Sequence Design for a Test Tube of Interacting Nucleic Acid Strands

ACS Synthetic Biology

Volumn 4, Issue 10, 2015, Pages 1086-1100

  Wolfe, Brian R ^a   Pierce, Niles A ^a,b  

^a California Institute of Technology   (United States)

^b California Institute of Technology   (United States)

Author keywords

dilute solution; equilibrium base pairing; hierarchical ensemble decomposition; target concentration; target secondary structure; test tube ensemble defect; test tube ensemble focusing

Indexed keywords

NUCLEIC ACID; NUCLEOTIDE; RNA;

ALGORITHM; ARTICLE; BASE PAIRING; LABORATORY DEVICE; MUTATION; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL; PROCESS OPTIMIZATION; PROTEIN SECONDARY STRUCTURE; SUBSTRATE CONCENTRATION; TEST TUBE; BIOLOGY; CHEMISTRY; CONFORMATION; PROCEDURES; SYNTHETIC BIOLOGY; THERMODYNAMICS;

ALGORITHMS; COMPUTATIONAL BIOLOGY; NUCLEIC ACID CONFORMATION; RNA; SYNTHETIC BIOLOGY; THERMODYNAMICS;

EID: 84944716127     PISSN: None     EISSN: 21615063     Source Type: Journal    
DOI: 10.1021/sb5002196     Document Type: Article

References (62)

