Name: rna secondary structure prediction using high-throughput shape
Uploaded: 2013-05-31T12:00:00
Description: Watch this Scientific Journal Video about RNA Secondary Structure Prediction Using High-throughput SHAPE at JoVE.com

S. Lusvarghi, J. Sztuba-Solinska, K.J. Purzycka, J.W. Rausch and S.F.J. Le Grice are supported by the Intramural Research Program of the National Cancer Institute, National Institutes of Health, USA.

Primer design and extension of the RNA 3' terminus
To analyze long RNAs by high-throughput SHAPE, a series of primer hybridization sites should be selected such that they (i) are separated by ~300 nt, (ii) are 20-30 nt in length, and (iii) that RNA/DNA hybrids produced by annealing DNA to these sites have an expected melting temperature of &gt;50 &deg;C. In addition, segments of RNA that are predicted to be highly structured should be avoided, although making such a determination requires some fo...

<ol>
	<li>Scott, W. G., Martick, M., Chi, Y. I. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Structure+and+function+of+regulatory+RNA+elements:+ribozymes+that+regulate+gene+expression.">Structure and function of regulatory RNA elements: ribozymes that regulate gene expression.</a> Biochim. Biophys. Acta. 1789, 634-641 (2009).</li><li>Moore, P. B., Steitz, T. A. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=The+roles+of+RNA+in+the+synthesis+of+protein.">The roles of RNA in the synthesis of protein.</a> Cold Spring Harb. Perspect. Biol. 3, a003780 (2011).</li><li>Wilkinson, K. A., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=High-throughput+SHAPE+analysis+reveals+structures+in+HIV-1+genomic+RNA+strongly+conserved+across+distinct+biological+states.">High-throughput SHAPE analysis reveals structures in HIV-1 genomic RNA strongly conserved across distinct biological states.</a> Plos Biol. 6, 883-899 (2008).</li><li>Merino, E. J., Wilkinson, K. A., Coughlan, J. L., Weeks, K. M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=RNA+structure+analysis+at+single+nucleotide+resolution+by+selective+2+'-hydroxyl+acylation+and+primer+extension+(SHAPE).">RNA structure analysis at single nucleotide resolution by selective 2 '-hydroxyl acylation and primer extension (SHAPE).</a> J. Am. Chem. Soc. 127, 4223-4231 (2005).</li><li>Watts, J. M., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Architecture+and+secondary+structure+of+an+entire+HIV-1+RNA+genome.">Architecture and secondary structure of an entire HIV-1 RNA genome.</a> Nature. 460, 711-716 (2009).</li><li>Xu, W., Bolduc, F., Hong, N., Perreault, J. P. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=The+use+of+a+combination+of+computer-assisted+structure+prediction+and+SHAPE+probing+to+elucidate+the+secondary+structures+of+five+viroids.">The use of a combination of computer-assisted structure prediction and SHAPE probing to elucidate the secondary structures of five viroids.</a> Mol. Plant Pathol. , (2012).</li><li>Novikova, I. V., Hennelly, S. P., Sanbonmatsu, K. Y. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Structural+architecture+of+the+human+long+non-coding+RNA,+steroid+receptor+RNA+activator.">Structural architecture of the human long non-coding RNA, steroid receptor RNA activator.</a> Nucleic Acids Res. 40, 5034-5051 (2012).</li><li>Leshin, J. A., Heselpoth, R., Belew, A. T., Dinman, J. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=High-throughput+structural+analysis+of+yeast+ribosomes+using+hSHAPE.">High-throughput structural analysis of yeast ribosomes using hSHAPE.</a> RNA Biol. 8, 478-487 (2011).</li><li>Souliere, M. F., Haller, A., Rieder, R., Micura, R. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=A+powerful+approach+for+the+selection+of+2-aminopurine+substitution+sites+to+investigate+RNA+folding.">A powerful approach for the selection of 2-aminopurine substitution sites to investigate RNA folding.</a> J. Am. Chem. Soc. 133, 16161-16167 (2011).</li><li>Wilkinson, K. A., Merino, E. J., Weeks, K. M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Selective+2+'-hydroxyl+acylation+analyzed+by+primer+extension+(SHAPE):+quantitative+RNA+structure+analysis+at+single+nucleotide+resolution.">Selective 2 '-hydroxyl acylation analyzed by primer extension (SHAPE): quantitative RNA structure analysis at single nucleotide resolution.</a> Nat. Protoc. 1, 1610-1616 (2006).</li><li>McGinnis, J. L., Duncan, C. D. S., Weeks, K. M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=High-Throughput+Shape+and+Hydroxyl+Radical+Analysis+of+Rna+Structure+and+Ribonucleoprotein+Assembly.">High-Throughput Shape and Hydroxyl Radical Analysis of Rna Structure and Ribonucleoprotein Assembly.</a> Method Enzymol. 468, 67-89 (2009).</li><li>Low, J. T., Weeks, K. M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=SHAPE-directed+RNA+secondary+structure+prediction.">SHAPE-directed RNA secondary structure prediction.</a> Methods. 52, 150-158 (2010).</li><li>Das, R., Laederach, A., Pearlman, S. M., Herschlag, D., Altman, R. B. S. A. F. A. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Semi-automated+footprinting+analysis+software+for+high-throughput+quantification+of+nucleic+acid+footprinting+experiments.">Semi-automated footprinting analysis software for high-throughput quantification of nucleic acid footprinting experiments.