Expanded sequence dependence of thermodynamic parameters improves prediction of RNA secondary structure
Open accessAbstract
An improved dynamic programming algorithm is reported for RNA secondary structure prediction by free energy minimization. Thermodynamic parameters for the stabilities of secondary structure motifs are revised to include expanded sequence dependence as revealed by recent experiments. Additional algorithmic improvements include reduced search time and storage for multibranch loop free energies and improved imposition of folding constraints. An extended database of 151,503 nt in 955 structures? determined by comparative sequence analysis was assembled to allow optimization of parameters not based on experiments and to test the accuracy of the algorithm. On average, the predicted lowest free energy structure contains 73 % of known base-pairs when domains of fewer than 700 nt are folded; this compares with 64 % accuracy for previous versions of the algorithm and parameters. For a given sequence, a set of 750 generated structures contains one structure that, on average, has 86 % of known base-pairs. Experimental constraints, derived from enzymatic and flavin mononucleotide cleavage, improve the accuracy of structure predictions.
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Integrity signals
Registry
Cites
Statistics
Claims the paper makes
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Claims other papers make about this one
Each is checked against this paper’s own text: does it say what the citing paper says it does?
The energy terms used for stacking and mismatches have an error of around 5-10%.
“These energy terms have an error of around 5–10% (32,33,35).”
From The prebiotic evolutionary advantage of transferring genetic information from RNA to DNA (2011) · cites this paper as [32]
The nearest-neighbor model was used to predict RNA and DNA duplex stabilities.
“To estimate ΔGn,m, we use the nearest-neighbor model for predicting RNA and DNA duplex stabilities (31,32,33).”
From The prebiotic evolutionary advantage of transferring genetic information from RNA to DNA (2011) · cites this paper as [32]
Self-check
Percentages, sums and reported differences re-computed from the paper’s own numbers.
The self-check needs the paper’s full text.
Cites
Adaptation in Natural and Artificial Systems
Holland, J. H. (1992) · The MIT Press eBooks · doi:10.7551/mitpress/1090.001.0001 · Cited by 47,340 · see citing works
Optimal computer folding of large RNA sequences using thermodynamics and auxiliary information
Zuker, M., & Stiegler, P. (1981) · Nucleic Acids Research · doi:10.1093/nar/9.1.133 · Cited by 3,604 · see citing works
Self-citationLight-Directed, Spatially Addressable Parallel Chemical Synthesis
Fodor, S. P. A., Read, J., Pirrung, M. C., Stryer, L., Lu, A. T., & Solas, D. W. (1991) · Science · doi:10.1126/science.1990438 · Cited by 2,697 · see citing works
Fast folding and comparison of RNA secondary structures
Hofacker, I. L., Fontana, W., Stadler, P. F., Bonhoeffer, S., Tacker, M., & Schuster, P. M. (1994) · Monatshefte für Chemie - Chemical Monthly · doi:10.1007/bf00818163 · Cited by 2,314 · see citing works
On Finding All Suboptimal Foldings of an RNA Molecule
Zuker, M. (1989) · Science · doi:10.1126/science.2468181 · Cited by 2,023 · see citing works
Self-citationCompilation of tRNA sequences and sequences of tRNA genes
Sprinzl, M. (2004) · Nucleic Acids Research · doi:10.1093/nar/gki012 · Cited by 1,916 · see citing works
Improved free-energy parameters for predictions of RNA duplex stability.
Freier, S. M., Kierzek, R., Jaeger, J. A., Sugimoto, N., Caruthers, M. H., Neilson, T., & Turner, D. H. (1986) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.83.24.9373 · Cited by 1,470 · see citing works
Self-citationIntramolecular Reaction in Polycondensations. I. The Theory of Linear Systems
Jacobson, H., & STOCKMAYER, W. H. (1950) · The Journal of Chemical Physics · doi:10.1063/1.1747547 · Cited by 1,410 · see citing works
The equilibrium partition function and base pair binding probabilities for RNA secondary structure
McCaskill, J. S. (1990) · Biopolymers · doi:10.1002/bip.360290621 · Cited by 1,288 · see citing works
Crystal Structure of a Group I Ribozyme Domain: Principles of RNA Packing
Cate, J. H. D., Gooding, A. R., Podell, E. R., Zhou, K., Golden, B. L., Kundrot, C. E., Cech, T. R., & Doudna, J. A. (1996) · Science · doi:10.1126/science.273.5282.1678 · Cited by 1,249 · see citing works
Michel, F., & Westhof, É. (1990) · Journal of Molecular Biology · doi:10.1016/0022-2836(90)90386-z · Cited by 1,239 · see citing works
Xia, T., SantaLucia, J., Burkard, M. E., Kierzek, R., Schroeder, S. J., Jiao, X., Cox, C., & Turner, D. H. (1998) · Biochemistry · doi:10.1021/bi9809425 · Cited by 1,140 · see citing works
Self-citationGenetic Algorithms: Principles of Natural Selection Applied to Computation
Forrest, S. (1993) · Science · doi:10.1126/science.8346439 · Cited by 882 · see citing works
Improved predictions of secondary structures for RNA.
