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Topic: RNA structure

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	An RNA Structure Primer
		RNA is ribonucleic acid, a close cousin of deoxyribonucleic acid or DNA.
		RNA molecules are built from three basic components: ribose, a five-carbon suger, phosphate, and a family of four heterocyclic bases.
		The structure of the RNA backbone is an alternating polymer of ribose and phosphate groups.
	www.rnabase.org /primer (962 words)

	RNA structure (Site not responding. Last check: 2007-11-06)
		The covalent structure of RNA differs from that of DNA in two basic ways (a) ribonucleic acid so the sugar unit in the nucleotides is ribose rather than deoxyribose (b) no thymine found in RNA its replaced by uracil U. Uracil can base pair with adenine.
		RNA molecules are single stranded except in some viruses however it is possible for RNA molecules to fold on themselves to form short regions of double helix by forming a hair-pin loop.
		Base pairing in RNA hairpin loops is frequently imperfect, often opposite bases cannot base pair, and one or more bases along a strand may be looped out in order for base pairing to occur by proper base pairing.
	www-biol.paisley.ac.uk /courses/stfunmac/glossary/RNA.html (350 words)

	RNA Structure and Function
		Since RNA has the extra hydroxyl group it is too bulky to form a double stranded molecule.
		It is the RNA referred to in the central dogma of biology (see Overview of Molecular Biology for more information).
		A spliceosome is a complex of proteins and small RNA molecules, and is where the removal of introns and the splicing together of exons takes place.
	www.scienceden.com /mbiology/concepts/rna (955 words)

	[No title]
		RNAforester implements a novel approach for structural motif detection in RNA secondary structures and is based on local RNA structure alignments.
		The calculation of a local RNA structure alignment means to search for the most similar substructures inside larger RNA secondary structures.
		Beside local alignment RNAforester can calculate global RNA structure alignments which gives a distance or similarity measure that is superior to pure sequence alignments of RNA structures.
	bibiserv.techfak.uni-bielefeld.de /rnaforester (141 words)

	Unprecedented View Of RNA Structure Captured
		Also, RNA's stature has risen extraordinarily in the past two decades with discoveries that RNA not only carries the genetic blueprint to the ribosomes for protein encoding, but also serves as the catalyst that carries out the reactions and does the major work of the ribosome.
		Even as scientists have begun to understand how significant RNA is to the origins of life, proper techniques for simply seeing its detailed structure have proved difficult to impossible to manage because of RNA's inherent tendency to be unstable.
		It was also important that Draper's group chose an RNA whose secondary structure had already been detected by previous scientists, but which also presented solid evidence that there was substantial additional structure at the tertiary level, the next significant level of complexity.
	www.eurekalert.org /pub_releases/1999-05/JHU-UVOR-140599.php (1096 words)

	An unusual RNA structure in the SARS virus offers a promising target for antiviral drugs
		Messenger RNA is the intermediary that carries genetic information from the DNA in the chromosomes to the cellular protein factories, called ribosomes, where the genetic information is translated into proteins.
		Noller, an expert on the ribosome, noticed that a sharp, 90-degree bend in the s2m RNA structure is similar to a part of the ribosome.
		A more common approach in structural genomics is to determine the three-dimensional shape of a novel protein and compare it to the shapes of proteins with known functions to find clues to the function of the unknown protein.
	www.innovations-report.com /html/reports/life_sciences/report-38282.html (1194 words)

	RNABase: The RNA Structure Database
		Analyze your PDB format structure the same way as official RNABase entries have been analyzed.
		A tabulation of all nucleotide conformations observed for RNA residues and their frequencies.
		A brief introduction to the structure of RNA and the nomenclature used to describe it.
	www.rnabase.org (264 words)

	Lin, J - The function of a complex RNA structure in the self-priming mechanism of Tf1 reverse transcription. (Site not responding. Last check: 2007-11-06)
		Lin, J - The function of a complex RNA structure in the self-priming mechanism of Tf1 reverse transcription.
		The function of a complex RNA structure in the self-priming mechanism of Tf1 reverse transcription.
		To determine the function of this structure, we systematically mutated sequences in the region encompassing the putative RNA structure.
	www.yeastgenome.org /yeast96/f2298.html (267 words)