</a> Rna-a Publication of the Rna Society. 11, 344-354 (2005).</li><li>Kertesz, M., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Genome-wide+measurement+of+RNA+secondary+structure+in+yeast.">Genome-wide measurement of RNA secondary structure in yeast.</a> Nature. 467, 103-107 (2010).</li><li>Underwood, J. G., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=FragSeq:+transcriptome-wide+RNA+structure+probing+using+high-throughput+sequencing.">FragSeq: transcriptome-wide RNA structure probing using high-throughput sequencing.</a> Nat. Methods. 7, 995-1001 (2010).</li><li>Mauger, D. M., Weeks, K. M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Toward+global+RNA+structure+analysis.">Toward global RNA structure analysis.</a> Nat. Biotechnol. 28, 1178-1179 (2010).</li><li>Lucks, J. B., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Multiplexed+RNA+structure+characterization+with+selective+2'-hydroxyl+acylation+analyzed+by+primer+extension+sequencing+(SHAPE-Seq).">Multiplexed RNA structure characterization with selective 2'-hydroxyl acylation analyzed by primer extension sequencing (SHAPE-Seq).</a> Proc. Natl. Acad. Sci. USA. 108, 11063-11068 (2011).</li><li>Vasa, S. M., Guex, N., Wilkinson, K. A., Weeks, K. M., Giddings, M. C. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=ShapeFinder:+a+software+system+for+high-throughput+quantitative+analysis+of+nucleic+acid+reactivity+information+resolved+by+capillary+electrophoresis.">ShapeFinder: a software system for high-throughput quantitative analysis of nucleic acid reactivity information resolved by capillary electrophoresis.</a> RNA. 14, 1979-1990 (2008).</li><li>Reuter, J. S., Mathews, D. H. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=RNAstructure:+software+for+RNA+secondary+structure+prediction+and+analysis.">RNAstructure: software for RNA secondary structure prediction and analysis.</a> BMC Bioinformatics. 11, 129 (2010).</li><li>Pang, P. S., Elazar, M., Pham, E. A., Glenn, J. S. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Simplified+RNA+secondary+structure+mapping+by+automation+of+SHAPE+data+analysis.">Simplified RNA secondary structure mapping by automation of SHAPE data analysis.</a> Nucleic Acids Res. 39, e151 (2011).</li><li>Deigan, K. E., Li, T. W., Mathews, D. H., Weeks, K. M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Accurate+SHAPE-directed+RNA+structure+determination.">Accurate SHAPE-directed RNA structure determination.</a> Proc. Natl. Acad. Sci. USA. 106, 97-102 (2009).</li><li>Darty, K., Denise, A., Ponty, Y. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=VARNA:+Interactive+drawing+and+editing+of+the+RNA+secondary+structure.">VARNA: Interactive drawing and editing of the RNA secondary structure.</a> Bioinformatics. 25, 1974-1975 (2009).</li><li>Byun, Y., Han, K. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=PseudoViewer:+web+application+and+web+service+for+visualizing+RNA+pseudoknots+and+secondary+structures.">PseudoViewer: web application and web service for visualizing RNA pseudoknots and secondary structures.</a> Nucleic Acids Res. 34, 416-422 (2006).</li><li>Brown, T., Brown, D. J. S., Eckstein, F. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=.">.</a> Oligonucleotides and Analogues - A Practical Approach. , 20 (1990).</li><li>Legiewicz, M., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=The+RNA+Transport+Element+of+the+Murine+musD+Retrotransposon+Requires+Long-range+Intramolecular+Interactions+for+Function.">The RNA Transport Element of the Murine musD Retrotransposon Requires Long-range Intramolecular Interactions for Function.</a> J. Biol. Chem. 285, 42097-42104 (2010).</li><li>Steen, K., Siegfried, N. A., Weeks, K. M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Syntheis+of+1-methyl-8-nitroisatoic+anhydride+(1M7).">Syntheis of 1-methyl-8-nitroisatoic anhydride (1M7).</a> Protocol Exchange. , (2011).</li><li>Mortimer, S. A., Weeks, K. M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=A+fast-acting+reagent+for+accurate+analysis+of+RNA+secondary+and+tertiary+structure+by+SHAPE+chemistry.">A fast-acting reagent for accurate analysis of RNA secondary and tertiary structure by SHAPE chemistry.</a> J. Am. Chem. Soc. 129, 4144-4145 (2007).</li><li>Mitra, S., Shcherbakova, I. V., Altman, R. B., Brenowitz, M., Laederach, A. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=High-throughput+single-nucleotide+structural+mapping+by+capillary+automated+footprinting+analysis.">High-throughput single-nucleotide structural mapping by capillary automated footprinting analysis.</a> Nucleic Acids Res. 36, e63 (2008).</li><li>Giddings, M. C., Severin, J., Westphall, M., Wu, J., Smith, L. M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=A+software+system+for+data+analysis+in+automated+DNA+sequencing.">A software system for data analysis in automated DNA sequencing.</a> Genome Res. 8, 644-665 (1998).</li><li>Aviran, S., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Modeling+and+automation+of+sequencing-based+characterization+of+RNA+structure.">Modeling and automation of sequencing-based characterization of RNA structure.</a> Proc. Natl. Acad. Sci. USA. 108, 11069-11074 (2011).</li></ol>