Jaeger, J. A., Turner, D. H., & Zuker, M. (1989) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.86.20.7706 · Cited by 817 · see citing works
Self-citationComparative and functional anatomy of group II catalytic introns — a review
Michel, F., Kazuhiko, U., & Haruo, O. (1989) · Gene · doi:10.1016/0378-1119(89)90026-7 · Cited by 790 · see citing works
Stability of ribonucleic acid double-stranded helices
Borer, P. N., Dengler, B., Tinoco, I., & Uhlenbeck, O. C. (1974) · Journal of Molecular Biology · doi:10.1016/0022-2836(74)90357-x · Cited by 762 · see citing works
Compilation of tRNA sequences and sequences of tRNA genes
Sprinzl, M. (1998) · Nucleic Acids Research · doi:10.1093/nar/26.1.148 · Cited by 750 · see citing works
Probing the structure of RNAs in solution
Ehresmann, C., Baudin, F., Mougel, M., Romby, P., Ebel, J., & Ehresmann, B. (1987) · Nucleic Acids Research · doi:10.1093/nar/15.22.9109 · Cited by 733 · see citing works
Detailed analysis of the higher-order structure of 16S-like ribosomal ribonucleic acids
Woese, C. R., Gutell, R. R., Gupta, R. C., et al. (1983) · Microbiological Reviews · doi:10.1128/mr.47.4.621-669.1983 · Cited by 652 · see citing works
Collection of small subunit (16S- and 16S-like) ribosomal RNA structures: 1994
Gutell, R. R. (1994) · Nucleic Acids Research · doi:10.1093/nar/22.17.3502 · Cited by 530 · see citing works
Architecture of ribosomal RNA: constraints on the sequence of "tetra-loops".
Woese, C. R., Winker, S., & Gutell, R. R. (1990) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.87.21.8467 · Cited by 523 · see citing works
Walter, A. E., Turner, D. H., Kim, J., Lyttle, M. H., Müller, P., Mathews, D. H., & Zuker, M. (1994) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.91.20.9218 · Cited by 466 · see citing works
Self-citationA compilation of large subunit (23S and 23S-like) ribosomal RNA structures: 1993
Gutell, R. R., Gray, M. W., & Schnare, M. N. (1993) · Nucleic Acids Research · doi:10.1093/nar/21.13.3055 · Cited by 447 · see citing works
Brown, J. (1998) · Nucleic Acids Research · doi:10.1093/nar/26.1.351 · Cited by 429 · see citing works
Metals, Motifs, and Recognition in the Crystal Structure of a 5S rRNA Domain
Correll, C. C., Freeborn, B., Moore, P. B., & Steitz, T. A. (1997) · Cell · doi:10.1016/s0092-8674(00)80457-2 · Cited by 393 · see citing works
Structure of an unusually stable RNA hairpin
Varani, G., Cheong, C., & Tinoco, I. (1991) · Biochemistry · doi:10.1021/bi00227a016 · Cited by 369 · see citing works
[11] Predicting thermodynamic properties of RNA
Serra, M. J., & Turner, D. H. (1995) · Methods in enzymology on CD-ROM/Methods in enzymology · doi:10.1016/0076-6879(95)59047-1 · Cited by 364 · see citing works
Self-citationFrequent use of the same tertiary motif by self‐folding RNAs.
