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2017 | OriginalPaper | Buchkapitel

1. Implementing Molecular Logic Gates, Circuits, and Cascades Using DNAzymes

verfasst von : Matthew R. Lakin, Milan N. Stojanovic, Darko Stefanovic

Erschienen in: Advances in Unconventional Computing

Verlag: Springer International Publishing

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Abstract

The programmable nature of DNA chemistry makes it an attractive framework for the implementation of unconventional computing systems. Our early work in this area was among the first to use oligonucleotide-based logic gates to perform computations in a bulk solution. In this chapter we chart the development of this technology over the course of almost 15 years. We review our work on the implementation of DNA-based logic gates and circuits, which we have used to demonstrate digital logic circuits, autonomous game-playing automata, trainable systems and, more recently, decision-making circuits with potential diagnostic applications.

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Literatur
1.
Adleman, L.M.: Molecular computation of solutions to combinatorial problems. Science 266, 1021–1024 (1994)CrossRef
2.
Aguirre, S.D., Ali, M.M., Kanda, P., Li, Y.: Detection of bacteria using fluorogenic DNAzymes. J. Vis. Exp. 63, e3961 (2012). doi:10.​3791/​3961
3.
Aguirre, S.D., Ali, M.M., Salena, B.J., Li, Y.: A sensitive DNA enzyme-based fluorescent assay for bacterial detection. Biomolecules 3, 563–577 (2013). doi:10.​3390/​biom3030563 CrossRef
4.
Ali, M.M., Aguirre, S.D., Lazim, H., Li, Y.: Fluorogenic DNAzyme probes as bacterial indicators. Angew. Chem. Int. Ed. 50, 3751–3754 (2011)CrossRef
5.
Ali, M.M., Aguirre, S.D., Mok, W.W.K., Li, Y.: Developing fluorogenic RNA-cleaving DNAzymes for biosensing applications. In: Hartig, J.S., (ed.) Ribozymes, Methods in Molecular Biology, vol. 848, pp. 395–418. Springer, New York (2012)
6.
Ali, M.M., Li, Y.: Colorimetric sensing using allosteric DNAzyme-coupled rolling circle amplification and a peptide nucleic acid-organic dye probe. Angew. Chem. Int. Ed. 48, 3512–3515 (2009)CrossRef
7.
Alon, U.: An Introduction to Systems Biology: Design Principles of Biological Circuits. Chapman & Hall/CRC, Boca Raton (2007)
8.
Bennett, C.H.: The thermodynamics of computation–a review. Int. J. Theor. Phys. 21(12), 905–940 (1982)CrossRef
9.
Bhatt, S., Gething, P.W., Brady, O.J., Messina, J.P., Farlow, A.W., Moyes, C.L., Drake, J.M., Brownstein, J.S., Hoen, A.G., Sankoh, O., Myers, M.F., George, D.B., Jaenisch, T., Wint, G.R.W., Simmons, C.P., Scott, T.W., Farrar, J.J., Hay, S.I.: The global distribution and burden of dengue. Nature 496, 504–507 (2013). doi:10.​1038/​nature12060 CrossRef
10.
Bone, S.M., Hasick, N.J., Lima, N.E., Erskine, S.M., Mokany, E., Todd, A.V.: DNA-only cascade: A universal tool for signal amplification, enhancing the detection of target analytes. Anal. Chem. 86(18), 9106–9113 (2014). doi:10.​1021/​ac501811r CrossRef
11.
Brandsen, B.M., Velez, T.E., Sachdeva, A., Ibrahim, N.A., Silverman, S.K.: DNA-catalyzed lysine side chain modification. Angew. Chem. Int. Ed. 53(34), 9045–9050 (2014). doi:10.​1002/​anie.​201404622 CrossRef
12.
Breaker, R.R.: In vitro selection of catalytic polynucleotides. Chem. Rev. 97(2), 371–390 (1997)CrossRef
13.
Breaker, R.R., Joyce, G.F.: A DNA enzyme with Mg\({}^{2+}\)-dependent RNA phosphoesterase activity. Chem. Biol. 2(10), 655–656 (1995)CrossRef
14.
Brown III, C.W., Lakin, M.R., Fabry-Wood, A., Horwitz, E.K., Baker, N.A., Stefanovic, D., Graves, S.W.: A unified sensor architecture for isothermal detection of double-stranded DNA, oligonucleotides, and small molecules. ChemBioChem 16, 725–730 (2015). doi:10.​1002/​cbic.​201402615 CrossRef
15.