We present here a detailed protocol for high-throughput SHAPE, a technique that allows secondary structure determination to single-nucleotide resolution for RNAs of any size. Moreover, coupling experimental SHAPE data with secondary structure prediction algorithms facilitates generation of RNA 2D models with a higher degree of accuracy than is possible with either method alone. The combination of fluorescently-labeled primers and automated CE provides significant advantages over the traditional gel-based SHAPE, facilitat...

To understand the functions of catalytic and non-coding RNAs involved in regulation of splicing, translation, virus replication and cancer, a detailed knowledge of RNA structure is required1,2. Unfortunately, accurate prediction of RNA folding presents a formidable challenge. Classical probing agents suffer from many disadvantages such as toxicity, incomplete nucleotide coverage and/or throughput limited to 100-150 nucleotides per experiment. Unaided secondary structure prediction algorithms are similarly disadvantageous, owing to inaccuracies resulting from their inability to effectively distinguish among energetically similar structures. Large RNAs in particular are also often refractory to methods of 3D structure determination such as X-ray crystallography and nuclear magnetic resonance (NMR) spectroscopy, due to their conformational flexibility and large quantities of highly pure samples required for these techniques.
High-throughput SHAPE solves many of these problems by providing an effective, simple approach to probing the structures of large RNAs at single-nucleotide resolution. Moreover, the reagents used for SHAPE are safe, easy to handle and, in contrast to most other chemical probing reagents, react with all four ribonucleotides. These reagents can also penetrate cellular membranes, making it possible to probe RNAs in their in vivo context(s)3. Originally developed in the Weeks laboratory4, SHAPE has been used to analyze a wide variety of RNAs, the most notable example being determination of the complete secondary structure of the ~9 kb HIV-1 RNA genome5. Other notable achievements using SHAPE include elucidation of the structures of infectious viroids6, human long non-coding RNAs7, yeast ribosomes8, and riboswitches9 as well as to identify protein binding sites in virion-associated HIV-1 RNA3. While the original and high-throughput variations of the SHAPE protocol have been published elsewhere10-12, the present work provides a detailed description of RNA secondary structure determination by high-throughput SHAPE using fluorescent oligonucleotides, the Beckman Coulter CEQ 8000 Genetic Analyzer, and SHAPEfinder and RNAStructure (v5.3) software. Previously unpublished technical details and troubleshooting advice are also included.
Variations of SHAPE
The essence of SHAPE and its variations is exposure of RNA in aqueous solution to electrophilic anhydrides that selectively acylate 2'-hydroxyl (2'-OH) ribose groups, producing bulky adducts at the sites of modification. This chemical reaction serves as a means of interrogating local RNA structural dynamics, as single-stranded nucleotides are more prone to adopt conformations conducive to electrophilic attack by these reagents, while base paired or architecturally constrained nucleotides are less or unreactive10. Sites of adduct formation are detected by reverse transcription initiating from fluorescently or radiolabeled primers hybridized to a specific site on the modified RNA (the "(+)" primer extension reaction). When reverse transcriptase (RT) fails to traverse the acylated ribonucleotides, a pool of cDNA products is produced whose lengths coincide with sites of modification. A control, "(-)" primer extension reaction utilizing RNA that has not been exposed to reagent is also performed so that premature termination of DNA synthesis (i.e. "stops") due to RNA structure, nonspecific RNA strand breakage, etc., may be distinguished from pausing produced by chemical modification. Finally, two dideoxy-sequencing reactions initiating from the same primers are used as markers to correlate reactive nucleotides with the RNA primary sequence following electrophoresis.
In the original application of SHAPE, the same 32P-end-labeled primer is utilized for the (+), (-), and two sequencing reactions. Products of these reactions are loaded into adjacent wells in a 5-8% polyacrylamide slab gel, and fractionated by denaturing polyacrylamide gel electrophoresis (PAGE; Figure 1). Quantitative analysis of the gel images produced by conventional SHAPE can be performed using SAFA, a semi-automated footprinting analysis software13.