Costa, M. C. R., & Michel, F. (1995) · The EMBO Journal · doi:10.1002/j.1460-2075.1995.tb07111.x · Cited by 356 · see citing works
Tuerk, C., Gauss, P., Thermes, C., Groebe, D. R., Gayle, M. A., Guild, N. A., Stormo, G. D., d’Aubenton-Carafa, Y., Uhlenbeck, O. C., & Tinoco, I. (1988) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.85.5.1364 · Cited by 355 · see citing works
The Computer Simulation of RNA Folding Pathways Using a Genetic Algorithm
Gultyaev, A. P., van Batenburg, F. H. D., & Pleij, C. W. A. (1995) · Journal of Molecular Biology · doi:10.1006/jmbi.1995.0356 · Cited by 321 · see citing works
Molecular Modeling of Nucleic Acids
Leontis, N. B., & Jr.2, J. S. (1997) · ACS symposium series · doi:10.1021/bk-1998-0682 · Cited by 304 · see citing works
A thermodynamic study of unusually stable RNA and DNA hairpins
Antao, V., Lai, S. Y., & Tinoco, I. (1991) · Nucleic Acids Research · doi:10.1093/nar/19.21.5901 · Cited by 303 · see citing works
McDowell, J. A., & Turner, D. H. (1996) · Biochemistry · doi:10.1021/bi9615710 · Cited by 297 · see citing works
Self-citationThe molecular mechanism of thermal unfolding of Escherichia coli formylmethionine transfer RNA
Crothers, D. M., Cole, P. E., Hilbers, C. W., et al. (1974) · Journal of Molecular Biology · doi:10.1016/0022-2836(74)90560-9 · Cited by 287 · see citing works
Lehnert, V., Jaeger, L., Francois, M., & Westhof, É. (1996) · Chemistry & Biology · doi:10.1016/s1074-5521(96)90166-0 · Cited by 287 · see citing works
Pley, H. W., Flaherty, K. M., & McKay, D. B. (1994) · Nature · doi:10.1038/372111a0 · Cited by 274 · see citing works
Thermodynamic parameters for loop formation in RNA and DNA hairpin tetraloops
Antao, V., & Tinoco, I. (1992) · Nucleic Acids Research · doi:10.1093/nar/20.4.819 · Cited by 249 · see citing works
GAAA Tetraloop and Conserved Bulge Stabilize Tertiary Structure of a Group I Intron Domain
Murphy, F. L., & Cech, T. R. (1994) · Journal of Molecular Biology · doi:10.1006/jmbi.1994.1117 · Cited by 244 · see citing works
Involvement of a GNRA tetraloop in long-range RNA tertiary interactions
Jaeger, L., Michel, F., & Westhof, É. (1994) · Journal of Molecular Biology · doi:10.1016/0022-2836(94)90055-8 · Cited by 237 · see citing works
Massire, C., Jaeger, L., & Westhof, É. (1998) · Journal of Molecular Biology · doi:10.1006/jmbi.1998.1797 · Cited by 234 · see citing works
Characterization of RNA hairpin loop stability
Groebe, D. R., & Uhlenbeck, O. C. (1988) · Nucleic Acids Research · doi:10.1093/nar/16.24.11725 · Cited by 211 · see citing works
Major Groove Accessibility of RNA
Weeks, K. M., & Crothers, D. M. (1993) · Science · doi:10.1126/science.7690496 · Cited by 205 · see citing works
[16] Enzymatic approaches to probing of RNA secondary and tertiary structure
Knapp, G. (1989) · Methods in enzymology on CD-ROM/Methods in enzymology · doi:10.1016/0076-6879(89)80102-8 · Cited by 198 · see citing works
Parallel thermodynamic analysis of duplexes on oligodeoxyribonucleotide microchips
Fotin, A., Drobyshev, A. L., Proudnikov, D., Perov, A. N., & Mirzabekov, A. D. (1998) · Nucleic Acids Research · doi:10.1093/nar/26.6.1515 · Cited by 195 · see citing works
An APL-programmed genetic algorithm for the prediction of RNA secondary structure
van Batenburg, F. H. D., Gultyaev, A. P., & Pleij, C. W. A. (1995) · Journal of Theoretical Biology · doi:10.1006/jtbi.1995.0098 · Cited by 193 · see citing works
Assessment of a model for intron RNA secondary structure relevant to RNA self-splicing — a review
Waring, R. B., & Davies, R. W. (1984) · Gene · doi:10.1016/0378-1119(84)90145-8 · Cited by 190 · see citing works
Using reliability information to annotate RNA secondary structures
Zuker, M., & Jacobson, A. B. (1998) · RNA · doi:10.1017/s1355838298980116 · Cited by 174 · see citing works
Self-citationSchnare, M. N., Damberger, S. H., Gray, M. W., et al. (1996) · Journal of Molecular Biology · doi:10.1006/jmbi.1996.0119 · Cited by 169 · see citing works
Banerjee, A. R., Jaeger, J. A., & Turner, D. H. (1993) · Biochemistry · doi:10.1021/bi00052a021 · Cited by 164 · see citing works
Self-citation4 Probing RNA Structure, Function, and History by Comparative Analysis
Pace, N. R., Thomas, B. C., & Woese, C. R. (1993) · doi:10.1101/087969589.37.113 · Cited by 161 · see citing works
Phylogenetic analysis of tmRNA secondary structure.