Brown III, C.W., Lakin, M.R., Horwitz, E.K., Fanning, M.L., West, H.E., Stefanovic, D., Graves, S.W.: Signal propagation in multi-layer DNAzyme cascades using structured chimeric substrates. Angew. Chem. Int. Ed. 53(28), 7183–7187 (2014). doi:10.​1002/​anie.​201402691 CrossRef
16.
17.
Chandra, M., Sachdeva, A., Silverman, S.K.: DNA-catalyzed sequence-specific hydrolysis of DNA. Nat. Chem. Biol. 5(10), 718–720 (2009)CrossRef
18.
19.
Chen, Y.J., Dalchau, N., Srinivas, N., Phillips, A., Cardelli, L., Soloveichik, D., Seelig, G.: Programmable chemical controllers made from DNA. Nat. Nanotechnol. 8, 755–762 (2013). doi:10.​1038/​nnano.​2013.​189 CrossRef
20.
Credi, A.: Molecules that make decisions. Angew. Chem. Int. Ed. 46(29), 5472–5475 (2007)CrossRef
21.
Dass, C.R.: Deoxyribozymes: cleaving a path to clinical trials. Trend. Pharmacol. Sci. 25(8), 395–397 (2004)CrossRef
22.
23.
24.
Dass, C.R., Saravolac, E.G., Li, Y., Sun, L.Q.: Cellular uptake, distribution, and stability of 10–23 deoxyribozymes. Antisense Nucl. Acid Drug Dev. 12, 289–299 (2002)CrossRef
25.
Dirks, R.M., Bois, J.S., Schaeffer, J.M., Winfree, E., Pierce, N.A.: Thermodynamic analysis of interacting nucleic acid strands. SIAM Rev. 49, 65–88 (2007)MathSciNetMATHCrossRef
26.
Dirks, R.M., Pierce, N.A.: A partition function algorithm for nucleic acid secondary structure including pseudoknots. J. Comput. Chem. 24, 1664–1677 (2003)CrossRef
27.
Dirks, R.M., Pierce, N.A.: An algorithm for computing nucleic acid base-pairing probabilities including pseudoknots. J. Comput. Chem. 25, 1295–1304 (2004)CrossRef
28.
Eckhoff, G., Codrea, V., Ellington, A.D., Chen, X.: Beyond allostery: catalytic regulation of a deoxyribozyme through an entropy-driven DNA amplifier. J. Syst. Chem. 1, 13 (2010). doi:10.​1186/​1759-2208-1-13 CrossRef
29.
30.
Elbaz, J., Lioubashevski, O., Wang, F., Remacle, F., Levine, R.D., Willner, I.: DNA computing circuits using libraries of DNAzyme subunits. Nat. Nanotechnol. 5(6), 417–422 (2010)CrossRef
31.
Elbaz, J., Moshe, M., Shlyahovsky, B., Willner, I.: Cooperative multicomponent self-assembly of nucleic acid structures for the activation of DNAzyme cascades: A paradigm for DNA sensors and aptasensors. Chemistry–A. Eur. J. 15, 3411–3418 (2009)CrossRef
32.
Elbaz, J., Wang, F., Remacle, F., Willner, I.: PH-programmable DNA logic arrays powered by modular DNAzyme libraries. Nano Lett. 12, 6049–6054 (2012). doi:10.​1021/​nl300051g
33.
Farfel, J., Stefanovic, D.: Towards practical biomolecular computers using microfluidic deoxyribozyme logic gate networks. In: Carbone, A., Pierce, N.A. (eds.) Proceedings of the 11th International Meeting on DNA Computing, Lecture Notes in Computer Science, vol. 3892, pp. 38–54. Springer, Heidelberg (2006)
34.
Flynn-Charlebois, A., Wang, Y., Prior, T.K., Rashid, I., Hoadley, K.A., Coppins, R.L., Wolf, A.C., Silverman, S.K.: Deoxyribozymes with 2’-5’ RNA ligase activity. J. Am. Chem. Soc. 125, 2444–2454 (2003). doi:10.​1021/​ja028774y CrossRef
35.