In contrast, high-throughput SHAPE employs fluorescently labeled primers and automated capillary electrophoresis. Specifically, for each region of RNA under investigation, a set of four DNA primers having a common sequence but different 5' fluorescent labels must be synthesized or purchased. These differently-labeled oligonucleotides serve to prime two SHAPE reactions and two sequencing reactions, the products of which are pooled and fractionated/detected by automated capillary electrophoresis (CE). Whereas the reactivity profile of 100-150 nt of RNA can be obtained from a set of four reactions using the original approach, high-throughput SHAPE allows resolution of 300-600 nt from a single pooled sample3. Up to 8 sets of reactions may be fractionated simultaneously, while as many as 96 samples can prepared for fractionation over the course of 12 consecutive CE runs (Figure 2). Moreover, the SHAPEfinder software, developed to process and analyze data emerging from the CEQ and other genetic analyzers, is more automated and require much less user intervention than SAFA13 or other gel-analysis packages.
More advanced high-throughput methodologies have recently emerged such as PARS (parallel analysis of RNA structure)14 and Frag-Seq (fragment-sequencing)15, which use structure-specific enzymes rather than alkylation reagents in conjunction with next generation sequencing techniques to obtain information about RNA structure. Despite the attractiveness of these techniques, the many limitations inherent to nuclease probing still remain16. These problems can be circumvented in the SHAPE sequencing (SHAPE-Seq)17 protocol, where next generation sequencing is preceded by chemical modification and reverse transcription of RNAs in a manner similar to that performed in conventional SHAPE. While these methods may represent the future of RNA structure determination, it is important to remember that next generation sequencing is very expensive, and remains unavailable to many laboratories.
SHAPE Data Analysis
Data produced in the genetic analyzer is presented in the form of an electropherogram, wherein the fluorescence intensity of the sample(s) flowing through the capillary detector is plotted against an index of migration time. This plot takes the form of overlapping traces corresponding to the four fluorescence channels used to detect the different fluorophores, and where each trace is comprised of peaks corresponding to individual cDNA or sequencing products. Electropherogram data is exported from the genetic analyzer as a tab-delimited text file and imported into ShapeFinder transformation and analysis software18.
ShapeFinder is initially used to perform a series of mathematical transformations on the data to ensure that migration times and peak volumes accurately reflect the identities and quantities of the reaction products, respectively. Peaks are then aligned and integrated, and the results tabulated together with the primary RNA sequence. A "reactivity profile" for the pertinent segment of RNA is obtained by subtracting control values from the (+) values associated with each RNA nucleotide, and normalizing the data as described below. This profile is imported into RNAstructure (v5.3) software19,20 , which converts the normalized reactivity values into pseudo-energy constraints that are incorporated into the RNA secondary structure folding algorithm. Combining chemical probing and folding algorithms in this way significantly improves the accuracy of structure prediction compared to either method alone12,21. The output of RNAstructure (v5.3) includes images of the lowest energy RNA secondary structures color-coded with the SHAPE reactivity profile(s), as well as the same structures in textual dot-bracket notation. The latter may subsequently be exported to software dedicated to the graphical display of RNA secondary structure such as Varna22 and PseudoViewer23.
<img alt="Figure 1" fo:content-width="4.8in" fo:src="/files/ftp_upload/50243/50243fig1highres.jpg" src="/files/ftp_upload/50243/50243fig1.jpg" /> 
Figure 1. Flowchart of RNA structure determination via SHAPE4,10. (A) RNA may be obtained from biological samples or by in vitro transcription. (B) Depending on the source, RNA is folded or otherwise processed and modified with SHAPE reagent. (C) Reverse transcription using fluorescently or radioactively labeled primers. (D) cDNA products are fractionated via either capillary or slab gel-based electrophoresis. (E) Fragment analysis. (F) RNA structure prediction. <a href="http://www.jove.com/files/ftp_upload/50243/50243fig1large.jpg" target="_blank">Click here to view larger figure.</a>
<img alt="Figure 2" fo:content-width="6in" fo:src="/files/ftp_upload/50243/50243fig2highres.jpg" src="/files/ftp_upload/50243/50243fig2.jpg" /> 
Figure 2. The high-throughput character of CE-based SHAPE allows rapid analysis of multiple RNAs, and/or multiple segments of the same RNA. (A) Represents how an RNA may be divided into 300-600 nt sections (color coded in green, blue and red) (B) Sections of the RNA are probed independently using different sets of fluorescent primers (black arrows) (C) Sets of reactions are pooled and loaded into wells A1, B1, C1, etc, respectively, providing complete coverage for the ~3 kb RNA1. Reaction products from RNAs 2, 3, 4, etc. may be similarly prepared for fractionation in consecutive electrophoretic runs. <a href="http://www.jove.com/files/ftp_upload/50243/50243fig2large.jpg" target="_blank">Click here to view larger figure.</a>

