In Vitro Selection for Small-Molecule-Triggered Strand Displacement and Riboswitch Activity

ACS Synthetic Biology

Volumn 4, Issue 10, 2015, Pages 1144-1150

  Martini, Laura ^a   Meyer, Adam J ^b   Ellefson, Jared W ^b   Milligan, John N ^b   Forlin, Michele ^a   Ellington, Andrew D ^b   Mansy, Sheref S ^a  

^a UNIVERSITY OF TRENTO   (Italy)

^b UNIVERSITY OF TEXAS AT AUSTIN   (United States)

Author keywords

aptamer; in vitro selection; riboswitch; SELEX; strand displacement

Indexed keywords

APTAMER; COCARBOXYLASE; DOUBLE STRANDED DNA; NUCLEIC ACID; RIBOSWITCH;

ARTICLE; BINDING SITE; CHEMICAL REACTION; CONFORMATIONAL TRANSITION; FLUORESCENCE; IN VITRO SELECTION; LIGAND BINDING; MOLECULAR SENSOR; NONHUMAN; NUCLEIC ACID SENSOR; PRIORITY JOURNAL; RIBOSWITCH; RNA BINDING; RNA SEQUENCE; STRAND DISPLACEMENT REACTION; CHEMISTRY; CONFORMATION; GENETIC PROCEDURES; GENETICS;

APTAMERS, NUCLEOTIDE; BIOSENSING TECHNIQUES; NUCLEIC ACID CONFORMATION; RIBOSWITCH;

EID: 84944747064     PISSN: None     EISSN: 21615063     Source Type: Journal    
DOI: 10.1021/acssynbio.5b00054     Document Type: Article

References (41)