1. Pinheiro, A. V., Han, D. R., Shih, W. M., and Yan, H. (2011) Challenges and opportunities for structural DNA nanotechnology Nat. Nanotechnol. 6, 763-772
2. Zhang, D. Y. and Seelig, G. (2011) Dynamic DNA nanotechnology using strand-displacement reactions Nat. Chem. 3, 103-113
3. Zuker, M. and Stiegler, P. (1981) Optimal computer folding of large RNA sequences using thermodynamics and auxiliary information Nucleic Acids Res. 9, 133-147
4. McCaskill, J. S. (1990) The equilibrium partition function and base pair binding probabilities for RNA secondary structure Biopolymers 29, 1105-1119
5. Hofacker, I. L., Fontana, W., Stadler, P. F., Bonhoeffer, L. S., Tacker, M., and Schuster, P. (1994) Fast folding and comparison of RNA secondary structures Monatsh. Chem. 125, 167-188
6. Lyngso, R. B., Zuker, M., and Pedersen, C. N. S. (1999) Fast evaluation of internal loops in RNA secondary structure prediction Bioinformatics 15, 440-445
7. 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
8. Dimitrov, R. A. and Zuker, M. (2004) Prediction of hybridization and melting for double-stranded nucleic acids Biophys. J. 87, 215-226
9. Andronescu, M., Zhang, Z. C., and Condon, A. (2005) Secondary structure prediction of interacting RNA molecules J. Mol. Biol. 345, 987-1001
10. Bernhart, S. H., Tafer, H., Muckstein, U., Flamm, C., Stadler, P. F., and Hofacker, I. L. (2006) Partition function and base pairing probabilities of RNA heterodimers Algorithm Mol. Biol. 1, 3 10.1186/1748-7188-1-3
11. Dirks, R. M., Bois, J. S., Schaeffer, J. M., Winfree, E., and Pierce, N. A. (2007) Thermodynamic analysis of interacting nucleic acid strands SIAM Rev. 49, 65-88
12. Zadeh, J. N., Steenberg, C. D., Bois, J. S., Wolfe, B. R., Pierce, M. B., Khan, A. R., Dirks, R. M., and Pierce, N. A. (2011) NUPACK: Analysis and design of nucleic acid systems J. Comput. Chem. 32, 170-173
13. Flamm, C., Hofacker, I. L., Maurer-Stroh, S., Stadler, P. F., and Zehl, M. (2001) Design of multistable RNA molecules RNA 7, 254-265
14. Dirks, R. M. and Pierce, N. A. (2003) A partition function algorithm for nucleic acid secondary structure including pseudoknots J. Comput. Chem. 24, 1664-1677
15. Dirks, R. M., Lin, M., Winfree, E., and Pierce, N. A. (2004) Paradigms for computational nucleic acid design Nucleic Acids Res. 32, 1392-1403
16. Andronescu, M., Fejes, A. P., Hutter, F., Hoos, H. H., and Condon, A. (2004) A new algorithm for RNA secondary structure design J. Mol. Biol. 336, 607-624
17. Busch, A. and Backofen, R. (2006) INFO-RNA-A fast approach to inverse RNA folding Bioinformatics 22, 1823-1831
18. Aguirre-Hernandez, R., Hoos, H. H., and Condon, A. (2007) Computational RNA secondary structure design: Empirical complexity and improved methods BMC Bioinformatics 8, 34 10.1186/1471-2105-8-34
19. Burghardt, B. and Hartmann, A. K. (2007) RNA secondary structure design Phys. Rev. E 75, 021920
20. Gao, J. Z. M., Li, L. Y. M., and Reidys, C. M. (2010) Inverse folding of RNA pseudoknot structures Algorithm Mol. Biol. 5, 27 10.1186/1748-7188-5-27
21. Shu, W. J., Liu, M., Chen, H. B., Bo, X. C., and Wang, S. Q. (2010) ARDesigner: A web-based system for allosteric RNA design J. Biotechnol. 150, 466-473
22. Zadeh, J. N., Wolfe, B. R., and Pierce, N. A. (2011) Nucleic acid sequence design via efficient ensemble defect optimization J. Comput. Chem. 32, 439-452
23. Avihoo, A., Churkin, A., and Barash, D. (2011) RNAexinv: An extended inverse RNA folding from shape and physical attributes to sequences BMC Bioinformatics 12, 319 10.1186/1471-2105-12-319
24. Ramlan, E. I. and Zauner, K. P. (2011) Design of interacting multi-stable nucleic acids for molecular information processing Biosystems 105, 14-24
25. Taneda, A. (2011) MODENA: A multi-objective RNA inverse folding Adv. Appl. Bioinforma. Chem. 4, 1-12
26. Levin, A., Lis, M., Ponty, Y., O'Donnell, C. W., Devadas, S., Berger, B., and Waldispuhl, J. (2012) A global sampling approach to designing and reengineering RNA secondary structures Nucleic Acids Res. 40, 10041-10052
27. Matthies, M. C., Bienert, S., and Torda, A. E. (2012) Dynamics in sequence space for RNA secondary structure design J. Chem. Theory Comput. 8, 3663-3670
28. Taneda, A. (2012) Multi-objective genetic algorithm for pseudoknotted RNA sequence design Front. Genet. 3, 36
29. Lyngso, R. B., Anderson, J. W. J., Sizikova, E., Badugu, A., Hyland, T., and Hein, J. (2012) Frnakenstein: Multiple target inverse RNA folding BMC Bioinformatics 13, 260 10.1186/1471-2105-13-260
30. Serra, M. J. and Turner, D. H. (1995) Predicting thermodynamic properties of RNA Methods Enzymol. 259, 242-261
31. Mathews, D. H., Sabina, J., Zuker, M., and Turner, D. H. (1999) Expanded sequence dependence of thermodynamic parameters improves prediction of RNA secondary structure J. Mol. Biol. 288, 911-940
32. SantaLucia, J., Jr. (1998) A unified view of polymer, dumbbell, and oligonucleotide DNA nearest-neighbor thermodynamics Proc. Natl. Acad. Sci. U.S.A. 95, 1460-1465