<table border="1">
	<tbody>
		<tr>
			<td>&nbsp;</td>
			<td>&nbsp;</td>
			<td>&nbsp;</td>
			<td>REAGENTS</td>
		</tr>
		<tr>
			<td>N-methylisatoic anhydride (NMIA)</td>
			<td>Life technologies</td>
			<td>M25</td>
			<td>Dissolve in anhydrous DMSO</td>
		</tr>
		<tr>
			<td>1-methyl-t-nitroisatoic anhydride (1M7)</td>
			<td>see ref. 22</td>
			<td>&nbsp;</td>
			<td>&nbsp;</td>
		</tr>
		<tr>
			<td>Superscript III Reverse Transcriptase</td>
			<td>Life technologies</td>
			<td>18080044</td>
			<td>10,000 units</td>
		</tr>
		<tr>
			<td>Thermo sequenase cycle sequencing kit</td>
			<td>Affymetrix</td>
			<td>78500</td>
			<td>&nbsp;</td>
		</tr>
		<tr>
			<td>&nbsp;</td>
			<td>&nbsp;</td>
			<td>&nbsp;</td>
			<td>Materials provided by the user</td>
		</tr>
		<tr>
			<td>RNA of interest</td>
			<td>&nbsp;</td>
			<td>&nbsp;</td>
			<td>6 pmol per reaction (the limit of detection will be determined by the instrument)</td>
		</tr>
		<tr>
			<td>Sets of four 5' labeled primers (Cy5, Cy5.5, WellRed D2 and WellRed D1/Licor IR800)</td>
			<td>&nbsp;</td>
			<td>&nbsp;</td>
			<td>Primers are complementary to the RNA and are used in reverse transcription and sequencing reactions. The listed fluorophores are optimal for the Beckman Coulter 8000 CEQ. Primers may be purchased or synthesized in house.</td>
		</tr>
		<tr>
			<td>DNA template</td>
			<td>&nbsp;</td>
			<td>&nbsp;</td>
			<td>DNA is used for sequencing reactions, and must contain the sequence of the RNA being studied - including any 3'terminal extension, if present. Where applicable, it is often convenient to use the RNA transcription template.</td>
		</tr>
		<tr>
			<td>&nbsp;</td>
			<td>&nbsp;</td>
			<td>&nbsp;</td>
			<td>Buffers</td>
		</tr>
		<tr>
			<td>10x RNA renaturation buffer</td>
			<td>&nbsp;</td>
			<td>&nbsp;</td>
			<td>100 mM Tris-HCl pH 8.0, 1 M KCl, 1 mM EDTA</td>
		</tr>
		<tr>
			<td>5X RNA folding buffer</td>
			<td>&nbsp;</td>
			<td>&nbsp;</td>
			<td>200 mM Tris-HCl pH 8.0, 25 mM MgCl2, 2.5 mM EDTA, 650 mM KCl. (This buffer might be changed depending on the case (e.g. pH, EDTA, Mg, RNase inhibitor)</td>
		</tr>
		<tr>
			<td>2.5X RT mix</td>
			<td>&nbsp;</td>
			<td>&nbsp;</td>
			<td>4 &mu;l 5X buffer, 1 &mu;l 100 mM DTT, 1.5 &mu;l water,1 &mu;l 10 mM dNTPs, 0.5 &mu;l SuperScript III. Note that the 5X buffer and 100 mM DTT are provided with purchase of SuperScript III (Invitrogen).</td>
		</tr>
		<tr>
			<td>GenomeLab Sample Loading Solution (Beckman Coulter)</td>
			<td>&nbsp;</td>
			<td>&nbsp;</td>
			<td>Attention: Avoid multiple freeze-thaw cycles</td>
		</tr>
		<tr>
			<td>&nbsp;</td>
			<td>&nbsp;</td>
			<td>&nbsp;</td>
			<td>EQUIPMENT</td>
		</tr>
		<tr>
			<td>Capillary electrophoresis</td>
			<td>Beckman</td>
			<td>CEQ8000</td>
			<td>&nbsp;</td>
		</tr>
		<tr>
			<td>Thermocycler</td>
			<td>varies</td>
			<td>&nbsp;</td>
			<td>&nbsp;</td>
		</tr>
	</tbody>
</table>