	Eddy lab :: Software (Site not responding. Last check: 2007-11-06)
		The algorithm is discussed in the paper "A dynamic programming algorithm for RNA structure prediction using pseudoknots".
		This is the code from Elena Rivas that accompanies the paper "Noncoding RNA gene detection using comparative sequence analysis".
		This is the code from Elena Rivas that goes with the paper "Secondary structure alone is generally not statistically significant for the detection of noncoding RNAs" by Elena Rivas and Sean Eddy.
	www.genetics.wustl.edu /eddy/software (836 words)

	RNA Structure Analysis (Site not responding. Last check: 2007-11-06)
		In the past we also developed a parallel version of the Zuker suboptimal RNA structure prediction algorithm (DPA ref.).
		RNA structure analysis is performed with help of a comprehensive computer workbench, STRUCTURELAB (STRUCTURELAB ref.), which permits the examination of 10,000's of optimal and suboptimal structures and offers motif searching capabilities.
		Various RNA structure analysis algorithms can be run on several different computer architectures including a Cray J90, Cray SV1, SGI Origin 2000, Digital Alpha 8400, 16,384 processor MasPar MP-2 SIMD machine, and various workstations.
	www-lmmb.ncifcrf.gov /~bshapiro/RNAstructure.html (277 words)

	The RNA Society WebSite
		The RNA Society was formed in 1993 to facilitate sharing and dissemination of experimental results and emerging concepts in ribonucleic acid research.
		The Society encompasses RNA research in the broadest sense: from the ribosome to the spliceosome, from RNA viruses to catalytic RNAs.
		It is a multidisciplinary society, representing molecular, evolutionary and structural biology, biochemistry, biomedical sciences, chemistry, genetics, and virology as they relate to questions of the structure and function of RNA and of ribonucleoprotein assemblies.
	www.rnasociety.org (374 words)

	The RNA World. by Brig Klyce
		It was prescient of Crick to guess that RNA could act as an enzyme, because that was not known for sure until it was proven in the 1980s by Nobel Prize-winning researcher Thomas R. Cech (2) and others.
		RNA is then relegated to the intermediate role it has today—no longer the center of the stage, displaced by DNA and the more effective protein enzymes.
		RNA is chemically fragile and difficult to synthesize abiotically.
	www.panspermia.org /rnaworld.htm (5641 words)

	Structure Of A Conserved RNA Element In The SARS Virus Genome Determined
		The genome of the SARS virus is a single strand of RNA that folds into regular repeating patterns to form secondary structures such as helices.
		This strong sequence conservation indicates that the tertiary structure of s2m could be important for viral function, and when the researchers solved the three-dimensional crystal structure of the element, they found that it had a unique tertiary structure.
		Finding a similar 90° kink in a region of ribosomal RNA that binds factors necessary for the initiation of protein synthesis, the researchers speculate that the SARS virus may use the s2m element to hijack its host cell's protein synthesis machinery.
	www.sciencedaily.com /releases/2005/02/050201191458.htm (729 words)

	RNA Structure and Function (Site not responding. Last check: 2007-11-06)
		The sugar in RNA is ribose, not the deoxyribose in DNA (as we previously learned).
		The base uracil is present in RNA instead of thymine.
		Ribosomes are small, granular structures where protein synthesis takes place.
	www.ncc.gmu.edu /dna/rna.htm (182 words)

	ISMB 2001 Poster Abstracts: DNA and RNA Structure
		Both a mathematical model of RNA secondary structure formation and its principally new algorithm developed on the basis of oriented, dynamically changing mathematical graph with corresponding computer implementation are described.
		The growth of RNA chain is associated to the set of discrete internal structural gaps from unstructured state to the final configuration when the molecule folds into locally stable structure.
		It was revealed that the accuracy of secondary structure prediction against the period of transcription grows rapidly while the increase of period of transcription from 1 to 20 nucleotides per step.
	ismb01.cbs.dtu.dk /DNARNAStructure.html (1401 words)

