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Engineering a Robust DNA Circuit for the Direct Detection of Biomolecular Interactions

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Abstract

The field of DNA circuitry started with the aim of developing DNA molecular machine for autonomous molecular computation. However, the field has since recognized that the speed and scale of DNA computation can never surpass that of silicon-based microelectronics (Regalado in MIT Technology Review, [1]).

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References

  1. Regalado, A. MIT Technology Review. https://www.technologyreview.com/s/400727/dna-computing/ (2000)

  2. Chen, X., Ellington, A.D.: Shaping up nucleic acid computation. Curr. Opin. Biotechnol. 21, 392 (2010)

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  3. Watson, J.D., Crick, F.H.C.: Molecular structure of nucleic acids. Nature 171, 737 (1953)

    Article  CAS  PubMed  Google Scholar 

  4. Yakovchuk, P., Protozanova, E., Frank-Kamenetskii, M.D.: Base-stacking and base-pairing contributions into thermal stability of the DNA double helix. Nucleic Acids Res. 34, 564 (2006)

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  5. Hunter, C.A.: Sequence-dependent DNA structure. J. Mol. Biol. 230, 1025 (1993)

    Article  CAS  PubMed  Google Scholar 

  6. Karabyk, H., Sevincek, R., Karabyk, H.: π-cooperativity effect on the base stacking interactions in DNA: is there a novel stabilization factor coupled with base pairing H-bonds? Phys. Chem. Chem. Phys. 16, 15527 (2014)

    Article  CAS  Google Scholar 

  7. Vallone, P.M., Paner, T.M., Hillario, J., Lane, M.J., Faldasz, B.D., Benight, A.S.: Melting studies of short DNA hairpins: influence of loop sequence and adjoining base pair identity on hairpin thermodynamic stability. Biopolymers 50, 425 (1999)

    Article  CAS  PubMed  Google Scholar 

  8. Rentzeperis, D., Alessi, K., Marky, L.A.: Thermodynamics of DNA hairpins: contribution of loop size to hairpin stability and ethidium binding. Nucleic Acids Res. 21, 2683 (1993)

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  9. Senior, M.M., Jones, R.A., Breslauer, K.J.: Influence of loop residues on the relative stabilities of DNA hairpin structures. Proc. Natl. Acad. Sci. U. S. A. 85, 6242 (1988)

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  10. Kuznetsov, S.V., Ren, C.-C., Woodson, S.A., Ansari, A.: Loop dependence of the stability and dynamics of nucleic acid hairpins. Nucleic Acids Res. 36, 1098 (2008)

    Article  CAS  PubMed  Google Scholar 

  11. SantaLucia, J., Hicks, D.: The thermodynamics of DNA structural motifs. Annu. Rev. Biophys. Biomol. Struct. 33, 415 (2004)

    Article  CAS  PubMed  Google Scholar 

  12. Kuznetsov, S.V., Ansari, A.: A kinetic zipper model with intrachain interactions applied to nucleic acid hairpin folding kinetics. Biophys. J. 102, 101 (2012)

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  13. Nelson, J.W., Tinoco, I.: Comparison of the kinetics of ribo-, deoxyribo- and hybrid oligonucleotide double-strand formation by temperature-jump kinetics. Biochemistry 21, 5289 (1982)

    Article  CAS  PubMed  Google Scholar 

  14. Owczarzy, R., Vallone, P.M., Gallo, F.J., Paner, T.M., Lane, M.J., Benight, A.S.: Predicting sequence-dependent melting stability of short duplex DNA oligomers. Biopolymers 44, 217 (1997)

    Article  CAS  PubMed  Google Scholar 

  15. Delcourt, S.G., Blake, R.D.: Stacking energies in DNA. J. Biol. Chem. 266, 15160 (1991)

    CAS  PubMed  Google Scholar 

  16. Frank-Kamenetskii, M.D.: Simplification of the empirical relationship between melting temperature of DNA, Its GC content and concentration of sodium ions in solution. Biopolymers 10, 2623 (1971)

    Article  CAS  PubMed  Google Scholar 

  17. Owczarzy, R., Moreira, B.G., You, Y., Behlke, M.A., Walder, J.A.: Predicting stability of DNA duplexes in solutions containing magnesium and monovalent cations. Biochemistry 47, 5336 (2008)

    Article  CAS  PubMed  Google Scholar 

  18. Crick, F.: Central dogma of molecular biology. Nature 227, 561 (1970)

    Article  CAS  PubMed  Google Scholar 

  19. Jackson, D.A., Symons, R.H., Berg, P.: Biochemical method for inserting new genetic information into DNA of Simian Virus 40: circular SV40 DNA molecules containing lambda phage genes and the galactose operon of Escherichia Coli. Proc. Natl. Acad. Sci. U. S. A. 69, 2904 (1972)

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  20. Seeman, N.C.: Nucleic acid junctions and lattices. J. Theor. Biol. 99, 237 (1982)

    Article  CAS  PubMed  Google Scholar 

  21. Seeman, N.C.: Structural DNA Nanotechnology. Cambridge University Press (2016)

    Google Scholar 

  22. Lu, Y., Liu, J.: Functional DNA nanotechnology: emerging applications of DNAzymes and aptamers. Curr. Opin. Biotechnol. 17, 580 (2006)