Gerasimova, Y.V., Cornett, E.M., Edwards, E., Su, X., Rohde, K.H., Kolpashchikov, D.M.: Deoxyribozyme cascade for visual detection of bacterial RNA. ChemBioChem 14, 2087–2090 (2013). doi:10.​1002/​cbic.​201300471 CrossRef
36.
Gerasimova, Y.V., Kolpashchikov, D.M.: Folding of 16S rRNA in a signal-producing structure for the detection of bacteria. Angew. Chem. Int. Ed. 52, 10586–10588 (2013). doi:10.​1002/​anie.​201303919 CrossRef
37.
Goldman, N., Bertone, P., Chen, S., Dessimoz, C., LeProust, E.M., Sipos, B., Birney, E.: Towards practical, high-capacity, low-maintenance information storage in synthesized DNA. Nature 494, 77–80 (2013). doi:10.​1038/​nature11875 CrossRef
38.
Goudarzi, A., Lakin, M.R., Stefanovic, D.: DNA reservoir computing: a novel molecular computing approach. In: Soloveichik, D., Yurke, B. (eds.) Proceedings of the 19th International Conference on DNA Computing and Molecular Programming, Lecture Notes in Computer Science, vol. 8141, pp. 76–89. Springer, Heidelberg (2013). doi:10.​1007/​978-3-319-01928-4_​6
39.
Gu, H., Furukawa, K., Weinberg, Z., Berenson, D.F., Breaker, R.R.: Small, highly active DNAs that hydrolyze DNA. J. Am. Chem. Soc. 135, 9121–9129 (2013). doi:10.​1021/​ja403585e
40.
He, S., Qu, L., Shen, Z., Tan, Y., Zeng, M., Liu, F., Jiang, Y., Li, Y.: Highly specific recognition of breast tumors by an RNA-cleaving fluorogenic DNAzyme probe. Anal. Chem. 87(1), 569–577 (2014). doi:10.​1021/​ac5031557 CrossRef
41.
42.
Huang, P.J.J., Vazin, M., Liu, J.: In vitro selection of a new lanthanide-dependent DNAzyme for ratiometric sensing lanthanides. Anal. Chem. 86(19), 9993–9999 (2014). doi:10.​1021/​ac5029962 CrossRef
43.
Huang, P.J.J., Vazin, M., Matuszek, Z., Liu, J.: A new heavy lanthanide-dependent DNAzyme displaying strong metal cooperativity and unrescuable phosphorothioate effect. Nucleic Acid. Res. 43(1), 461–469 (2015). doi:10.​1093/​nar/​gku1296 CrossRef
44.
Hwang, K., Wu, P., Kim, T., Lei, L., Tian, S., Wang, Y., Lu, Y.: Photocaged DNAzymes as a general method for sensing metal ions in living cells. Angew. Chem. Int. Ed. 53, 13798–13802 (2014)CrossRef
45.
Hayden, J.E., Riley, C.A., Burton, A.S., Lehman, N.: RNA-directed construction of structurally complex and active ligase ribozymes through recombination. RNA 11(11), 1678–1687 (2005). doi:10.​1261/​rna.​2125305
46.
Kahan-Hanum, M., Douek, Y., Adar, R., Shapiro, E.: A library of programmable DNAzymes that operate in a cellular environment. Sci. Rep. 3, 1535 (2013)CrossRef
47.
Katz, E., Privman, V.: Enzyme-based logic systems for information processing. Chem. Soc. Rev. 39(5), 1835–1857 (2010)CrossRef
48.
49.
50.
51.
Kolpashchikov, D.M.: A binary deoxyribozyme for nucleic acid analysis. ChemBioChem 8, 2039–2042 (2007)CrossRef
52.
Kolpashchikov, D.M.: Binary probes for nucleic acid analysis. Chem. Rev. 110, 4709–4723 (2010)CrossRef
53.
Kolpashchikov, D.M., Gerasimova, Y.V., Khan, M.S.: DNA nanotechnology for nucleic acid analysis: DX motif-based sensor. ChemBioChem 12, 2564–2567 (2011)CrossRef
54.
55.
Lakin, M.R., Brown III, C.W., Horwitz, E.K., Fanning, M.L., West, H.E., Stefanovic, D., Graves, S.W.: Biophysically inspired rational design of structured chimeric substrates for DNAzyme cascade engineering. PLoS ONE 9(10), e110986 (2014). doi:10.​1371/​journal.​pone.​0110986
56.