rna secondary structure prediction using high-throughput shape

Understanding the function of RNA involved in biological processes requires a thorough knowledge of RNA structure. Toward this end, the methodology dubbed "high-throughput selective 2' hydroxyl acylation analyzed by primer extension", or SHAPE, allows prediction of RNA secondary structure with single nucleotide resolution. This approach utilizes chemical probing agents that preferentially acylate single stranded or flexible regions of RNA in aqueous solution. Sites of chemical modification are detected by reverse transcription of the modified RNA, and the products of this reaction are fractionated by automated capillary electrophoresis (CE). Since reverse transcriptase pauses at those RNA nucleotides modified by the SHAPE reagents, the resulting cDNA library indirectly maps those ribonucleotides that are single stranded in the context of the folded RNA. Using ShapeFinder software, the electropherograms produced by automated CE are processed and converted into nucleotide reactivity tables that are themselves converted into pseudo-energy constraints used in the RNAStructure (v5.3) prediction algorithm. The two-dimensional RNA structures obtained by combining SHAPE probing with in silico RNA secondary structure prediction have been found to be far more accurate than structures obtained using either method alone.

RNA containing the HIV-1 rev response element (RRE) and a 3' terminal structure cassette4 was prepared from a linearized plasmid by in vitro transcription, after which it was folded by heating, cooling, and incubation at 37 &deg;C in the presence of MgCl2. RNA was exposed to NMIA and then reverse transcribed from a 5'-end-labeled DNA primer hybridized to the 3' terminal structure cassette. The resulting SHAPE cDNA library, together with control and sequencing reactions, was then fractionate...

Watch this Scientific Journal Video about RNA Secondary Structure Prediction Using High-throughput SHAPE at JoVE.com

RNA Secondary Structure Prediction Using High-throughput SHAPE

High-throughput selective 2' hydroxyl acylation analyzed by primer extension (SHAPE) utilizes a novel chemical probing technology, reverse transcription, capillary electrophoresis and secondary structure prediction software to determine the structures of RNAs from several hundred to several thousand nucleotides at single nucleotide resolution.

Understanding the function of RNA involved in biological processes requires a thorough knowledge of RNA structure. Toward this end, the methodology dubbed ...

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