    Article  CAS  PubMed  Google Scholar 

  23. Ellington, A.D., Szostak, J.W.: In vitro selection of RNA molecules that bind specific ligands. Nature 346, 818 (1990)

    Article  CAS  PubMed  Google Scholar 

  24. Ellington, A.D., Szostak, J.W.: Selection in vitro of single-stranded DNA molecules that fold into specific ligand-binding structures. Nature 355, 850 (1992)

    Article  CAS  PubMed  Google Scholar 

  25. Adleman, L.M.: Molecular computation of solutions to combinatorial problems. Science 266, 1021 (1994)

    Article  CAS  PubMed  Google Scholar 

  26. Yurke, B., Turberfield, A.J., Mills, A.P., Simmel, F.C., Neumann, J.L.: A DNA-fuelled molecular machine made of DNA. Nature 406, 605 (2000)

    Article  CAS  PubMed  Google Scholar 

  27. Zhang, D.Y., Seelig, G.: Dynamic DNA nanotechnology using strand-displacement reactions. Nat. Chem. 3, 103 (2011)

    Article  CAS  PubMed  Google Scholar 

  28. Zhang, D.Y., Turberfield, A.J., Yurke, B., Winfree, E.: Engineering entropy-driven reactions and networks catalyzed by DNA. Science 318, 1121 (2007)

    Article  CAS  PubMed  Google Scholar 

  29. Reynaldo, L.P., Vologodskii, A.V., Neri, B.P., Lyamichev, V.I.: The kinetics of oligonucleotide replacements. J. Mol. Biol. 297, 511 (2000)

    Article  CAS  PubMed  Google Scholar 

  30. Yurke, B., Mills, A.P.: Using DNA to power nanostructures. Genet. Program. Evol. M. 4, 111 (2003)

    Article  Google Scholar 

  31. Zhang, D.Y., Winfree, E.: Control of DNA strand Displacement kinetics using toehold exchange. J. Am. Chem. Soc. 131, 17303 (2009)

    Article  CAS  PubMed  Google Scholar 

  32. Panyutin, I.G., Hsieh, P.: The kinetics of spontaneous DNA branch migration. Proc. Natl. Acad. Sci. U. S. A. 91, 2021 (1994)

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  33. Srinivas, N., Ouldridge, T.E., Šulc, P., Schaeffer, J.M., Yurke, B., Louis, A.A., Doye, J.P.K., Winfree, E.: On the biophysics and kinetics of toehold-mediated DNA strand displacement. Nucleic Acids Res. 41, 10641 (2013)

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  34. 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 (2011)

    Article  CAS  PubMed  Google Scholar 

  35. Owczarzy, R., Tataurov, A.V., Wu, Y., Manthey, J.A., McQuisten, K.A., Almabrazi, H.G., Pedersen, K.F., Lin, Y., Garretson, J., McEntaggart, N.O., Sailor, C.A., Dawson, R.B., Peek, A.S.: IDT SciTools: a suite for analysis and design of nucleic acid oligomers. Nucleic Acids Res. 36, W163 (2008)

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  36. Zuker, M.: Mfold web server for nucleic acid folding and hybridization prediction. Nucleic Acids Res. 31, 3406 (2003)

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  37. SantaLucia, J.: A unified view of polymer, dumbbell, and oligonucleotide DNA nearest-neighbor thermodynamics. Proc. Natl. Acad. Sci. U. S. A. 95, 1460 (1998)

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  38. Lakin, M.R., Youssef, S., Polo, F., Emmott, S., Phillips, A.: Visual DSD: a design and analysis tool for DNA strand displacement systems. Bioinformatics 27, 3211 (2011)

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  39. Ouldridge, T.E., Louis, A.A., Doye, J.P.K.: Structural, mechanical, and thermodynamic properties of a coarse-grained DNA model. J. Chem. Phys. 134, 085101 (2011)

    Article  CAS  PubMed  Google Scholar 

  40. Seelig, G., Soloveichik, D., Zhang, D.Y., Winfree, E.: Enzyme-free nucleic acid logic circuits. Science 314, 1585 (2006)

    Article  CAS  PubMed  Google Scholar 

  41. Green, S.J., Lubrich, D., Turberfield, A.J.: DNA hairpins: fuel for autonomous DNA devices. Biophys. J. 91, 2966 (2006)

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  42. Genot, A.J., Zhang, D.Y., Bath, J., Turberfield, A.J.: Remote toehold: a mechanism for flexible control of DNA hybridization kinetics. J. Am. Chem. Soc. 133, 2177 (2011)

    Article  CAS  PubMed  Google Scholar 

  43. Zhu, J., Zhang, L., Zhou, Z., Dong, S., Wang, E.: Molecular aptamer beacon tuned DNA strand displacement to transform small molecules into DNA logic outputs. Chem. Commun. 50, 3321 (2014)

    Article  CAS  Google Scholar 

  44. Xing, Y., Yang, Z., Liu, D.: A responsive hidden toehold to enable controllable DNA strand displacement reactions. Angew. Chem. Int. Ed. 50, 11934 (2011)

    Article  CAS  Google Scholar 

  45. Zhang, L., Guo, S., Zhu, J., Zhou, Z., Li, T., Li, J., Dong, S., Wang, E.: Engineering DNA three-way junction with multifunctional moieties: sensing platform for bioanalysis. Anal. Chem. 87, 11295 (2015)