Lam, B.J., Joyce, G.F.: Autocatalytic aptazymes enable ligand-dependent exponential amplification of RNA. Nat. Biotechnol. 27(3), 288–292 (2009). doi:10.​1038/​nbt.​1528 CrossRef
57.
Lan, T., Furuya, K., Lu, Y.: A highly selective lead sensor based on a classic lead DNAzyme. Chem. Commun. 46, 3896–3898 (2010)CrossRef
58.
Lederman, H., Macdonald, J., Stefanovic, D., Stojanovic, M.N.: Deoxyribozyme-based three-input logic gates and construction of a molecular full adder. Biochemistry 45(4), 1194–1199 (2006)CrossRef
59.
Lee, C.S., Mui, T.P., Silverman, S.K.: Improved deoxyribozymes for synthesis of covalently branched DNA and RNA. Nucleic Acid. Res. 39(1), 269–279 (2011). doi:10.​1093/​nar/​gkq753 CrossRef
60.
Lee, J.H., Wang, Z., Liu, J., Lu, Y.: Highly sensitive and selective colorimetric sensors for uranyl (\({\rm {UO}}_{2}^{2+}\)): development and comparison of labeled and label-free DNAzyme-gold nanoparticle systems. J. Am. Chem. Soc. 130, 14217–14226 (2008)CrossRef
61.
62.
Lincoln, T.A., Joyce, G.F.: Self-sustained replication of an RNA enzyme. Science 323, 1229–1232 (2009)CrossRef
63.
64.
Lu, C.H., Wang, F., Willner, I.: Zn\(^{2+}\)-ligation DNAzyme-driven enzymatic and nonenzymatic cascades for the amplified detection of DNA. J. Am. Chem. Soc. 134(25), 10651–10658 (2012)CrossRef
65.
Lund, K., Manzo, A.J., Dabby, N., Michelotti, N., Johnson-Buck, A., Nangreave, J., Taylor, S., Pei, R., Stojanovic, M.N., Walter, N.G., Winfree, E., Yan, H.: Molecular robots guided by prescriptive landscapes. Nature 465, 206–209 (2010)
66.
Macdonald, J., Li, Y., Sutovic, M., Lederman, H., Pendri, K., Lu, W., Andrews, B.L., Stefanovic, D., Stojanovic, M.N.: Medium scale integration of molecular logic gates in an automaton. Nano Lett. 6(11), 2598–2603 (2006)CrossRef
67.
Macdonald, J., Stefanovic, D., Stojanovic, M.N.: DNA computers for work and play. Sci. Am. 299(5), 84–91 (2008)CrossRef
68.
McManus, S.A., Li, Y.: Turning a kinase deoxyribozyme into a sensor. J. Am. Chem. Soc. 135(19), 7181–7186 (2013)CrossRef
69.
Mitchell, A., Dass, C.R., Sun, L.Q., Khachigian, L.M.: Inhibition of human breast carcinoma proliferation, migration, chemoinvasion and solid tumour growth by DNAzymes targeting the zinc finger transcription factor EGR-1. Nucleic Acid. Res. 32(10), 3065–3069 (2004). doi:10.​1093/​nar/​gkh626 CrossRef
70.
Mokany, E., Bone, S.M., Young, P.E., Doan, T.B., Todd, A.V.: MNAzymes, a versatile new class of nucleic acid enzymes that can function as biosensors and molecular switches. J. Am. Chem. Soc. 132, 1051–1059 (2010). doi:10.​1021/​ja9076777 CrossRef
71.
Montagne, K., Plasson, R., Sakai, Y., Fujii, T., Rondelez, Y.: Programming an in vitro DNA oscillator using a molecular networking strategy. Mol. Syst. Biol. 7, 466 (2011). doi:10.​1038/​msb.​2011.​12 CrossRef
72.
Mui, T.P., Silverman, S.K.: Convergent and general one-step DNA-catalyzed synthesis of multiply branched DNA. Organ. Lett. 10(20), 4417–4420 (2008)CrossRef
73.
Muscat, R.A., Strauss, K., Ceze, L., Seelig, G.: DNA-based molecular architecture with spatially localized components. In: ISCA ’13: Proceedings of the 40th Annual International Symposium on Computer Architecture, pp. 177–188. ACM, New York (2013)
74.
75.
