicroRNA and Small Interfering RNA Pathways with Virus-Encoded Suppressors of RNA Silencing -- Dunoyer et al. 16 (5): 1235 -- THE PLANT CELL
		One of the Two Dicer-like Proteins in the Filamentous Fungi Magnaporthe oryzae Genome Is Responsible for Hairpin RNA-triggered RNA Silencing and Related Small Interfering RNA Accumulation
		Probing the MicroRNA and Small Interfering RNA Pathways with Virus-Encoded Suppressors of RNA Silencing
		Probing the MicroRNA and Small Interfering RNA Pathways with Virus-Encoded Suppressors of RNA Silencing -- Dunoyer et al.
	www.plantcell.org /cgi/content/abstract/16/5/1235 (1049 words)

	Ambion - RNA interference (RNAi) Resource Page
		Structural Requirements of Potent Small Hairpin RNAs (shRNAs) - May 2002
		Small RNAs May Cause Genomic Rearrangements in Tetrahymena - Oct 2002
		The Role of RDE-4 in RNA Interference - Sept 2002
	www.ambion.com /techlib/resources/RNAi/jclub.html (226 words)

	University of California, Santa Cruz Chemistry Department
		Scott, J. Finch, and A. Klug, "Three-Dimensional Structure of an all- RNA Hammerhead Ribozyme: A Proposed Mechanism for RNA Catalytic Cleavage," Cell 81, 991-1002, 1995.
		Scott, J. Murray, B. Stoddard, and A. Klug, "Capturing the Structure of a Catalytic RNA Intermediate: The Hammerhead Ribozyme," Science 274, 2065-2069, 1996.
		Murray, A. Seyhan, N. Walter, J. Burke, and W. Scott, "The Hammerhead, Hairpin and VS Ribozymes are Catalytically Proficient in Monovalent Cations Alone," Chemistry and Biology 5, 587-595, 1998.
	www.chemistry.ucsc.edu /scott_w.html (969 words)

	Catalytic Nucleic Acids: From Lab to Applications -- Sun et al. 52 (3): 325 -- Pharmacological Reviews
		This diagram is a proposed schematic representation of the catalytic cycle typical for small RNA-cleaving nucleic acid enzymes such as the hammerhead ribozyme and the 10-23 deoxyribozyme, which bind to their substrate via Watson-Crick interactions.
		hammerhead and hairpin ribozymes, the presence of Mg is essential for the cleavage, and the convincing evidence suggested
		Hammerhead and hairpin motifs have often found application in the design of trans-acting ribozymes.
	pharmrev.aspetjournals.org /cgi/content/full/52/3/325 (8819 words)

	University of California, Santa Cruz Chemistry Department
		Scott, J. Finch, and A. Klug, "Three-Dimensional Structure of an all- RNA Hammerhead Ribozyme: A Proposed Mechanism for RNA Catalytic Cleavage," Cell 81, 991-1002, 1995.
		Scott, J. Murray, B. Stoddard, and A. Klug, "Capturing the Structure of a Catalytic RNA Intermediate: The Hammerhead Ribozyme," Science 274, 2065-2069, 1996.
		Murray, A. Seyhan, N. Walter, J. Burke, and W. Scott, "The Hammerhead, Hairpin and VS Ribozymes are Catalytically Proficient in Monovalent Cations Alone," Chemistry and Biology 5, 587-595, 1998.
	www.chemistry.ucsc.edu /scott_w.html (969 words)

	About siRNA
		For DNA-vector based siRNA technology, a small DNA insert (about 70 bp) encoding a short hairpin RNA targeting the gene of interest is cloned into a vector.
		Two single-stranded 19-22 nt RNA oligos are chemically synthesized, and annealed to form a siRNA duplex.
		Chemically synthesized siRNA and siRNA cassette are mainly used for initial screening to identify the most potent target sequence.
	www.genscript.com /sirna_ca_intro.html (969 words)

	Molecular Dynamics Simulation of the Human U2B" Protein Complex with U2 snRNA Hairpin IV in Aqueous Solution -- Guo and Gmeiner 81 (2): 630 -- Biophysical Journal
		Molecular dynamics simulations of the complex between human U1A protein and hairpin II of U1 small nuclear RNA and of free RNA in solution.
		Water molecules in DNA recognition 1: hydration lifetimes of trp operator DNA in solution measured by NMR spectroscopy.
		FIGURE 3 RMSD, relative to the initial coordinates, during the 2200-ps molecular dynamics trajectory.
	www.biophysj.org /cgi/content/full/81/2/630 (5568 words)

	siRNA Database and RNA Interference Resources
		The target sequence (19 to 29 nucleotides) is placed in a sense and antisense orientation with a small spacer group in between (short hairpin RNA or shRNA).
		Once transcribed, a hairpin structure is formed that can be recognized and cleaved by Dicer.
		Some of the requirements include using sequences shorter than 30 nucleotides to avoid PKR activation, sequence stability at the 5' end of the antisense strand relative to the 3' terminus and inserting a TT overhang.
	www.RNAinterference.org (5568 words)

	Functional Mapping of the U3 Small Nucleolar RNA from the Yeast Saccharomyces cerevisiae -- Samarsky and Fournier 18 (6): 3431 -- Molecular and Cellular Biology
		The U3* RNA has a different sequence in the nonconserved hairpin 4 region; however, the secondary structure of the hairpin is preserved.
		The structural and functional information available for the U3 small nucleolar RNA from S.
		Characterization and expression of a maize U3 snRNA gene.
	mcb.asm.org /cgi/content/full/18/6/3431 (8667 words)

	Folding of RNA – The Hairpin Ribozyme as a model system
		The Hairpin Ribozyme is a small catalytic RNA found in plant virus satellite RNAs.
		Freely-diffusing single hairpin ribozymes provide insights into the role of secondary structure and partially folded states in RNA folding.
		Folding of RNA– The Hairpin Ribozyme as a model system
	www.scripps.edu /mb/millar/research/hairpin.htm (430 words)

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Topic: Small hairpin RNA

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