    Article  CAS  PubMed  Google Scholar 

  46. Feng, S., Wu, F., Xu, J., Chen, Y., Zhou, X.: Regulation of DNA strand displacement using a G-quadruplex-mediated toehold. RSC Adv. 4, 55367 (2014)

    Article  CAS  Google Scholar 

  47. Amodio, A., Zhao, B., Porchetta, A., Idili, A., Castronovo, M., Fan, C., Ricci, F.: Rational design of pH-controlled DNA strand displacement. J. Am. Chem. Soc. 136, 16469 (2014)

    Article  CAS  PubMed  Google Scholar 

  48. Deng, W., Xu, H., Ding, W., Liang, H.: DNA logic gate based on metallo-toehold strand displacement. PLoS ONE 9, e111650 (2014)

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  49. Tang, W., Wang, H., Wang, D., Zhao, Y., Li, N., Liu, F.: DNA tetraplexes-based toehold activation for controllable DNA strand displacement reactions. J. Am. Chem. Soc. 135, 13628 (2013)

    Article  CAS  PubMed  Google Scholar 

  50. Prokup, A., Hemphill, J., Deiters, A.: DNA computation: a photochemically controlled and gate. J. Am. Chem. Soc. 134, 3810 (2012)

    Article  CAS  PubMed  Google Scholar 

  51. Prokup, A., Hemphill, J., Liu, Q., Deiters, A.: Optically controlled signal amplification for DNA computation. ACS Synth. Biol. 4, 1064 (2015)

    Article  CAS  PubMed  Google Scholar 

  52. Huang, F., You, M., Han, D., Xiong, X., Liang, H., Tan, W.: DNA branch migration reactions through photocontrollable toehold formation. J. Am. Chem. Soc. 135, 7967 (2013)

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  53. Chen, X.: Expanding the rule set of DNA circuitry with associative toehold activation. J. Am. Chem. Soc. 134, 263 (2012)

    Article  CAS  PubMed  Google Scholar 

  54. Genot, A.J., Bath, J., Turberfield, A.J.: Combinatorial displacement of DNA strands: application to matrix multiplication and weighted sums. Angew. Chem. Int. Ed. 125, 1227 (2013)

    Article  Google Scholar 

  55. Zhu, J., Zhang, L., Dong, S., Wang, E.: Four-way junction-driven DNA strand displacement and its application in building majority logic circuit. ACS Nano 7, 10211 (2013)

    Article  CAS  PubMed  Google Scholar 

  56. Picuri, J.M., Frezza, B.M., Ghadiri, M.R.: Universal translators for nucleic acid diagnosis. J. Am. Chem. Soc. 131, 9368 (2009)

    Article  CAS  PubMed  Google Scholar 

  57. Tang, W., Hu, S., Wang, H., Zhao, Y., Li, N., Liu, F.: A universal molecular translator for non-nucleic acid targets that enables dynamic DNA assemblies and logic operations. Chem. Commun. 50, 14352 (2014)

    Article  CAS  Google Scholar 

  58. Zhu, J., Wang, L., Jiang, W.: A binding-induced sutured toehold activation for controllable DNA strand displacement reactions. Chem. Commun. 51, 2903 (2015)

    Article  CAS  Google Scholar 

  59. Zhu, J., Wang, L., Xu, X., Wei, H., Jiang, W.: Modular nuclease-responsive DNA Three-way junction-based dynamic assembly of a DNA device and its sensing application. Anal. Chem. 88, 3817 (2016)

    Article  CAS  PubMed  Google Scholar 

  60. Li, F., Zhang, H., Lai, C., Li, X.-F., Le, X.C.: A molecular translator that acts by binding-induced DNA strand displacement for a homogeneous protein assay. Angew. Chem. Int. Ed. 51, 9317 (2012)

    Article  CAS  Google Scholar 

  61. Zhang, H., Li, F., Dever, B., Wang, C., Li, X.-F., Le, X.C.: Assembling DNA through affinity binding to achieve ultrasensitive protein detection. Angew. Chem. Int. Ed. 52, 10698 (2013)

    Article  CAS  Google Scholar 

  62. Dirks, R.M., Pierce, N.A.: Triggered amplification by hybridization chain reaction. Proc. Natl. Acad. Sci. U. S. A. 101, 15275 (2004)

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  63. Bi, S., Chen, M., Jia, X., Dong, Y., Wang, Z.: Hyperbranched hybridization chain reaction for triggered signal amplification and concatenated logic circuits. Angew. Chem. Int. Ed. 54, 8144 (2015)

    Article  CAS  Google Scholar 

  64. Chandran, H., Rangnekar, A., Shetty, G., Schultes, E.A., Reif, J.H., LaBean, T.H.: An autonomously self-assembling dendritic DNA nanostructure for target DNA detection. Biotechnol. J. 8, 221 (2013)

    Article  CAS  PubMed  Google Scholar 

  65. Yin, P., Choi, H.M.T., Calvert, C.R., Pierce, N.A.: Programming biomolecular self-assembly pathways. Nature 451, 318 (2008)

    Article  CAS  PubMed  Google Scholar 

  66. Xuan, F., Hsing, I.M.: Triggering hairpin-free chain-branching growth of fluorescent DNA dendrimers for nonlinear hybridization chain reaction. J. Am. Chem. Soc. 136, 9810 (2014)

