Using an RNA Secondary Structure Partition Function to Determine Confidence in Base Pairs Predicted by Free Energy Minimization

Overview

Journal RNA

Specialty Molecular Biology

Date 2004 Jul 24

PMID 15272118

Citations 187

Authors

David H Mathews

Affiliations

Soon will be listed here.

Abstract

A partition function calculation for RNA secondary structure is presented that uses a current set of nearest neighbor parameters for conformational free energy at 37 degrees C, including coaxial stacking. For a diverse database of RNA sequences, base pairs in the predicted minimum free energy structure that are predicted by the partition function to have high base pairing probability have a significantly higher positive predictive value for known base pairs. For example, the average positive predictive value, 65.8%, is increased to 91.0% when only base pairs with probability of 0.99 or above are considered. The quality of base pair predictions can also be increased by the addition of experimentally determined constraints, including enzymatic cleavage, flavin mono-nucleotide cleavage, and chemical modification. Predicted secondary structures can be color annotated to demonstrate pairs with high probability that are therefore well determined as compared to base pairs with lower probability of pairing.

Citing Articles

The RNA Revolution in the Central Molecular Biology Dogma Evolution.

Haseltine W, Patarca R Int J Mol Sci. 2024; 25(23).

PMID: 39684407 PMC: 11641533. DOI: 10.3390/ijms252312695.

Automated Design of Oligopools and Rapid Analysis of Massively Parallel Barcoded Measurements.

Hossain A, Cetnar D, LaFleur T, McLellan J, Salis H ACS Synth Biol. 2024; 13(12):4218-4232.

PMID: 39641628 PMC: 11669329. DOI: 10.1021/acssynbio.4c00661.

New insights and investigation: Morphomolecular notes on the infraciliature, taxonomy, and systematics of pleurostomatid ciliates (Protozoa, Ciliophora), with establishment of a new suborder, two new genera, and three new species.

Zhang G, Zhang T, Chi Y, Pan H, Zhang Z, Zhang J Zool Res. 2024; 45(6):1327-1346.

PMID: 39479998 PMC: 11668957. DOI: 10.24272/j.issn.2095-8137.2024.128.

DecoyFinder: Identification of Contaminants in Sets of Homologous RNA Sequences.

Zhu M, Zuber J, Tan Z, Sharma G, Mathews D bioRxiv. 2024; .

PMID: 39464058 PMC: 11507696. DOI: 10.1101/2024.10.12.618037.

Template switching enables chemical probing of native RNA structures.

Hall I, OSteen M, Gold S, Keane S, Weidmann C RNA. 2024; 31(1):113-125.

PMID: 39438135 PMC: 11648929. DOI: 10.1261/rna.079926.123.

References

Hansen J, Schmeing T, Moore P, Steitz T . Structural insights into peptide bond formation. Proc Natl Acad Sci U S A. 2002; 99(18):11670-5. PMC: 129327. DOI: 10.1073/pnas.172404099. View

Waterston R, Lindblad-Toh K, Birney E, Rogers J, Abril J, Agarwal P . Initial sequencing and comparative analysis of the mouse genome. Nature. 2002; 420(6915):520-62. DOI: 10.1038/nature01262. View

Chamberlin S, Weeks K . Differential helix stabilities and sites pre-organized for tertiary interactions revealed by monitoring local nucleotide flexibility in the bI5 group I intron RNA. Biochemistry. 2003; 42(4):901-9. DOI: 10.1021/bi026817h. View

Hoffmann B, Mitchell G, Gendron P, Major F, Andersen A, Collins R . NMR structure of the active conformation of the Varkud satellite ribozyme cleavage site. Proc Natl Acad Sci U S A. 2003; 100(12):7003-8. PMC: 165820. DOI: 10.1073/pnas.0832440100. View

Hofacker I . Vienna RNA secondary structure server. Nucleic Acids Res. 2003; 31(13):3429-31. PMC: 169005. DOI: 10.1093/nar/gkg599. View

Dirks R, Pierce N . A partition function algorithm for nucleic acid secondary structure including pseudoknots. J Comput Chem. 2003; 24(13):1664-77. DOI: 10.1002/jcc.10296. View

Matveeva O, Mathews D, Tsodikov A, Shabalina S, GESTELAND R, Atkins J . Thermodynamic criteria for high hit rate antisense oligonucleotide design. Nucleic Acids Res. 2003; 31(17):4989-94. PMC: 212809. DOI: 10.1093/nar/gkg710. View

Cannone J, Subramanian S, Schnare M, Collett J, DSouza L, Du Y . The comparative RNA web (CRW) site: an online database of comparative sequence and structure information for ribosomal, intron, and other RNAs. BMC Bioinformatics. 2002; 3:2. PMC: 65690. DOI: 10.1186/1471-2105-3-2. View

Ding Y, Lawrence C . A statistical sampling algorithm for RNA secondary structure prediction. Nucleic Acids Res. 2003; 31(24):7280-301. PMC: 297010. DOI: 10.1093/nar/gkg938. View

10.

Ruan J, Stormo G, Zhang W . An iterated loop matching approach to the prediction of RNA secondary structures with pseudoknots. Bioinformatics. 2003; 20(1):58-66. DOI: 10.1093/bioinformatics/btg373. View

11.

Mathews D, Disney M, Childs J, Schroeder S, Zuker M, Turner D . Incorporating chemical modification constraints into a dynamic programming algorithm for prediction of RNA secondary structure. Proc Natl Acad Sci U S A. 2004; 101(19):7287-92. PMC: 409911. DOI: 10.1073/pnas.0401799101. View

12.

Brennan T, Sundaralingam M . Structlre of transfer RNA molecules containing the long variable loop. Nucleic Acids Res. 1976; 3(11):3235-50. PMC: 343166. DOI: 10.1093/nar/3.11.3235. View

13.

Speek M, Lind A . Structural analyses of E. coli 5S RNA fragments, their associates and complexes with proteins L18 and L25. Nucleic Acids Res. 1982; 10(3):947-65. PMC: 326213. DOI: 10.1093/nar/10.3.947. View

14.

Walter P, Blobel G . Signal recognition particle contains a 7S RNA essential for protein translocation across the endoplasmic reticulum. Nature. 1982; 299(5885):691-8. DOI: 10.1038/299691a0. View

15.

Fekete M, Hofacker I, Stadler P . Prediction of RNA base pairing probabilities on massively parallel computers. J Comput Biol. 2000; 7(1-2):171-82. DOI: 10.1089/10665270050081441. View

16.

Schultes E, Bartel D . One sequence, two ribozymes: implications for the emergence of new ribozyme folds. Science. 2000; 289(5478):448-52. DOI: 10.1126/science.289.5478.448. View

17.

Ban N, Nissen P, Hansen J, Moore P, Steitz T . The complete atomic structure of the large ribosomal subunit at 2.4 A resolution. Science. 2000; 289(5481):905-20. DOI: 10.1126/science.289.5481.905. View

18.

Michel F, Umesono K, Ozeki H . Comparative and functional anatomy of group II catalytic introns--a review. Gene. 1989; 82(1):5-30. DOI: 10.1016/0378-1119(89)90026-7. View

19.

Knapp G . Enzymatic approaches to probing of RNA secondary and tertiary structure. Methods Enzymol. 1989; 180:192-212. DOI: 10.1016/0076-6879(89)80102-8. View

20.

McCaskill J . The equilibrium partition function and base pair binding probabilities for RNA secondary structure. Biopolymers. 1990; 29(6-7):1105-19. DOI: 10.1002/bip.360290621. View