Olea, Jr. C., Horning, D.P., Joyce, G.F.: Ligand-dependent exponential amplification of a self-replicating lRNA enzyme. J. Am. Chem. Soc. 134, 8050–8053 (2012). doi:10.​1021/​ja302197x
76.
Orbach, R., Remacle, F., Levine, R.D., Willner, I.: DNAzyme-based 2:1 and 4:1 multiplexers and 1:2 demultiplexer. Chem. Sci. 5, 1074–1081 (2014)CrossRef
77.
Osborne, S.E., Ellington, A.D.: Nucleic acid selection and the challenge of combinatorial chemistry. Chem. Rev. 97(2), 349–370 (1997)CrossRef
78.
Parker, D.J., Xiao, Y., Aguilar, J.M., Silverman, S.K.: DNA catalysis of a normally disfavored RNA hydrolysis reaction. J. Am. Chem. Soc. 135(23), 8472–8475 (2013). doi:10.​1021/​ja4032488 CrossRef
79.
80.
81.
82.
Pei, R., Matamoros, E., Liu, M., Stefanovic, D., Stojanovic, M.N.: Training a molecular automaton to play a game. Nat. Nanotechnol. 5, 773–777 (2010)CrossRef
83.
Pei, R., Taylor, S.K., Stefanovic, D., Rudchenko, S., Mitchell, T.E., Stojanovic, M.N.: Behavior of polycatalytic assemblies in a substrate-displaying matrix. J. Am. Chem. Soc. 128(39), 12693–12699 (2006)CrossRef
84.
85.
Plotnikov, A., Zehorai, E., Procaccia, S., Seger, R.: The MAPK cascades: Signaling components, nuclear roles and mechanisms of nuclear translocation. Biochimica et Biophysica Acta 1813, 1619–1633 (2011)CrossRef
86.
Poje, J.E., Kastratovic, T., Macdonald, A.R., Guillermo, A.C., Troetti, S.E., Jabado, O.J., Fanning, M.L., Stefanovic, D., Macdonald, J.: Visual displays that directly interface and provide read-outs of molecular states via molecular graphics processing units. Angew. Chem. Int. Ed. 53(35), 9222–9225 (2014)CrossRef
87.
Purtha, W.E., Coppins, R.L., Smalley, M.K., Silverman, S.K.: General deoxyribozyme-catalyzed synthesis of native 3’-5’ RNA linkages. J. Am. Chem. Soc. 127, 13124–13125 (2005). doi:10.​1021/​ja0533702 CrossRef
88.
Qian, L., Soloveichik, D., Winfree, E.: Efficient Turing-universal computation with DNA polymers. In: Sakakibara, Y., Mi, Y. (eds.) Proceedings of the 16th International Conference on DNA Computing and Molecular Programming, Lecture Notes in Computer Science, vol. 6518, pp. 123–140. Springer, New York (2011)
89.
90.
Qian, L., Winfree, E.: Parallel and scalable computation and spatial dynamics with DNA-based chemical reaction networks on a surface. In: Murata, S., Kobayashi, S. (eds.) Proceedings of the 20th International Conference on DNA Computing and Molecular Programming, Lecture Notes in Computer Science, vol. 8727, pp. 114–131. Springer, New York (2014)
91.
92.
Robertson, M.P., Ellington, A.: In vitro selection of an allosteric ribozyme that transduces analytes to amplicons. Nat. Biotechol. 17(1), 62–66 (1999)CrossRef
93.
Santoro, S.W., Joyce, G.F.: A general purpose RNA-cleaving DNA enzyme. Proc. Natl. Acad. Sci. U.S. Am. 94, 4262–4266 (1997)CrossRef
94.
Saunders, M.J., Edwards, B.S., Zhu, J., Sklar, L.A., Graves, S.W.: Microsphere-based flow cytometry protease assays for use in protease activity detection and high-throughput screening. In: Robinson, J.P. (ed.) Current Protocols in Cytometry Unit 13.12. Wiley, Hoboken (2010). doi:10.​1002/​0471142956.​cy1312s54
95.
Schaeffer, H.J., Weber, M.J.: Mitogen-activated protein kinases: specific messages from ubiquitous messengers. Mol. Cell. Biol. 19(4), 2435–2444 (1999)CrossRef
96.
97.
98.
Silverman, S.K.: Deoxyribozymes: DNA catalysts for bioorganic chemistry. Organ. Biomol. Chem. 2, 2701–2706 (2004)CrossRef
99.
