RNA Secondary Structure Analysis Using RNAstructure
互联网
1078
- Abstract
- Table of Contents
- Figures
- Literature Cited
Abstract
RNAstructure is a user?friendly program for the prediction and analysis of RNA secondary structure under Microsoft Windows. This unit provides protocols for RNA secondary structure prediction and prediction of high?affinity oligonucleotide binding sites to a structured RNA target.
Keywords: RNA Secondary Structure Prediction; Free Energy Minimization; Thermodynamics
GO TO THE FULL PROTOCOL:
PDF or HTML at Wiley Online LibraryTable of Contents
- Basic Protocol 1: Predicting Secondary Structure and Predicting Base‐Pair Probabilities
- Basic Protocol 2: Predicting Binding Affinities of Oligonucleotides Complementary to an RNA Target with OligoWalk
- Guidelines for Understanding Results
- Commentary
- Literature Cited
- Figures
- Tables
GO TO THE FULL PROTOCOL:
PDF or HTML at Wiley Online LibraryMaterials
GO TO THE FULL PROTOCOL:
PDF or HTML at Wiley Online LibraryFigures
-
Figure 12.6.1 Screen shot of the RNAstructure sequence editor. The D. melanogaster 5S rRNA sequence is entered and formatted using the Format Sequence button. View Image -
Figure 12.6.2 Screen shot of the RNA secondary structure prediction window. View Image -
Figure 12.6.3 The lowest free energy secondary structure predicted for the D. melanogaster 5S rRNA sequence as drawn by RNAstructure. View Image -
Figure 12.6.4 The probability dot plot for base pairs in the D. melanogaster 5S rRNA sequence. Each dot in this plot is a single base pair and is associated with a base‐pairing probability. For pairs between nucleotides i and j , with i < j , i is down the right‐hand side of the plot and j is across the top. In RNAstructure, dots are colored to indicate a probability interval, with the most probable pairs in red and the least probable in blue. The current base pairs displayed have pairing probability of ≥1%. A color key is drawn at the bottom of the window (not shown in this view). After clicking on a dot, the pair and −log10 (base‐pair probability) are indicated at the bottom of the RNAstructure window. The current display shows that the base pair between G75 and C102 was clicked and has −log10 (base‐pair probability) of 5.33232 × 10−2 (88.4457%). View Image -
Figure 12.6.5 The lowest free energy secondary structure predicted for the D. melanogaster 5S rRNA sequence with color annotation. The color annotation key is shown in the lower right‐hand corner. The most probable base pairs are red and least probable are violet. The predicted pairs with the highest base pair probabilities are more likely to be correctly predicted pairs (Mathews, ). View Image -
Figure 12.6.6 The OligoWalk input window. View Image -
Figure 12.6.7 The OligoWalk output display. View Image
Videos
Literature Cited
| Bohula, E.A., Salisbury, A.J., Sohail, M., Playford, M.P., Riedemann, J., Southern, E.M., and Macaulay, V.M. 2003. The efficacy of small interfering RNAs targeted to the type 1 insulin‐like growth factor receptor (IGF1R) is influenced by secondary structure in the IGF1R transcript. J. Biol. Chem. 278:15991‐15997. | |
| Brown, J.W. 1999. The ribonuclease P database. Nucl. Acids Res. 27:314. | |
| Burgstaller, P., Hermann, T., Huber, C., Westhof, E., and Famulok, M. 1997. Isoalloxazine derivatives promote photocleavage of natural RNAs at GU base pairs embedded within helices. Nucl. Acids Res. 25:4018‐4027. | |
| Condon, A., Davy, B., Rastegari, B., Tarrant, F., and Zhao, S. 2004. Classifying RNA pseudoknotted structures. Theor. Comp. Sci. 320:35‐50. | |
| Dirks, R.M. and Pierce, N.A. 2004. An algorithm for computing nucleic acid base‐pairing probabilities including pseudoknots. J. Comput. Chem. 25:1295‐1304. | |
| Dowell, R.D. and Eddy, S.R. 2004. Evaluation of several lightweight stochastic context‐free grammars for RNA secondary structure prediction. BMC Bioinformatics 5:71. | |
| Eddy, S.R. 2004. How do RNA folding algorithms work? Nat. Biotechnol. 22:1457‐1458. | |