33. SantaLucia, J., Jr. and Hicks, D. (2004) The thermodynamics of DNA structural motifs Annu. Rev. Biophys. Biomol. Struct. 33, 415-440
34. Koehler, R. T. and Peyret, N. (2005) Thermodynamic properties of DNA sequences: Characteristic values for the human genome Bioinformatics 21, 3333-3339
35. Genot, A. J., Zhang, D. Y., Bath, J., and Turberfield, A. J. (2011) Remote toehold: A mechanism for flexible control of DNA hybridization kinetics J. Am. Chem. Soc. 133, 2177-2182
36. Genot, A. J., Bath, J., and Turberfield, A. J. (2011) Reversible logic circuits made of DNA J. Am. Chem. Soc. 133, 20080-20083
37. Delebecque, C. J., Silver, P. A., and Lindner, A. B. (2012) Designing and using RNA scaffolds to assemble proteins in vivo Nat. Protoc. 7, 1797-1807
38. Greene, D. G., Keum, J. W., and Bermudez, H. (2012) The role of defects on the assembly and stability of DNA nanostructures Small 8, 1320-1325
39. Padirac, A., Fujii, T., and Rondelez, Y. (2012) Quencher-free multiplexed monitoring of DNA reaction circuits Nucleic Acids Res. 40, e118
40. Tang, H., Deschner, R., Allen, P., Cho, Y. J., Sermas, P., Maurer, A., Ellington, A. D., and Willson, C. G. (2012) Analysis of DNA-guided self-assembly of microspheres using imaging flow cytometry J. Am. Chem. Soc. 134, 15245-15248
41. Zhang, X. J. and Yadavalli, V. K. (2012) Functional self-assembled DNA nanostructures for molecular recognition Nanoscale 4, 2439-2446
42. Goodman, D. B., Church, G. M., and Kosuri, S. (2013) Causes and effects of N-terminal codon bias in bacterial genes Science 342, 475-479
43. Xu, X. W. and Yang, X. R. (2014) Reversion of DNA strand displacement using functional nucleic acids as toeholds Chem. Commun. 50, 805-807
44. Dirks, R. M. and Pierce, N. A. (2004) Triggered amplification by hybridization chain reaction Proc. Natl. Acad. Sci. U.S.A. 101, 15275-15278
45. Patzel, V., Rutz, S., Dietrich, I., Köberle, C., Sheffold, A., and Kaufmann, S. H. E. (2005) Design of siRNAs producing unstructured guide-RNAs results in improved RNA interference efficiency Nat. Biotechnol. 23, 1440-1444
46. Penchovsky, R. and Breaker, R. R. (2005) Computational design and experimental validation of oligonucleotide-sensing allosteric ribozymes Nat. Biotechnol. 23, 1424-1433
47. Venkataraman, S., Dirks, R. M., Rothemund, P. W. K., Winfree, E., and Pierce, N. A. (2007) An autonomous polymerization motor powered by DNA hybridization Nat. Nanotechnol. 2, 490-494
48. Yin, P., Choi, H. M. T., Calvert, C. R., and Pierce, N. A. (2008) Programming biomolecular self-assembly pathways Nature 451, 318-322
49. Salis, H. M., Mirsky, E. A., and Voigt, C. A. (2009) Automated design of synthetic ribosome binding sites to control protein expression Nat. Biotechnol. 27, 946-950
50. Li, B. L., Ellington, A. D., and Chen, X. (2011) Rational, modular adaptation of enzyme-free DNA circuits to multiple detection methods Nucleic Acids Res. 39, e110
51. Dong, J., Cui, X., Deng, Y., and Tang, Z. (2012) Amplified detection of nucleic acid by G-quadruplex based hybridization chain reaction Biosens. Bioelectron. 38, 258-263
52. Nishimura, T., Ogura, Y., and Tanida, J. (2012) Fluorescence resonance energy transfer-based molecular logic circuit using a DNA scaffold Appl. Phys. Lett. 101, 233703
53. Schade, M., Knoll, A., Vogel, A., Seitz, O., Liebscher, J., Huster, D., Herrmann, A., and Arbuzova, A. (2012) Remote control of lipophilic nucleic acids domain partitioning by DNA hybridization and enzymatic cleavage J. Am. Chem. Soc. 134, 20490-20497
54. Vieregg, J. R., Nelson, H. M., Stoltz, B. M., and Pierce, N. A. (2013) Selective nucleic acid capture with shielded covalent probes J. Am. Chem. Soc. 135, 9691-9699
55. Hochrein, L. M., Schwarzkopf, M., Shahgholi, M., Yin, P., and Pierce, N. A. (2013) Conditional Dicer substrate formation via shape and sequence transduction with small conditional RNAs J. Am. Chem. Soc. 135, 17322-17330
56. Genot, A. J., Bath, J., and Turberfield, A. J. (2013) Combinatorial displacement of DNA strands: Application to matrix multiplication and weighted sums Angew. Chem., Int. Ed. 52, 1189-1192
57. Hamblin, G. D., Hariri, A. A., Carneiro, K. M. M., Lau, K. L., Cosa, G., and Sleiman, H. F. (2013) Simple design for DNA nanotubes from a minimal set of unmodified strands: Rapid, room-temperature assembly, and readily tunable structure ACS Nano 7, 3022-3028
58. Santini, C. C., Bath, J., Tyrrell, A. M., and Turberfield, A. J. (2013) A clocked finite state machine built from DNA Chem. Commun. 49, 237-239
59. Jiang, Y. S., Bhadra, S., Li, B. L., and Ellington, A. D. (2014) Mismatches improve the performance of strand-displacement nucleic acid circuits Angew. Chem., Int. Ed. 53, 1845-1848
60. Geary, C., Rothemund, P. W. K., and Andersen, E. S. (2014) A single-stranded architecture for cotranscriptional folding of RNA nanostructures Science 345, 799-804
61. 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
62. Hunter, J. D. (2007) Matplotlib: A 2D graphics environment Comput. Sci. Eng. 9, 90-95