Williams, K. P., & Bartel, D. P. (1996) · PubMed · Cited by 158 · see citing works
Thermodynamic and spectroscopic study of bulge loops in oligoribonucleotides
Longfellow, C. E., Kierzek, R., & Turner, D. H. (1990) · Biochemistry · doi:10.1021/bi00453a038 · Cited by 151 · see citing works
Self-citationSolution Structure of the CUUG Hairpin Loop: A Novel RNA Tetraloop Motif
Jucker, F. M., & Pardi, A. (1995) · Biochemistry · doi:10.1021/bi00044a019 · Cited by 150 · see citing works
SantaLucia, J., Kierzek, R., & Turner, D. H. (1991) · Biochemistry · doi:10.1021/bi00247a021 · Cited by 140 · see citing works
Self-citationProbing the structure of the Escherichia coli 10Sa RNA (tmRNA).
Felden, B., Himeno, H., Muto, A., McCutcheon, J. P., Atkins, J. F., & Gesteland, R. F. (1997) · PubMed Central · Cited by 136 · see citing works
Freier, S. M., Sugimoto, N., Sinclair, A., et al. (1986) · Biochemistry · doi:10.1021/bi00359a020 · Cited by 128 · see citing works
A comparative database of group I intron structures
Damberger, S. H., & Gutell, R. R. (1994) · Nucleic Acids Research · doi:10.1093/nar/22.17.3508 · Cited by 119 · see citing works
A Periodic Table of Tandem Mismatches in RNA
Wu, M., McDowell, J. A., & Turner, D. H. (1995) · Biochemistry · doi:10.1021/bi00010a009 · Cited by 119 · see citing works
Self-citationSolution structure of a GAAA tetraloop receptor RNA
Butcher, S. E., Dieckmann, T., & Feigon, J. F. (1997) · The EMBO Journal · doi:10.1093/emboj/16.24.7490 · Cited by 116 · see citing works
Assessing the reliability of RNA folding using statistical mechanics
Huynen, M. A., Gutell, R. R., & Konings, D. A. M. (1997) · Journal of Molecular Biology · doi:10.1006/jmbi.1997.0889 · Cited by 114 · see citing works
Free energy of imperfect nucleic acid helices
Fink, T. R., & Crothers, D. M. (1972) · Journal of Molecular Biology · doi:10.1016/s0022-2836(72)80002-0 · Cited by 111 · see citing works
He, L., Kierzek, R., SantaLucia, J., et al. (1991) · Biochemistry · doi:10.1021/bi00110a015 · Cited by 111 · see citing works
Effects of 3' dangling end stacking on the stability of GGCC and CCGG double helixes
Freier, S. M., Burger, B. J., Alkema, D., Neilson, T., & Turner, D. H. (1983) · Biochemistry · doi:10.1021/bi00295a025 · Cited by 110 · see citing works
Self-citationThermodynamics of RNA Folding in a Conserved Ribosomal RNA Domain
Laing, L. G., & Draper, D. E. (1994) · Journal of Molecular Biology · doi:10.1006/jmbi.1994.1255 · Cited by 106 · see citing works
Monitoring of the Cooperative Unfolding of the sunY Group I Intron of Bacteriophage T4
Jaeger, L., Westhof, É., & Michel, F. (1993) · Journal of Molecular Biology · doi:10.1006/jmbi.1993.1590 · Cited by 101 · see citing works
Zuker, M., & Jacobson, A. B. (1995) · Nucleic Acids Research · doi:10.1093/nar/23.14.2791 · Cited by 101 · see citing works
Self-citation[18] Phylogenetic comparative analysis of RNA secondary structure
James, B. D., Olsen, G. J., & Pace, N. R. (1989) · Methods in enzymology on CD-ROM/Methods in enzymology · doi:10.1016/0076-6879(89)80104-1 · Cited by 99 · see citing works
SantaLucia, J., Kierzek, R., & Turner, D. H. (1991) · Journal of the American Chemical Society · doi:10.1021/ja00011a039 · Cited by 98 · see citing works
Self-citationThe Signal Recognition Particle Database (SRPDB)
Samuelsson, T., & Zwieb, C. W. (1999) · Nucleic Acids Research · doi:10.1093/nar/27.1.169 · Cited by 98 · see citing works
Mathews, D. H., Banerjee, A. R., Luan, D. D., Eickbush, T. H., & Turner, D. H. (1997) · PubMed Central · Cited by 92 · see citing works
Self-citationEnergetics of internal GU mismatches in ribooligonucleotide helixes
Sugimoto, N., Kierzek, R., Freier, S. M., et al. (1986) · Biochemistry · doi:10.1021/bi00367a061 · Cited by 89 · see citing works