	Vienna RNA Secondary Structure Package
		The Vienna RNA Package consists of a C code library and several stand-alone programs for the prediction and comparison of RNA secondary structures.
		RNA secondary structure prediction through energy minimization is the most used function in the package.
		Structure prediction for moderate size RNAs can be done interactively on our server.
	www.tbi.univie.ac.at /~ivo/RNA (486 words)

	Johnson & Schneeman Publication Page (Site not responding. Last check: 2007-11-06)
		Structures of the native and swollen forms of cowpea chlorotic mottle virus determined by X-ray crystallography and cryo electron microscopy.
		Influence of 3- dimensional structure on the immunogenicity of a peptide expressed on the surface of a plant virus.
		Taylor, D. J., Krishna, N. K., Canady, M. A., Schneemann, A., and Johnson, J. Large-scale, pH-dependent, quaternary structure changes in an RNA virus capsid are reversible in the absence of subunit autoproteolysis.
	lav.scripps.edu /recpapers/recpapers.shtml (7929 words)

	Phylogenetic conservation of RNA secondary and tertiary structure in the trpEDCFBA operon leader transcript in Bacillus ...
		The tertiary structure model (lower structure) predicts that 24 nt in the 5' (magenta) and the 3' (blue) sides of the pyrimidine-rich internal loop base pair with the same colored residues between nt 33 and 60 containing the single-stranded (G/U)AG repeats (the secondary structure defects are omitted for clarity; Schaak et al.
		P-labeled RNA (1–232) was renatured under various salt conditions and fractionated on a 6% native polyacrylamide gel.
		RNAs were melted from 5°C–95°C at pH 7.0 and 8.0, and from 20°C–60°C at pH 6.0 at a step of 0.1°C, and the data were smoothed over 3°C before taking the first derivative.
	www.rnajournal.org /cgi/content/full/9/12/1502 (6188 words)

	Dr Chromo's school: RNA structure
		An RNA molecule is a linear polymer in which the monomers (nucleotides) are linked together by means of phosphodiester bridges, or bonds.
		Although each RNA molecule has only a single polynucleotide chain, it is not a smooth linear structure.
		In the base paired region, the RNA molecule adopts a helical structure as in DNA.
	www.rothamsted.bbsrc.ac.uk /notebook/courses/guide/rnast.htm (452 words)

	RNA Structure
		The structure shown here (that we just looked at on th Linking Nucleotides page) is essentially the structure of ribonucleic acid because the sugar shown here is ribose.
		Whichever diagram of RNA you use, note that RNA includes adenine, cytosine, guanine and uracil.
		Another source of good diagrams and much additional information about the structure of RNA (and also DNA) is the Biochemistry in 3D web site maintained by Worth Publishers as a supplement to an excellent Biochemistry text by Lehninger.
	dl.clackamas.cc.or.us /ch106-09/rna.htm (242 words)

	Ambion - The RNA Company : Structure/Function
		The types of experiments performed to structurally characterize RNA utilize a variety of reagents that are not readily available from a single source and typically are not optimized for these applications.
		As The RNA Company, Ambion is making a concerted effort to provide kits, reagents and protocols as a service to the community of scientists that perform these experiments.
		RNA Structure/Function Protocols: Alkaline Hydrolysis, RNA Sequencing and RNA Structure Analyses with Nucleases
	www.ambion.com /techlib/resources/structure (258 words)

	IMB Jena Image Library: Index of RNA structures
		The ribosome entries 1gix and 1giy are counted as two structures because the PDB has released them in two separate files (size limitation of the PDB format).
		The same is true for a number of further lareg structures.
		If you are aware of RNA structures deposited at the PDB or NDB but not included here, let me know.
	www.imb-jena.de /IMAGE_RNA.html (773 words)

	RNAsoft - home page
		PairFold can be used, for example, to predict interactions between a probe and target RNA molecule, or between pairs of strands in biomolecular nanostructures.
		RNA Designer designs an RNA sequence that folds to a given input secondary structure.
		The tool is intended for designers of RNA molecules with particular structural or functional properties.
	www.rnasoft.ca (132 words)