    Article  CAS  PubMed  Google Scholar 

  67. Qian, L., Winfree, E.: A simple DNA gate motif for synthesizing large-scale circuits. J. R. Soc. Interface (2011)

    Google Scholar 

  68. Qian, L., Winfree, E.: Scaling up digital circuit computation with DNA strand displacement cascades. Science 332, 1196 (2011)

    Article  CAS  PubMed  Google Scholar 

  69. Turberfield, A.J., Mitchell, J.C., Yurke, B., Mills, A.P., Blakey, M.I., Simmel, F.C.: DNA fuel for free-running nanomachines. Phys. Rev. Lett. 90, 118102 (2003)

    Article  CAS  PubMed  Google Scholar 

  70. Muscat, R.A., Strauss, K., Ceze, L., Seelig, G.: In: Proceedings of the 40th Annual International Symposium on Computer Architecture, p. 177. ACM, Tel-Aviv, Israel (2013)

    Google Scholar 

  71. Dunn, K.E., Trefzer, M.A., Johnson, S., Tyrrell, A.M.: Investigating the dynamics of surface-immobilized DNA nanomachines. Sci. Rep. 6, 29581 (2016)

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  72. Gu, H., Chao, J., Xiao, S.-J., Seeman, N.C.: A proximity-based programmable DNA nanoscale assembly line. Nature 465, 202 (2010)

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  73. Rotaru, A., Gothelf, K.V.: DNA nanotechnology: steps towards automated synthesis. Nat. Nanotechnol. 5, 760 (2010)

    Article  CAS  PubMed  Google Scholar 

  74. Wickham, S.F.J., Bath, J., Katsuda, Y., Endo, M., Hidaka, K., Sugiyama, H., Turberfield, A.J.: A DNA-based molecular motor that can navigate a network of tracks. Nat. Nanotechnol. 7, 169 (2012)

    Article  CAS  PubMed  Google Scholar 

  75. 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 (2010)

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  76. Chandran, H.; Gopalkrishnan, N.; Phillips, A.; Reif, J. In: Cardelli, L., Shih, W. (eds.) DNA Computing and Molecular Programming: 17th International Conference, DNA 17, Pasadena, CA, USA, September 19–23, 2011. Proceedings, p. 64. Springer Berlin Heidelberg, Berlin, Heidelberg (2011)

    Google Scholar 

  77. Ruiz, I.M., Arbona, J.-M., Lad, A., Mendoza, O., Aime, J.-P., Elezgaray, J.: Connecting localized DNA strand displacement reactions. Nanoscale 7, 12970 (2015)

    Article  CAS  PubMed  Google Scholar 

  78. Teichmann, M., Kopperger, E., Simmel, F.C.: Robustness of localized DNA strand displacement cascades. ACS Nano 8, 8487 (2014)

    Article  CAS  PubMed  Google Scholar 

  79. Peterson, A.W., Heaton, R.J., Georgiadis, R.M.: The effect of surface probe density on DNA hybridization. Nucleic Acids Res. 29, 5163 (2001)

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  80. Mendoza, O., Mergny, J.-L., Aimé, J.-P., Elezgaray, J.: G-quadruplexes light up localized DNA circuits. Nano Lett. 16, 624 (2016)

    Article  CAS  PubMed  Google Scholar 

  81. Dunn, K.E., Morgan, T.L., Trefzer, M.A., Johnson, S.D., Tyrrell, A.M.: In: Lones, M., Tyrrell, A., Smith, S., Fogel, G. (eds.) Information Processing in Cells and Tissues: 10th International Conference, IPCAT 2015, San Diego, CA, USA, September 14–16, 2015, Proceedings, p. 3. Springer International Publishing, Cham (2015)

    Google Scholar 

  82. Zhang, D.Y., Hariadi, R.F., Choi, H.M.T., Winfree, E.: Integrating DNA strand-displacement circuitry with DNA tile self-assembly. Nat. Commun. 4, 1965 (2013)

    Article  CAS  PubMed  Google Scholar 

  83. Zhang, H., Li, X.-F., Le, X.C.: Binding-induced DNA assembly and its application to yoctomole detection of proteins. Anal. Chem. 84, 877 (2012)

    Article  CAS  PubMed  Google Scholar 

  84. Tang, Y., Lin, Y., Yang, X., Wang, Z., Le, X.C., Li, F.: Universal strategy to engineer catalytic DNA hairpin assemblies for protein analysis. Anal. Chem. 87, 8063 (2015)

    Article  CAS  PubMed  Google Scholar 

  85. Li, F., Lin, Y., Le, X.C.: Binding-induced formation of DNA three-way junctions and its application to protein detection and DNA strand displacement. Anal. Chem. 85, 10835 (2013)

    Article  CAS  PubMed  Google Scholar 

  86. Li, F., Tang, Y., Traynor, S.M., Li, X.-F., Le, X.C.: Kinetics of proximity-induced intramolecular DNA strand displacement. Anal. Chem. 88, 8152 (2016)

    Article  CAS  PubMed  Google Scholar 

  87. Li, F., Zhang, H., Wang, Z., Li, X., Li, X.-F., Le, X.C.: Dynamic DNA assemblies mediated by binding-induced DNA strand displacement. J. Am. Chem. Soc. 135, 2443 (2013)

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  88. Tyagi, S., Kramer, F.R.: Molecular beacons: probes that fluoresce upon hybridization. Nat. Biotechnol. 14, 303 (1996)