Peritz, A. E., Kierzek, R., Sugimoto, N., et al. (1991) · Biochemistry · doi:10.1021/bi00240a013 · Cited by 85 · see citing works
Free energy contributions of G.cntdot.U and other terminal mismatches to helix stability
Freier, S. M., Kierzek, R., Caruthers, M. H., et al. (1986) · Biochemistry · doi:10.1021/bi00359a019 · Cited by 84 · see citing works
Walter, A. E., & Turner, D. H. (1994) · Biochemistry · doi:10.1021/bi00208a024 · Cited by 83 · see citing works
Self-citationHarris, M. E., Kazantsev, A. V., Chen, J. J. ‐., & Pace, N. R. (1997) · PubMed Central · Cited by 80 · see citing works
RNA hairpin loop stability depends on closing base pair
Serra, M. J., Lyttle, M. H., Axenson, T. J., et al. (1993) · Nucleic Acids Research · doi:10.1093/nar/21.16.3845 · Cited by 79 · see citing works
The Stability and Structure of Tandem GA Mismatches in RNA Depend on Closing Base Pairs
Walter, A. E., Wu, M., & Turner, D. H. (1994) · Biochemistry · doi:10.1021/bi00203a033 · Cited by 74 · see citing works
Self-citationThermodynamics of Nonsymmetric Tandem Mismatches Adjacent to G·C Base Pairs in RNA
Xia, T., McDowell, J. A., & Turner, D. H. (1997) · Biochemistry · doi:10.1021/bi971069v · Cited by 73 · see citing works
Self-citationSerra, M. J., Axenson, T. J., & Turner, D. H. (1994) · Biochemistry · doi:10.1021/bi00251a042 · Cited by 72 · see citing works
Self-citationLück, R., Steger, G., & Riesner, D. (1996) · Journal of Molecular Biology · doi:10.1006/jmbi.1996.0289 · Cited by 69 · see citing works
Comparative structural analysis of nuclear RNase P RNAs from yeast
Tranguch, A. J., & Engelke, D. R. (1993) · Journal of Biological Chemistry · doi:10.1016/s0021-9258(19)85207-9 · Cited by 65 · see citing works
Thermal stability of RNA hairpins containing a four-membered loop and a bulge nucleotide
Groebe, D. R., & Uhlenbeck, O. C. (1989) · Biochemistry · doi:10.1021/bi00428a049 · Cited by 57 · see citing works
Thermodynamics of Coaxially Stacked Helixes with GA and CC Mismatches
Kim, J., Walter, A. E., & Turner, D. H. (1996) · Biochemistry · doi:10.1021/bi960913z · Cited by 54 · see citing works
Self-citationThermodynamic Analysis of an RNA Combinatorial Library Contained in a Short Hairpin
Bevilacqua, J. M., & Bevilacqua, P. C. (1998) · Biochemistry · doi:10.1021/bi981732v · Cited by 52 · see citing works
Stability of RNA Hairpins Closed by Wobble Base Pairs
Giese, M. R., Betschart, K., Dale, T., et al. (1998) · Biochemistry · doi:10.1021/bi972050v · Cited by 50 · see citing works
Gaspin, C., & Westhof, É. (1995) · Journal of Molecular Biology · doi:10.1006/jmbi.1995.0608 · Cited by 49 · see citing works
The development of microfabricated arrays for DNA sequencing and analysis
O'Donnell-Maloney, M. J., Smith, C. L., & Cantor, C. R. (1996) · Trends in biotechnology · doi:10.1016/0167-7799(96)10052-4 · Cited by 49 · see citing works
Burgstaller, P. (1997) · Nucleic Acids Research · doi:10.1093/nar/25.20.4018 · Cited by 48 · see citing works
McDowell, J. A., He, L., Chen, X., et al. (1997) · Biochemistry · doi:10.1021/bi970122c · Cited by 47 · see citing works
Flavin-Dependent Photocleavage of RNA at G·U Base Pairs
Burgstaller, P., & Famulok, M. (1997) · Journal of the American Chemical Society · doi:10.1021/ja962918p · Cited by 45 · see citing works
Improved Parameters for the Prediction of RNA Hairpin Stability
Serra, M. J., Barnes, T. W., Betschart, K., et al. (1997) · Biochemistry · doi:10.1021/bi962608j · Cited by 45 · see citing works
Thermal unfolding of yeast glycine transfer RNA
Hilbers, C. W., Robillard, G. T., Shulman, R. G., et al. (1976) · Biochemistry · doi:10.1021/bi00654a013 · Cited by 44 · see citing works
Szymański, M. (1998) · Nucleic Acids Research · doi:10.1093/nar/26.1.156 · Cited by 42 · see citing works
Morse, S. E., & Draper, D. E. (1995) · Nucleic Acids Research · doi:10.1093/nar/23.2.302 · Cited by 40 · see citing works