| Ehresmann, C., Baudin, F., Mougel, M., Romby, P., Ebel, J., and Ehresmann, B. 1987. Probing the structure of RNAs in solution. Nucl. Acids Res. 15:9109‐9128. | |
| Far, R.K. and Sczakiel, G. 2003. The activity of siRNA in mammalian cells is related to structural target accessibility: A comparison with antisense oligonucleotides. Nucl. Acids Res. 31:4417‐4424. | |
| Heale, B.S., Soifer, H.S., Bowers, C., and Rossi, J.J. 2005. siRNA target site secondary structure predictions using local stable substructures. Nucl. Acids Res. 33:e30. | |
| Hofacker, I.L. 2003. Vienna RNA secondary structure server. Nucl. Acids Res. 31:3429‐3431. | |
| Knapp, G. 1989. Enzymatic approaches to probing RNA secondary and tertiary structure. Methods Enzymol. 180:192‐212. | |
| Mathews, D.H. 2004. Using an RNA secondary structure partition function to determine confidence in base pairs predicted by free energy minimization. RNA 10:1178‐1190. | |
| Mathews, D.H. 2005. Predicting a set of minimal free energy RNA secondary structures common to two sequences. Bioinformatics 21:2246‐2253. | |
| Mathews, D.H. and Turner, D.H. 2002. Dynalign: An algorithm for finding the secondary structure common to two RNA sequences. J. Mol. Biol. 317:191‐203. | |
| Mathews, D.H. and Zuker, M. 2004. Predictive methods using RNA sequences. In Bioinformatics: A Practical Guide to the Analysis of Genes and Proteins, 3rd Ed. (A. Baxevenis and F. Oullette, eds.) pp. 143‐170, John Wiley & Sons, Hoboken, N.J. | |
| Mathews, D.H., Burkard, M.E., Freier, S.M., Wyatt, J.R., and Turner, D.H. 1999a. Predicting oligonucleotide affinity to nucleic acid targets. RNA 5:1458‐1469. | |
| Mathews, D.H., Sabina, J., Zuker, M., and Turner, D.H. 1999b. Expanded sequence dependence of thermodynamic parameters provides improved prediction of RNA secondary structure. J. Mol. Biol. 288:911‐940. | |
| Mathews, D.H., Turner, D.H., and Zuker, M. 2000. RNA secondary structure prediction. In Current Protocols in Nucleic Acid Chemistry (S.L. Beaucage, D.E. Bergstrom, P. Herdewijn, and A. Matsuda, eds.) pp. 11.2.1‐11.2.10. John Wiley & Sons, Hoboken, N.J. | |
| Mathews, D.H., Disney, M.D., Childs, J.L., Schroeder, S.J., Zuker, M., and Turner, D.H. 2004. Incorporating chemical modification constraints into a dynamic programming algorithm for prediction of RNA secondary structure. Proc. Natl. Acad. Sci. U.S.A. 101:7287‐7292. | |
| Matveeva, O.V., Mathews, D.H., Tsodikov, A.D., Shabalina, S.A., Gesteland, R.F., Atkins, J.F., and Freier, S.M. 2003. Thermodynamic criteria for high hit rate antisense oligonucleotide design. Nucl. Acids Res. 31:4989‐4994. | |
| Petch, A.K., Sohail, M., Hughes, M.D., Benter, I., Darling, J., Southern, E.M., and Akhtar, S. 2003. Messenger RNA expression profiling of genes involved in epidermal growth factor receptor signalling in human cancer cells treated with scanning array‐designed antisense oligonucleotides. Biochem. Pharmacol. 66:819‐830. | |
| Rivas, E. and Eddy, S.R. 1999. A dynamic programming algorithm for RNA structure prediction including pseudoknots. J. Mol. Biol. 285:2053‐2068. | |
| Szymanski, M., Barciszewska, M.Z., Barciszewski, J., and Erdmann, V.A. 2000. 5S ribosomal RNA database Y2K. Nucl. Acids Res. 28:166‐167. | |
| Williams, K.P. and Bartel, D.P. 1996. Phylogenetic analysis of tmRNA secondary structure. RNA 2:1306‐1310. | |
| Xia, T., SantaLucia, J. Jr., Burkard, M.E., Kierzek, R., Schroeder, S.J., Jiao, X., Cox, C., and Turner, D.H. 1998. Thermodynamic parameters for an expanded nearest‐neighbor model for formation of RNA duplexes with Watson‐Crick pairs. Biochemistry 37:14719‐14735. | |
| Zuker, M. 1989. On finding all suboptimal foldings of an RNA molecule. Science 244:48‐52. | |
| Zuker, M. 2003. Mfold web server for nucleic acid folding and hybridization prediction. Nucl. Acids Res. 31:3406‐3415. | |
| Internet Resources | |
| http://rna.urmc.rochester.edu | |
| Mathews lab Web site, where RNAstructure can be downloaded. |
GO TO THE FULL PROTOCOL:
PDF or HTML at Wiley Online Library