    Article  CAS  PubMed  Google Scholar 

  89. Tsourkas, A., Behlke, M.A., Rose, S.D., Bao, G.: Hybridization kinetics and thermodynamics of molecular beacons. Nucleic Acids Res. 31, 1319 (2003)

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  90. Li, B., Ellington, A.D., Chen, X.: Rational, modular adaptation of enzyme-free DNA circuits to multiple detection methods. Nucleic Acids Res. 39, e110 (2011)

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  91. Huang, J., Su, X., Li, Z.: Enzyme-free and amplified fluorescence DNA detection using bimolecular beacons. Anal. Chem. 84, 5939 (2012)

    Article  CAS  PubMed  Google Scholar 

  92. Jiang, Z., Wang, H., Zhang, X., Liu, C., Li, Z.: An enzyme-free signal amplification strategy for sensitive detection of MicroRNA via catalyzed hairpin assembly. Anal. Methods 6, 9477 (2014)

    Article  CAS  Google Scholar 

  93. Hun, X., Xie, G., Luo, X.: Scaling up an electrochemical signal with a catalytic hairpin assembly coupling nanocatalyst label for DNA detection. Chem. Commun. 51, 7100 (2015)

    Article  CAS  Google Scholar 

  94. Chen, X., Briggs, N., McLain, J.R., Ellington, A.D.: Stacking nonenzymatic circuits for high signal gain. Proc. Natl. Acad. Sci. U. S. A. 110, 5386 (2013)

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  95. Milligan, J.N., Ellington, A.D.: Using RecA protein to enhance kinetic rates of DNA circuits. Chem. Commun. 51, 9503 (2015)

    Article  CAS  Google Scholar 

  96. Li, C., Li, Y., Xu, X., Wang, X., Chen, Y., Yang, X., Liu, F., Li, N.: Fast and quantitative differentiation of single-base mismatched DNA by initial reaction rate of catalytic hairpin assembly. Biosens. Bioelectron. 60, 57 (2014)

    Article  CAS  PubMed  Google Scholar 

  97. Zhang, S., Wang, K., Li, Z., Feng, Z., Sun, T.: Lab in a tube: a fast-assembled colorimetric sensor for highly sensitive detection of oligonucleotides based on a hybridization chain reaction. RSC Adv. 5, 44714 (2015)

    Article  CAS  Google Scholar 

  98. Li, B., Chen, X., Ellington, A.D.: Adapting enzyme-free DNA circuits to the detection of loop-mediated isothermal amplification reactions. Anal. Chem. 84, 8371 (2012)

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  99. Jiang, Y., Li, B., Milligan, J.N., Bhadra, S., Ellington, A.D.: Real-time detection of isothermal amplification reactions with thermostable catalytic hairpin assembly. J. Am. Chem. Soc. 135, 7430 (2013)

    Article  CAS  PubMed  Google Scholar 

  100. Song, W., Zhang, Q., Sun, W.: Ultrasensitive detection of nucleic acids by template enhanced hybridization followed by rolling circle amplification and catalytic hairpin assembly. Chem. Commun. 51, 2392 (2015)

    Article  CAS  Google Scholar 

  101. Dong, J., Cui, X., Deng, Y., Tang, Z.: Amplified detection of nucleic acid by G-quadruplex based hybridization chain reaction. Biosens. Bioelectron. 38, 258 (2012)

    Article  CAS  PubMed  Google Scholar 

  102. Huang, J., Wu, Y., Chen, Y., Zhu, Z., Yang, X., Yang, C.J., Wang, K., Tan, W.: Pyrene-excimer probes based on the hybridization chain reaction for the detection of nucleic acids in complex biological fluids. Angew. Chem. Int. Ed. 50, 401 (2011)

    Article  CAS  Google Scholar 

  103. Liu, L., Li, Q., Tang, L.-J., Yu, R.-Q., Jiang, J.-H.: Silver nanocluster-lightened hybridization chain reaction. RSC Adv. 6, 57502 (2016)

    Article  CAS  Google Scholar 

  104. Qiu, X., Wang, P., Cao, Z.: Hybridization chain reaction modulated DNA-hosted silver nanoclusters for fluorescent identification of single nucleotide polymorphisms in the let-7 miRNA family. Biosens. Bioelectron. 60, 351 (2014)

    Article  CAS  PubMed  Google Scholar 

  105. Liu, P., Yang, X., Sun, S., Wang, Q., Wang, K., Huang, J., Liu, J., He, L.: Enzyme-free colorimetric detection of DNA by using gold nanoparticles and hybridization chain reaction amplification. Anal. Chem. 85, 7689 (2013)

    Article  CAS  PubMed  Google Scholar 

  106. Ma, C., Wang, W., Mulchandani, A., Shi, C.: A simple colorimetric DNA detection by target-induced hybridization chain reaction for isothermal signal amplification. Anal. Biochem. 457, 19 (2014)

    Article  CAS  PubMed  Google Scholar 

  107. Chen, Y., Xu, J., Su, J., Xiang, Y., Yuan, R., Chai, Y.: In situ hybridization chain reaction amplification for universal and highly sensitive electrochemiluminescent detection of DNA. Anal. Chem. 84, 7750 (2012)