Structure-Sensitive RNA Footprinting of Yeast Nuclear Ribonuclease P
Tranguch, A. J., Kindelberger, D. W., Rohlman, C. E., Lee, J.-Y., & Engelke, D. R. (1994) · Biochemistry · doi:10.1021/bi00173a022 · Cited by 39 · see citing works
Thermodynamics of RNA hairpins containing single internal mismatches
Meroueh, M. (1999) · Nucleic Acids Research · doi:10.1093/nar/27.4.1118 · Cited by 39 · see citing works
Mathews, D. H., André, T. C., Kim, J., Turner, D. H., & Zuker, M. (1997) · ACS symposium series · doi:10.1021/bk-1998-0682.ch015 · Cited by 39 · see citing works
Self-citationG·A and U·U Mismatches Can Stabilize RNA Internal Loops of Three Nucleotides
Schroeder, S. J., Kim, J., & Turner, D. H. (1996) · Biochemistry · doi:10.1021/bi961789m · Cited by 35 · see citing works
Self-citationImproved free energies for G · C base-pairs
Freier, S. M., Sinclair, A., Neilson, T., et al. (1985) · Journal of Molecular Biology · doi:10.1016/0022-2836(85)90077-4 · Cited by 35 · see citing works
The Signal Recognition Particle Database (SRPDB)
Larsen, N. (1998) · Nucleic Acids Research · doi:10.1093/nar/26.1.177 · Cited by 34 · see citing works
Jabri, E., Aigner, S., & Cech, T. R. (1997) · Biochemistry · doi:10.1021/bi9718595 · Cited by 23 · see citing works
Speek, M., & Artur, L. I. N. D. (1982) · Nucleic Acids Research · doi:10.1093/nar/10.3.947 · Cited by 21 · see citing works
Zhu, J., & Wartell, R. M. (1997) · Biochemistry · doi:10.1021/bi9716783 · Cited by 21 · see citing works
Kean, J. M., & Draper, D. E. (1985) · Biochemistry · doi:10.1021/bi00340a015 · Cited by 21 · see citing works
Flagged first, then by citations
Research works printed but not linked: 1
- Holland, J. H. (1975). Adaption in Natural and Arti®cial Systems, University of Michigan Press.
Cited by
Sorted by citations
Mfold web server for nucleic acid folding and hybridization prediction
Zuker, M. (2003) · Nucleic Acids Research · doi:10.1093/nar/gkg595 · Cited by 13,404 · see citing works
Self-citationRNA-Guided Human Genome Engineering via Cas9
Mali, P., Yang, L., Esvelt, K. M., Aach, J., Guell, M., DiCarlo, J. E., Norville, J. E., & Church, G. M. (2013) · Science · doi:10.1126/science.1232033 · Cited by 9,210 · see citing works
Lorenz, R., Bernhart, S. H., Höner zu Siederdissen, C., Tafer, H., Flamm, C., Stadler, P. F., & Hofacker, I. L. (2011) · Algorithms for Molecular Biology · doi:10.1186/1748-7188-6-26 · Cited by 5,098 · see citing works
Automated design of synthetic ribosome binding sites to control protein expression
Salis, H. M., Mirsky, E. A., & Voigt, C. A. (2009) · Nature Biotechnology · doi:10.1038/nbt.1568 · Cited by 1,844 · see citing works
Makarova, K. S., Grishin, N. V., Shabalina, S. A., Wolf, Y. I., & Koonin, E. V. (2006) · Biology Direct · doi:10.1186/1745-6150-1-7 · Cited by 1,199 · see citing works
Fragile X mental retardation protein targets G quartet mRNAs important for neuronal function
Darnell, J. C., Jensen, K. B., Jin, P., Brown, V., Warren, S. T., & Darnell, R. B. (2001) · Cell · doi:10.1016/s0092-8674(01)00566-9 · Cited by 952 · see citing works
Nackley, A. G., Shabalina, S. A., Tchivileva, I. E., Satterfield, K., Korchynskyi, O., Makarov, S. S., Maixner, W., & Diatchenko, L. (2006) · Science · doi:10.1126/science.1131262 · Cited by 848 · see citing works
Selection of tRNA by the Ribosome Requires a Transition from an Open to a Closed Form
Ogle, J. M., Murphy, F. V., Tarry, M. J., & Ramakrishnan, V. (2002) · Cell · doi:10.1016/s0092-8674(02)01086-3 · Cited by 663 · see citing works
Turner, D. H., & Mathews, D. H. (2010) · Nucleic Acids Research · doi:10.1093/nar/gkp892 · Cited by 575 · see citing works
Self-citationSecondary Structure of Vertebrate Telomerase RNA
Chen, J.-L., Blasco, M. A., & Greider, C. W. (2000) · Cell · doi:10.1016/s0092-8674(00)80687-x · Cited by 605 · see citing works