	RNA STRUCTURE
		The basic components of RNA are the same than for DNA (see the DNA page) with two major differences.
		For RNA, nucleosides are formed similarly to DNA with ribose replacing deoxyribose Uracil 5' monophosphate is given as an example.
		RNA also contain "unusual" nucleotides (formed after the RNA synthesis is complete).
	www-scf.usc.edu /%7Echem203/resources/DNA/rna_structure.html (244 words)

	[3C] RNA Structure and Function (Site not responding. Last check: 2007-11-06)
		They may form secondary structures such as stem-loop and hairpin.
		The major role of RNA is to participate in protein synthesis.
		A guide to ions and RNA structure - RNA, 2004.
	www.web-books.com /MoBio/Free/Ch3C.htm (31 words)

	Compilation of tRNA sequences and sequences of tRNA genes
		Positions in particular sequence which are not filled (gaps in the generalised structure) are indicated by a dash.
		Terminology and structure of the modified nucleosides occurring in tRNAs were used according to (5) and (6).
		Nucleotides involved in Watson-Crick pairs are marked with '=', the GU pairs are indicated with the sign '*', tertiary interactions are not annotated.
	www.uni-bayreuth.de /departments/biochemie/trna (1010 words)

	RNA Structure Logos
		The structure logo is an extension of the sequence logo by Schneider and Stephens.
		The mutual information between indicated (given from the structural alignment) basepair is symmetric so each involved position do Only obtain half of the shared mutual information.
		The mutual information is calculated as the relative entropy between the fractions of complementary bases at indicated basepaired positions in the alignment and the number of basepairs one would expect by chance from the distribution of nucleotides at the involved positions.
	www.cbs.dtu.dk /~gorodkin/appl/slogo.html (521 words)

	BioMed Central \| Abstract \| Accelerated probabilistic inference of RNA structure evolution
		Pairwise stochastic context-free grammars (Pair SCFGs) are powerful tools for evolutionary analysis of RNA, including simultaneous RNA sequence alignment and secondary structure prediction, but the associated algorithms are intensive in both CPU and memory usage.
		It is therefore desirable to constrain such algorithms, by pre-processing the sequences and using this first pass to limit the range of structures and/or alignments that can be considered.
		It is now possible to combine independent structural and alignment constraints of unprecedented general flexibility in Pair SCFG alignment algorithms.
	www.biomedcentral.com /1471-2105/6/73/abstract (221 words)

	Citations: Computer Prediction of RNA Structure - Zuker (ResearchIndex) (Site not responding. Last check: 2007-11-06)
		A new method to predict the consensus secondary structure..
		The domain knowledge and experimental data have been also formalized for RNA structure prediction, and a framework for combining knowledge from several....
		....in [20] are not permitted in secondary structure calculations.
	citeseer.ist.psu.edu /context/117185/0 (579 words)

	The Bioinformatics Center at Rensselaer and Wadsworth. RNA and DNA Folding Applications
		Michael Zuker, professor of mathematical sciences, develops tools for predicting the secondary structure of RNA and DNA, mainly by using thermodynamic methods.
		Much of his work has been on RNA structure, which is important in understanding many biological processes, including translation regulation in messenger RNA, replication of single-stranded RNA viruses, and the function of structural RNAs and RNA/protein complexes.
		Recent work in his laboratory includes the development of methods to predict folding hybridization and melting curves for two strands of RNA or DNA, and he is developing statistically based rules for RNA folding.
	www.bioinfo.rpi.edu /applications/mfold (239 words)

	Posttranscription Initiation Control of Tryptophan Metabolism in Bacillus subtilis by the trp RNA-Binding Attenuation ...
		The overlap between the antiterminator and terminator structures is shown.
		In this case the trp leader RNA adopts a structure such that the trpE SD sequence is single stranded and available for translation.
		SCHAAK, J. Phylogenetic conservation of RNA secondary and tertiary structure in the trpEDCFBA operon leader transcript in Bacillus.
	jb.asm.org /cgi/content/full/183/20/5795 (4421 words)

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