1. Win, M. N. and Smolke, C. D. (2008) Higher-order cellular information processing with synthetic RNA devices Science 322, 456
2. Ogawa, A. and Maeda, M. (2008) An artificial aptazyme-based riboswitch and its cascading system in E. coli ChemBioChem 9, 206
3. Soukup, G. A. and Breaker, R. R. (1999) Engineering precision RNA molecular switches Proc. Natl. Acad. Sci. U.S.A. 96, 3584
4. Robertson, M. P. and Ellington, A. D. (2000) Design and optimization of effector-activated ribozyme ligases Nucleic Acids Res. 28, 1751
5. Soukup, G. A., Emilsson, G. A., and Breaker, R. R. (2000) Altering molecular recognition of RNA aptamers by allosteric selection J. Mol. Biol. 298, 623
6. Wieland, M., Benz, A., Klauser, B., and Hartig, J. S. (2009) Artificial ribozyme switches containing natural riboswitch aptamer domains Angew. Chem., Int. Ed. 48, 2715
7. Yurke, B., Turberfield, A. J., Mills, A. P., Jr., Simmel, F. C., and Neumann, J. L. (2000) A DNA-fuelled molecular machine made of DNA Nature 406, 605
8. Zhang, D. Y. and Winfree, E. (2009) Control of DNA strand displacement kinetics using toehold exchange J. Am. Chem. Soc. 131, 17303
9. Li, Q., Luan, G., Guo, Q., and Liang, J. (2002) A new class of homogeneous nucleic acid probes based on specific displacement hybridization Nucleic Acids Res. 30, E5
10. Zhang, D. Y. and Seelig, G. (2011) Dynamic DNA nanotechnology using strand-displacement reactions Nat. Chem. 3, 103
11. Seeman, N. C. (2010) Structural DNA nanotechnology: growing along with Nano Letters Nano Lett. 10, 1971
12. Yan, H., Zhang, X., Shen, Z., and Seeman, N. C. (2002) A robust DNA mechanical device controlled by hybridization topology Nature 415, 62
13. Yin, P., Choi, H. M., Calvert, C. R., and Pierce, N. A. (2008) Programming biomolecular self-assembly pathways Nature 451, 318
14. Jiang, Y. S., Li, B., Milligan, J. N., Bhadra, S., and Ellington, A. D. (2013) Real-time detection of isothermal amplification reactions with thermostable catalytic hairpin assembly J. Am. Chem. Soc. 135, 7430
15. Compton, J. (1991) Nucleic acid sequence-based amplification Nature 350, 91
16. Li, B., Ellington, A. D., and Chen, X. (2011) Rational, modular adaptation of enzyme-free DNA circuits to multiple detection methods Nucleic Acids Res. 39, e110
17. Bhadra, S. and Ellington, A. D. (2014) A spinach molecular beacon triggered by strand displacement RNA 20, 1183
18. Bhadra, S. and Ellington, A. D. (2014) Design and application of cotranscriptional non-enzymatic RNA circuits and signal transducers Nucleic Acids Res. 42, e58
19. Green, A. A., Silver, P. A., Collins, J. J., and Yin, P. (2014) Toehold switches: de-novo-designed regulators of gene expression Cell 159, 925
20. Akter, F. and Yokobayashi, Y. (2015) RNA signal amplifier circuit with integrated fluorescence output ACS Synth. Biol. 4, 655
21. Ellington, A. D. and Szostak, J. W. (1990) In vitro selection of RNA molecules that bind specific ligands Nature 346, 818
22. Tuerk, C. and Gold, L. (1990) Systematic evolution of ligands by exponential enrichment: RNA ligands to bacteriophage T4 DNA polymerase Science 249, 505
23. Bartel, D. P. and Szostak, J. W. (1993) Isolation of new ribozymes from a large pool of random sequences [see comment] Science 261, 1411
24. Wieland, M., Benz, A., Haar, J., Halder, K., and Hartig, J. S. (2010) Small molecule-triggered assembly of DNA nanoarchitectures Chem. Commun. 46, 1866
25. Nomura, Y. and Yokobayashi, Y. (2007) Reengineering a natural riboswitch by dual genetic selection J. Am. Chem. Soc. 129, 13814
26. Nutiu, R. and Li, Y. (2005) In vitro selection of structure-switching signaling aptamers Angew. Chem., Int. Ed. 44, 1061
27. Stoltenburg, R., Nikolaus, N., and Strehlitz, B. (2012) Capture-SELEX: selection of DNA aptamers for aminoglycoside antibiotics J. Anal. Methods Chem. 2012, 415697
28. Winkler, W. C. and Breaker, R. R. (2003) Genetic control by metabolite-binding riboswitches ChemBioChem 4, 1024
29. Sudarsan, N., Hammond, M. C., Block, K. F., Welz, R., Barrick, J. E., Roth, A., and Breaker, R. R. (2006) Tandem riboswitch architectures exhibit complex gene control functions Science 314, 300
30. Goodson, M. S., Harbaugh, S. V., Chushak, Y. G., and Kelley-Loughnane, N. (2015) Integrating and amplifying signal from riboswitch biosensors Methods Enzymol. 550, 73
31. Lentini, R., Santero, S. P., Chizzolini, F., Cecchi, D., Fontana, J., Marchioretto, M., Del Bianco, C., Terrell, J. L., Spencer, A. C., Martini, L., Forlin, M., Assfalg, M., Dalla Serra, M., Bentley, W. E., and Mansy, S. S. (2014) Integrating artificial with natural cells to translate chemical messages that direct E. coli behaviour Nat. Commun. 5, 4012
32. Lynch, S. A. and Gallivan, J. P. (2009) A flow cytometry-based screen for synthetic riboswitches Nucleic Acids Res. 37, 184
33. Mishler, D. M. and Gallivan, J. P. (2014) A family of synthetic riboswitches adopts a kinetic trapping mechanism Nucleic Acids Res. 42, 6753
34. Martini, L. and Mansy, S. S. (2011) Cell-like systems with riboswitch controlled gene expression Chem. Commun. 47, 10734
35. Lemay, J. F., Desnoyers, G., Blouin, S., Heppell, B., Bastet, L., St-Pierre, P., Masse, E., and Lafontaine, D. A. (2011) Comparative study between transcriptionally- and translationally-acting adenine riboswitches reveals key differences in riboswitch regulatory mechanisms PLoS Genet. 7, e1001278
36. Rajendran, M. and Ellington, A. D. (2008) Selection of fluorescent aptamer beacons that light up in the presence of zinc Anal. Bioanal. Chem. 390, 1067
37. Rajendran, M. and Ellington, A. D. (2003) In vitro selection of molecular beacons Nucleic Acids Res. 31, 5700
38. Culler, S. J., Hoff, K. G., and Smolke, C. D. (2010) Reprogramming cellular behavior with RNA controllers responsive to endogenous proteins Science 330, 1251
39. Topp, S. and Gallivan, J. P. (2007) Guiding bacteria with small molecules and RNA J. Am. Chem. Soc. 129, 6807
40. Ichihashi, N., Usui, K., Kazuta, Y., Sunami, T., Matsuura, T., and Yomo, T. (2013) Darwinian evolution in a translation-coupled RNA replication system within a cell-like compartment Nat. Commun. 4, 2494
41. Lentini, R., Forlin, M., Martini, L., Del Bianco, C., Spencer, A. C., Torino, D., and Mansy, S. S. (2013) Fluorescent proteins and in vitro genetic organization for cell-free synthetic biology ACS Synth. Biol. 2, 482