Busch, A., Richter, A. S., & Backofen, R. (2008) · Bioinformatics · doi:10.1093/bioinformatics/btn544 · Cited by 552 · see citing works
Algorithm for optimized mRNA design improves stability and immunogenicity
Zhang, H., Zhang, L., Lin, A., Xu, C., Li, Z., Liu, K., Liu, B., Ma, X., Zhao, F., Jiang, H., et al. (2023) · Nature · doi:10.1038/s41586-023-06127-z · Cited by 498 · see citing works
Self-citationIncreasing the specificity of CRISPR systems with engineered RNA secondary structures
Kocak, D. D., Josephs, E. A., Bhandarkar, V., Adkar, S. S., Kwon, J. B., & Gersbach, C. A. (2019) · Nature Biotechnology · doi:10.1038/s41587-019-0095-1 · Cited by 351 · see citing works
RNA Pseudoknot Prediction in Energy-Based Models
Lyngsø, R. B., & Pedersen, C. N. S. (2000) · Journal of Computational Biology · doi:10.1089/106652700750050862 · Cited by 359 · see citing works
Gu, W., Zhou, T., & Wilke, C. O. (2010) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1000664 · Cited by 313 · see citing works
Zhang, X., Rice, K., Wang, Y., Chen, W., Zhong, Y., Nakayama, Y., Zhou, Y., & Klibanski, A. (2010) · Endocrinology · doi:10.1210/en.2009-0657 · Cited by 325 · see citing works
MicroRNAs regulate the expression of the alternative splicing factor nPTB during muscle development
Boutz, P. L., Chawla, G., Stoilov, P., & Black, D. L. (2007) · Genes & Development · doi:10.1101/gad.1500707 · Cited by 304 · see citing works
Darnell, J. C., Fraser, C. E., Mostovetsky, O., Stefani, G., Jones, T. A., Eddy, S. R., & Darnell, R. B. (2005) · Genes & Development · doi:10.1101/gad.1276805 · Cited by 287 · see citing works
Efficient search, mapping, and optimization of multi-protein genetic systems in diverse bacteria
Farasat, I., Kushwaha, M., Collens, J., Easterbrook, M., Guido, M., & Salis, H. M. (2014) · Molecular Systems Biology · doi:10.15252/msb.20134955 · Cited by 235 · see citing works
Multiple roles of the coding sequence 5′ end in gene expression regulation
Tuller, T., & Zur, H. (2015) · Nucleic Acids Research · doi:10.1093/nar/gku1313 · Cited by 206 · see citing works
LinearFold: linear-time approximate RNA folding by 5'-to-3' dynamic programming and beam search
Huang, L., Zhang, H., Deng, D., Zhao, K., Liu, K., Hendrix, D. A., & Mathews, D. H. (2019) · Bioinformatics · doi:10.1093/bioinformatics/btz375 · Cited by 207 · see citing works
“8% of the optimal structure (Zuker et al., 1991; Mathews et al., 1999).”
Self-citationRivas, E., Lang, R., & Eddy, S. R. (2012) · RNA · doi:10.1261/rna.030049.111 · Cited by 145 · see citing works
von der Haar, T., & McCarthy, J. E. G. (2002) · Molecular Microbiology · doi:10.1046/j.1365-2958.2002.03172.x · Cited by 137 · see citing works
Testa, S. M., Disney, M. D., Turner, D. H., & Kierzek, R. (1999) · Biochemistry · doi:10.1021/bi991187d · Cited by 122 · see citing works
Self-citationAptamer base: a collaborative knowledge base to describe aptamers and SELEX experiments
Cruz-Toledo, J., McKeague, M., Zhang, X., Giamberardino, A., McConnell, E., Francis, T., DeRosa, M. C., & Dumontier, M. (2012) · Database · doi:10.1093/database/bas006 · Cited by 95 · see citing works
The prebiotic evolutionary advantage of transferring genetic information from RNA to DNA
Leu, K., Obermayer, B., Rajamani, S., Gerland, U., & Chen, I. A. (2011) · Nucleic Acids Research · doi:10.1093/nar/gkr525 · Cited by 85 · see citing works
Manrubia, S., Cuesta, J. A., Aguirre, J., Ahnert, S. E., Altenberg, L., Cano, A. V., Catalán, P., Diaz-Uriarte, R., Elena, S. F., García-Martín, J. A., et al. (2021) · Physics of Life Reviews · doi:10.1016/j.plrev.2021.03.004 · Cited by 88 · see citing works
Complex RNA Folding Kinetics Revealed by Single-Molecule FRET and Hidden Markov Models