    Article  CAS  PubMed  Google Scholar 

  108. Wang, X., Lau, C., Kai, M., Lu, J.: Hybridization chain reaction-based instantaneous derivatization technology for chemiluminescence detection of specific DNA sequences. Analyst 138, 2691 (2013)

    Article  CAS  PubMed  Google Scholar 

  109. Niu, S., Jiang, Y., Zhang, S.: Fluorescence detection for DNA using hybridization chain reaction with enzyme-amplification. Chem. Commun. 46, 3089 (2010)

    Article  CAS  Google Scholar 

  110. Yu, X., Zhang, Z.-L., Zheng, S.-Y.: Highly sensitive DNA detection using cascade amplification strategy based on hybridization chain reaction and enzyme-induced metallization. Biosens. Bioelectron. 66, 520 (2015)

    Article  CAS  PubMed  Google Scholar 

  111. Yang, D., Ning, L., Gao, T., Ye, Z., Li, G.: Enzyme-free dual amplification strategy for protein assay by coupling toehold-mediated DNA strand displacement reaction with hybridization chain reaction. Electrochem. Commun. 58, 33 (2015)

    Article  CAS  Google Scholar 

  112. Feng, C., Zhu, J., Sun, J., Jiang, W., Wang, L.: Hairpin assembly circuit-based fluorescence cooperative amplification strategy for enzyme-free and label-free detection of small molecule. Talanta 143, 101 (2015)

    Article  CAS  PubMed  Google Scholar 

  113. Zou, P., Liu, Y., Wang, H., Wu, J., Zhu, F., Wu, H.: G-quadruplex DNAzyme-based chemiluminescence biosensing platform based on dual signal amplification for label-free and sensitive detection of protein. Biosens. Bioelectron. 79, 29 (2016)

    Article  CAS  PubMed  Google Scholar 

  114. Chen, J., Wen, J., Yang, G., Zhou, S.: A target-induced three-way G-quadruplex Junction for 17β-Estradiol monitoring with a naked-eye readout. Chem. Commun. 51, 12373 (2015)

    Article  CAS  Google Scholar 

  115. Guo, Y., Wu, J., Ju, H.: Target-driven DNA association to initiate cyclic assembly of hairpins for biosensing and logic gate operation. Chem. Sci. 6, 4318 (2015)

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  116. Kim, D., Garner, O.B., Ozcan, A., Di Carlo, D.: Homogeneous entropy-driven amplified detection of biomolecular interactions. ACS Nano 10, 7467 (2016)

    Article  CAS  PubMed  Google Scholar 

  117. Zong, C., Wu, J., Liu, M., Yan, F., Ju, H.: High-throughput imaging assay of multiple proteins via target-induced DNA assembly and cleavage. Chem. Sci. 6, 2602 (2015)

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  118. Choi, H.M.T., Chang, J.Y., Trinh, L.A., Padilla, J.E., Fraser, S.E., Pierce, N.A.: Programmable in situ amplification for multiplexed imaging of mRNA expression. Nat. Biotechnol. 28, 1208 (2010)

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  119. Tyagi, S.: Imaging intracellular RNA distribution and dynamics in living cells. Nat. Methods 6, 331 (2009)

    Article  CAS  PubMed  Google Scholar 

  120. Choi, H.M.T., Beck, V.A., Pierce, N.A.: Next-generation in situ hybridization chain reaction: higher gain, lower cost, greater durability. ACS Nano 8, 4284 (2014)

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  121. Huang, J., Wang, H., Yang, X., Quan, K., Yang, Y., Ying, L., Xie, N., Ou, M., Wang, K.: Fluorescence resonance energy transfer-based hybridization chain reaction for in situ visualization of tumor-related mRNA. Chem. Sci. 7, 3829 (2016)

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  122. Schweller, R.M., Zimak, J., Duose, D.Y., Qutub, A.A., Hittelman, W.N., Diehl, M.R.: Multiplexed in situ immunofluorescence using dynamic DNA complexes. Angew. Chem. Int. Ed. 51, 9292 (2012)

    Article  CAS  Google Scholar 

  123. Hemphill, J., Deiters, A.: DNA Computation in mammalian cells: microRNA logic operations. J. Am. Chem. Soc. 135, 10512 (2013)

    Article  CAS  PubMed  Google Scholar 

  124. Wu, C., Cansiz, S., Zhang, L., Teng, I.T., Qiu, L., Li, J., Liu, Y., Zhou, C., Hu, R., Zhang, T., Cui, C., Cui, L., Tan, W.: A nonenzymatic hairpin DNA cascade reaction provides high signal gain of mRNA imaging inside live cells. J. Am. Chem. Soc. 137, 4900 (2015)

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  125. Wu, Z., Liu, G.-Q., Yang, X.-L., Jiang, J.-H.: Electrostatic nucleic acid nanoassembly enables hybridization chain reaction in living cells for ultrasensitive mRNA imaging. J. Am. Chem. Soc. 137, 6829 (2015)

    Article  CAS  PubMed  Google Scholar 

  126. Cheglakov, Z., Cronin, T.M., He, C., Weizmann, Y.: Live cell microRNA imaging using cascade hybridization reaction. J. Am. Chem. Soc. 137, 6116 (2015)

    Article  CAS  PubMed  Google Scholar 

  127. Ellis, R.J.: Macromolecular crowding: an important but neglected aspect of the intracellular environment. Curr. Opin. Struc. Biol. 11, 114 (2001)