Silverman, S.K.: Catalytic DNA (deoxyribozymes) for synthetic applications—current abilities and future prospects. Chem. Commun. pp. 3467–3485 (2008). doi:10.​1039/​b807292m
100.
Simmons, C.P., Farrar, J.J., van Vin Chau, N., Wills, B.: Dengue. New Engl. J. Med. 366, 1423–1432 (2012)
101.
102.
Stefanovic, D., Stojanovic, M.N.: Computing game strategies. In: Computability in Europe: The Nature of Computation, pp. 383–392. Milano (2013)
103.
Stojanovic, M.N., Mitchell, T.E., Stefanovic, D.: Deoxyribozyme-based logic gates. J. Am. Chem. Soc. 124, 3555–3561 (2002)CrossRef
104.
Stojanovic, M.N., de Prada, P., Landry, D.W.: Catalytic molecular beacons. ChemBioChem 2, 411–415 (2001)CrossRef
105.
Stojanovic, M.N., Semova, S., Kolpashchikov, D., Macdonald, J., Morgan, C., Stefanovic, D.: Deoxyribozyme-based ligase logic gates and their initial circuits. J. Am. Chem. Soc. 127, 6914–6915 (2005). doi:10.​1021/​ja043003a CrossRef
106.
Stojanovic, M.N., Stefanovic, D.: Deoxyribozyme-based half adder. J. Am. Chem. Soc. 125(22), 6673–6676 (2003)CrossRef
107.
Stojanovic, M.N., Stefanovic, D.: A deoxyribozyme-based molecular automaton. Nat. Biotechnol. 21(9), 1069–1074 (2003)CrossRef
108.
Stojanovic, M.N., Stefanovic, D., Rudchenko, S.: Exercises in molecular computing. Acc. Chem. Res. 47, 1845–1852 (2014)CrossRef
109.
Tabor, J.J., Levy, M., Ellington, A.D.: Deoxyribozymes that recode sequence information. Nucleic Acid. Res. 34, 2166–2172 (2006)CrossRef
110.
Tang, J., Breaker, R.R.: Rational design of allosteric ribozymes. Chem. Biol. 4(6), 453–459 (1997)CrossRef
111.
Teichmann, M., Kopperger, E., Simmel, F.C.: Robustness of localized DNA strand displacement cascades. ACS Nano 8(8), 8487–8496 (2014)CrossRef
112.
Teller, C., Shimron, S., Willner, I.: Aptamer-DNAzyme hairpins for amplified biosensing. Anal. Chem. 81, 9114–9119 (2009)CrossRef
113.
114.
Tram, K., Kanda, P., Salena, B.J., Huan, S., Li, Y.: Translating bacterial detection by DNAzymes into a litmus test. Angew. Chem. Int. Ed. 53(47), 12799–12802 (2014). doi:10.​1002/​anie.​201407021
115.
Tyagi, S., Kramer, F.R.: Molecular beacons: probes that fluoresce upon hybridization. Nat. Biotechnol. 14(3), 303–309 (1996)CrossRef
116.
Vaidya, N., Manapat, M.L., Chen, I.A., Xulvi-Brunet, R., Hayden, E.J., Lehman, N.: Spontaneous network formation among cooperative RNA replicators. Nature 491, 72–77 (2012). doi:10.​1038/​nature11549 CrossRef
117.
118.
Wang, F., Elbaz, J., Orbach, R., Magen, N., Willner, I.: Amplified analysis of DNA by the autonomous assembly of polymers consisting of DNAzyme wires. J. Am. Chem. Soc. 133, 17149–17151 (2011)CrossRef
119.
Wang, F., Elbaz, J., Teller, C., Willner, I.: Amplified detection of DNA through an autocatalytic and catabolic DNAzyme-mediated process. Angew. Chem. Int. Ed. 50, 295–299 (2011)CrossRef
120.
Wang, F., Elbaz, J., Willner, I.: Enzyme-free amplified detection of DNA by an autonomous ligation DNAzyme machinery. J. Am. Chem. Soc. 134, 5504–5507 (2012)
121.
Wang, F., Lu, C.H., Willner, I.: From cascaded catalytic nucleic acids to enzyme-DNA nanostructures: controlling reactivity, sensing, logic operations, and assembly of complex structures. Chem. Rev. 114, 2881–2941 (2014). doi:10.​1021/​cr400354z CrossRef
122.
123.