Keller, B. G., Kobitski, A., Jäschke, A., Nienhaus, G. U., & Noé, F. (2014) · Journal of the American Chemical Society · doi:10.1021/ja4098719 · Cited by 84 · see citing works
Bush, J. A., Aikawa, H., Fuerst, R., Li, Y., Ursu, A., Meyer, S. M., Benhamou, R. I., Chen, J. L., Khan, T., Wagner-Griffin, S., et al. (2021) · Science Translational Medicine · doi:10.1126/scitranslmed.abd5991 · Cited by 77 · see citing works
Kaukinen, U. (2002) · Nucleic Acids Research · doi:10.1093/nar/30.2.468 · Cited by 69 · see citing works
A novel mechanism for translation initiation operates in haloarchaea
Hering, O., Brenneis, M., Beer, J., Suess, B., & Soppa, J. (2009) · Molecular Microbiology · doi:10.1111/j.1365-2958.2009.06615.x · Cited by 64 · see citing works
RNA Folding Argues Against a Hot-Start Origin of Life
Moulton, V., Gardner, P. P., Pointon, R. F., Creamer, L. K., Jameson, G. B., & Penny, D. (2000) · Journal of Molecular Evolution · doi:10.1007/s002390010104 · Cited by 56 · see citing works
The four ingredients of single-sequence RNA secondary structure prediction. A unifying perspective
Rivas, E. (2013) · RNA Biology · doi:10.4161/rna.24971 · Cited by 57 · see citing works
A tRNA aminoacylation system for non-natural amino acids based on a programmable ribozyme
Bessho, Y., Hodgson, D. R. W., & Suga, H. (2002) · Nature Biotechnology · doi:10.1038/nbt0702-723 · Cited by 56 · see citing works
Polymorphic GGC repeat differentially regulates human reelin gene expression levels
Persico, A. M., Levitt, P., & Pimenta, A. F. (2006) · Journal of Neural Transmission · doi:10.1007/s00702-006-0441-6 · Cited by 52 · see citing works
Hairpin‐DNA memory Using Molecular Addressing
Takinoue, M., & Suyama, A. (2006) · Small · doi:10.1002/smll.200600237 · Cited by 37 · see citing works
Terai, G., Kamegai, S., & Asai, K. (2016) · Bioinformatics · doi:10.1093/bioinformatics/btv678 · Cited by 36 · see citing works
Natural Selection and Algorithmic Design of mRNA
Cohen, B., & Skiena, S. (2003) · Journal of Computational Biology · doi:10.1089/10665270360688101 · Cited by 35 · see citing works
- Authors
- Mathews, D. H., Sabina, J., Zuker, M., & Turner, D. H.
- Affiliations
- University of Rochester (US)
- Washington University in St. Louis (US)
- Corresponding author
- Turner, Douglas H.
- Venue
- Journal of Molecular Biology
- Publisher
- Elsevier BV
- Published
- 1999-05
- Volume
- 288
- Issue
- 5
- Pages
- 911-940
- ISSN
- 0022-2836 (ISSN-L)
- OpenAlex
- W2009818318
- Cited by
- 3,795
- References
- 104
- Citations by year
- 2026: 49 · 2025: 42 · 2024: 72 · 2023: 61 · 2022: 61 · 2021: 54 · 2020: 66 · 2019: 80 · 2018: 72 · 2017: 56 · 2016: 85 · 2015: 103 · 2014: 117 · 2013: 142 · 2012: 168
- FWCI
- 63.62
- Type
- journal article
- Language
- en
- Open access
- hybrid
- doi.org
- Licence
- Locations
- Journal of Molecular Biology (publishedVersion, cc-by-nc-nd)
- PubMed (publishedVersion)
- Funders
- National Institutes of Health (GM 22939)
- National Institute of General Medical Sciences (GM 22939, 5-T32-GM07356, GM54250, R01GM022939, T32GM007356, R01GM054250)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA and protein synthesis mechanisms
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein Structure and Dynamics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA Research and Splicing
- Keywords
- RNA secondary structure prediction, free energy minimization, dynamic programming algorithm, sequence comparison, RNA folding
- MeSH terms
- Algorithms, Amino Acid Sequence, Escherichia coli, Flavin Mononucleotide, Kinetics, Models, Genetic, Molecular Sequence Data, Nucleic Acid Conformation, RNA, Ribosomal, 5S, Thermodynamics, Time Factors, Models, Statistical, Databases, Factual, Bacteriophage T4, Protein Structure, Secondary
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
Are you an author, or do you see a problem with this page? Request a review