    Article  CAS  Google Scholar 

  128. Zhu, G., Zhang, S., Song, E., Zheng, J., Hu, R., Fang, X., Tan, W.: Building fluorescent DNA nanodevices on target living cell surfaces. Angew. Chem. Int. Ed. 52, 5490 (2013)

    Article  CAS  Google Scholar 

  129. Rudchenko, M., Taylor, S., Pallavi, P., Dechkovskaia, A., Khan, S., Butler Jr., V.P., Rudchenko, S., Stojanovic, M.N.: Autonomous molecular cascades for evaluation of cell surfaces. Nat. Nanotechnol. 8, 580 (2013)

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  130. Han, D., Zhu, Z., Wu, C., Peng, L., Zhou, L., Gulbakan, B., Zhu, G., Williams, K.R., Tan, W.: A logical molecular circuit for programmable and autonomous regulation of protein activity using DNA aptamer-protein interactions. J. Am. Chem. Soc. 134, 20797 (2012)

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  131. Han, D., Zhu, G., Wu, C., Zhu, Z., Chen, T., Zhang, X., Tan, W.: Engineering a cell-surface aptamer circuit for targeted and amplified photodynamic cancer therapy. ACS Nano 7, 2312 (2013)

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  132. Wang, Y.-M., Wu, Z., Liu, S.-J., Chu, X.: Structure-switching aptamer triggering hybridization chain reaction on the cell surface for activatable theranostics. Anal. Chem. 87, 6470 (2015)

    Article  CAS  PubMed  Google Scholar 

  133. Lei, Y., Tang, J., Shi, H., Ye, X., He, X., Xu, F., Yan, L.A., Qiao, Z., Wang, K.: Nature-inspired smart dna nanodoctor for activatable in vivo cancer imaging and in situ drug release based on recognition-triggered assembly of split aptamer. Anal. Chem. (2016)

    Google Scholar 

  134. You, M., Peng, L., Shao, N., Zhang, L., Qiu, L., Cui, C., Tan, W.: DNA “Nano-Claw”: logic-based autonomous cancer targeting and therapy. J. Am. Chem. Soc. 136, 1256 (2014)

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  135. You, M., Zhu, G., Chen, T., Donovan, M.J., Tan, W.: Programmable and multiparameter DNA-based logic platform for cancer recognition and targeted therapy. J. Am. Chem. Soc. 137, 667 (2015)

    Article  CAS  PubMed  Google Scholar 

  136. Collins, F.S., Varmus, H.: A new initiative on precision medicine. New Engl. J. Med. 372, 793 (2015)

    Article  CAS  PubMed  Google Scholar 

  137. Kusumi, A., Fujiwara, T.K., Chadda, R., Xie, M., Tsunoyama, T.A., Kalay, Z., Kasai, R.S., Suzuki, K.G.N.: Dynamic organizing principles of the plasma membrane that regulate signal transduction: commemorating the fortieth anniversary of singer and Nicolson’s fluid-mosaic model. Annu. Rev. Cell Dev. Biol. 28, 215 (2012)

    Article  CAS  PubMed  Google Scholar 

  138. Hooper, L.V., Littman, D.R., Macpherson, A.J.: Interactions between the microbiota and the immune system. Science 336, 1268 (2012)

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  139. Wu, H.: Higher-order assemblies in a new paradigm of signal transduction. Cell 153, 287 (2013)

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  140. Legrain, P., Rain, J.-C.: Twenty years of protein interaction studies for biological function deciphering. J. Proteomics 107, 93 (2014)

    Article  CAS  PubMed  Google Scholar 

  141. Nam, J.-M., Stoeva, S.I., Mirkin, C.A.: Bio-bar-code-based DNA detection with PCR-like sensitivity. J. Am. Chem. Soc. 126, 5932 (2004)

    Article  CAS  PubMed  Google Scholar 

  142. Nam, J.-M., Thaxton, C.S., Mirkin, C.A.: Nanoparticle-based bio-bar codes for the ultrasensitive detection of proteins. Science 301, 1884 (2003)

    Article  CAS  PubMed  Google Scholar 

  143. Obernosterer, G., Martinez, J., Alenius, M.: Locked nucleic acid-based in situ detection of microRNAs in mouse tissue sections. Nat. Protoc. 2, 1508 (2007)

    Article  CAS  PubMed  Google Scholar 

  144. Ngounou Wetie, A.G., Sokolowska, I., Woods, A.G., Roy, U., Loo, J.A., Darie, C.C.: Investigation of stable and transient protein-protein interactions: past, present, and future. Proteomics 13, 538 (2013)

    Article  CAS  PubMed  Google Scholar 

  145. Berggård, T., Linse, S., James, P.: Methods for the detection and analysis of protein-protein interactions. Proteomics 7, 2833 (2007)

    Article  CAS  PubMed  Google Scholar 

  146. Fields, S., Song, O.-K.: A novel genetic system to detect protein-protein interactions. Nature 340, 245 (1989)

    Article  CAS  PubMed  Google Scholar 

  147. Morell, M., Ventura, S., Avilés, F.X.: Protein complementation assays: approaches for the in vivo analysis of protein interactions. FEBS Lett. 583, 1684 (2009)