Wang, Z., Lee, J.H., Lu, Y.: Label-free colorimetric detection of lead ions with a nanomolar detection limit and tunable dynamic range by using gold nanoparticles and DNAzyme. Adv. Mater. 20(17), 3263–3267 (2008)CrossRef
124.
125.
Wolfe, B.R., Pierce, N.A.: Sequence design for a test tube of interacting nucleic acid strands. ACS Synth. Biol. 4(10), 1086–1100 (2015). doi:10.​1021/​sb5002196
126.
Wu, P., Hwang, K., Lan, T., Lu, Y.: A DNAzyme-gold nanoparticle probe for uranyl ion in living cells. J. Am. Chem. Soc. 135, 5254–5257 (2013). doi:10.​1021/​ja400150v CrossRef
127.
128.
Xiang, Y., Lu, Y.: Expanding targets of DNAzyme-based sensors through deactivation and activation of DNAzymes by single uracil removal: Sensitive fluorescent assay of uracil-DNA glycosylase. Anal. Chem. 84, 9981–9987 (2012). doi:10.​1021/​ac302424f CrossRef
129.
Xiang, Y., Wang, Z., Xing, H., Lu, Y.: Expanding DNAzyme functionality through enzyme cascades with applications in single nucleotide repair and tunable DNA-directed assembly of nanomaterials. Chem. Sci. 4, 398–404 (2013). doi:10.​1039/​c2sc20763j CrossRef
130.
Xiang, Y., Wu, P., Tan, L.H., Lu, Y.: DNAzyme-functionalized gold nanoparticles for biosensing. In: Gu, M.B., Kim, H.S. (eds.) Biosensors Based on Aptamers and Enzymes, Advances in Biochemical Engineering/Biotechnology, vol. 140, pp. 93–120. Springer, New York (2014)
131.
Xiao, Y., Wehrmann, R.J., Ibrahim, N.A., Silverman, S.K.: Establishing broad generality of DNA catalysts for site-specific hydrolysis of single-stranded DNA. Nucleic Acid. Res. 40(4), 1778–1786 (2012). doi:10.​1093/​nar/​gkr860 CrossRef
132.
Yashin, R., Rudchenko, S., Stojanovic, M.N.: Networking particles over distance using oligonucleotide-based devices. J. Am. Chem. Soc. 129(50), 15581–15584 (2007)CrossRef
133.
134.
Yurke, B., Turberfield, A.J., Mills Jr., A.P., Simmel, F.C., Neumann, J.L.: A DNA-fuelled molecular machine made of DNA. Nature 406, 605–608 (2000). doi:10.​1038/​35020524 CrossRef
135.
Zadeh, J.N., Steenberg, C.D., Bois, J.S., Wolfe, B.R., Pierce, M.B., Khan, A.R., Dirks, R.M., Pierce, N.A.: NUPACK: analysis and design of nucleic acid systems. J. Comput. Chem. 32, 170–173 (2011)
136.
Zadeh, J.N., Wolfe, B.R., Pierce, N.A.: Nucleic acid sequence design via efficient ensemble defect optimization. J. Comput. Chem. 32, 439–452 (2011)CrossRef
137.
Zenisek, S.F.M., Hayden, E.J., Lehman, N.: Genetic exchange leading to self-assembling RNA species upon encapsulation in artificial protocells. Artif. Life 13(3), 279–289 (2007). doi:10.​1162/​artl.​2007.​13.​3.​279
138.
139.
140.
Zhang, D.Y., Turberfield, A.J., Yurke, B., Winfree, E.: Engineering entropy-driven reactions and networks catalyzed by DNA. Science 318, 1121–1125 (2007)CrossRef
141.
Zhang, X.B., Kong, R.M., Lu, Y.: Metal ion sensors based on DNAzymes and related DNA molecules. Annu. Rev. Anal. Chem. 4, 105–128 (2011)CrossRef
Metadaten
Titel
Implementing Molecular Logic Gates, Circuits, and Cascades Using DNAzymes
verfasst von
Matthew R. Lakin
Milan N. Stojanovic
Darko Stefanovic
Copyright-Jahr
2017
Buch
Advances in Unconventional Computing

Print ISBN: 978-3-319-33920-7

Electronic ISBN: 978-3-319-33921-4

Copyright-Jahr: 2017

DOI
https://doi.org/10.1007/978-3-319-33921-4_1