    Article  CAS  PubMed  Google Scholar 

  148. Stynen, B., Tournu, H., Tavernier, J., Van Dijck, P.: Diversity in Genetic in vivo methods for protein-protein interaction studies: from the yeast two-hybrid system to the mammalian split-luciferase system. Microbiol. Mol. Biol. R. 76, 331 (2012)

    Article  CAS  Google Scholar 

  149. Soderberg, O., Gullberg, M., Jarvius, M., Ridderstrale, K., Leuchowius, K.-J., Jarvius, J., Wester, K., Hydbring, P., Bahram, F., Larsson, L.-G., Landegren, U.: Direct observation of individual endogenous protein complexes in situ by proximity ligation. Nat. Methods 3, 995 (2006)

    Article  CAS  PubMed  Google Scholar 

  150. Gullberg, M., Fredriksson, S., Taussig, M., Jarvius, J., Gustafsdottir, S., Landegren, U.: A sense of closeness: protein detection by proximity ligation. Curr. Opin. Biotechnol. 14, 82 (2003)

    Article  CAS  PubMed  Google Scholar 

  151. Mocanu, M.-M., Váradi, T., Szöllősi, J., Nagy, P.: Comparative Analysis of Fluorescence Resonance Energy Transfer (FRET) and Proximity Ligation Assay (PLA). Proteomics 11, 2063 (2011)

    Article  CAS  PubMed  Google Scholar 

  152. Clausson, C.-M., Arngården, L., Ishaq, O., Klaesson, A., Kühnemund, M., Grannas, K., Koos, B., Qian, X., Ranefall, P., Krzywkowski, T., Brismar, H., Nilsson, M., Wählby, C., Söderberg, O.: Compaction of rolling circle amplification products increases signal integrity and signal-to-noise ratio. Sci. Rep. 5, 12317 (2015)

    Article  PubMed  PubMed Central  Google Scholar 

  153. Clausson, C.-M., Allalou, A., Weibrecht, I., Mahmoudi, S., Farnebo, M., Landegren, U., Wahlby, C., Soderberg, O.: Increasing the dynamic range of in situ PLA. Nat. Methods 8, 892 (2011)

    Article  CAS  PubMed  Google Scholar 

  154. Koos, B., Cane, G., Grannas, K., Lof, L., Arngarden, L., Heldin, J., Clausson, C.-M., Klaesson, A., Hirvonen, M.K., de Oliveira, F.M.S., Talibov, V.O., Pham, N.T., Auer, M., Danielson, U.H., Haybaeck, J., Kamali-Moghaddam, M., Soderberg, O.: Proximity-dependent initiation of hybridization chain reaction. Nat. Commun. 6, 7294 (2015)

    Article  CAS  PubMed  Google Scholar 

  155. Koussa, M.A., Halvorsen, K., Ward, A., Wong, W.P.: DNA nanoswitches: a quantitative platform for gel-based biomolecular interaction analysis. Nat. Methods 12, 123 (2015)

    Article  CAS  PubMed  Google Scholar 

  156. Chandrasekaran, A.R., Zavala, J., Halvorsen, K.: Programmable DNA nanoswitches for detection of nucleic acid sequences. ACS Sens. 1, 120 (2016)

    Article  CAS  Google Scholar 

  157. Hecker, K.H., Rill, R.L.: Error analysis of chemically synthesized polynucleotides. Biotechniques 24, 256 (1998)

    Article  CAS  PubMed  Google Scholar 

  158. Li, B., Jiang, Y., Chen, X., Ellington, A.D.: Probing spatial organization of DNA strands using enzyme-free hairpin assembly circuits. J. Am. Chem. Soc. 134, 13918 (2012)

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  159. Krueger, A., Protozanova, E., Frank-Kamenetskii, M.D.: Sequence-dependent basepair opening in DNA double helix. Biophys. J. 90, 3091 (2006)

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  160. von Hippel, P.H., Johnson, N.P., Marcus, A.H.: Fifty years of DNA “Breathing”: reflections on old and new approaches. Biopolymers 99, 923 (2013)

    Google Scholar 

  161. Zhang, D.Y.: In: Sakakibara, Y., Mi, Y. (eds.) DNA Computing and Molecular Programming: 16th International Conference, DNA 16, Hong Kong, China, June 14–17, 2010, Revised Selected Papers, p. 162. Springer Berlin Heidelberg, Berlin, Heidelberg (2011)

    Google Scholar 

  162. Jiang, Y.S., Bhadra, S., Li, B., Ellington, A.D.: Mismatches improve the performance of strand-displacement nucleic acid circuits. Angew. Chem. Int. Ed. 53, 1845 (2014)

    Article  CAS  Google Scholar 

  163. Tang, Y., Wang, Z., Yang, X., Chen, J., Liu, L., Zhao, W., Le, X.C., Li, F.: Constructing real-time, wash-free, and reiterative sensors for cell surface proteins using binding-induced dynamic DNA assembly. Chem. Sci. 6, 5729 (2015)

    Article  CAS  PubMed  PubMed Central  Google Scholar 

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  1. Department of Chemical and Biomolecular Engineering, National University of Singapore, Singapore, 117585, Singapore

    Dr. Ang Yan Shan

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Yan Shan, A. (2018). Literature Review. In: Engineering a Robust DNA Circuit for the Direct Detection of Biomolecular Interactions. Springer Theses. Springer, Singapore. https://doi.org/10.1007/978-981-13-2188-7_2

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