1932

Abstract

Biosensors represent biomimetic analytical tools for addressing increasing needs in medical diagnosis, environmental monitoring, security, and biodefense. Nevertheless, widespread real-world applications of biosensors remain challenging due to limitations of performance, including sensitivity, specificity, speed, and reproducibility. In this review, we present a DNA nanotechnology-enabled interfacial engineering approach for improving the performance of biosensors. We first introduce the main challenges of the biosensing interfaces, especially under the context of controlling the DNA interfacial assembly. We then summarize recent progress in DNA nanotechnology and efforts to harness DNA nanostructures to engineer various biological interfaces, with a particular focus on the use of framework nucleic acids. We also discuss the implementation of biosensors to detect physiologically relevant nucleic acids, proteins, small molecules, ions, and other biomarkers. This review highlights promising applications of DNA nanotechnology in interfacial engineering for biosensors and related areas.

Loading

Article metrics loading...

/content/journals/10.1146/annurev-anchem-061417-010007
2018-06-12
2024-05-18
Loading full text...

Full text loading...

/deliver/fulltext/11/1/annurev-anchem-061417-010007.html?itemId=/content/journals/10.1146/annurev-anchem-061417-010007&mimeType=html&fmt=ahah

Literature Cited

  1. 1.  Kelley SO 2017. Advancing ultrasensitive molecular and cellular analysis methods to speed and simplify the diagnosis of disease. Acc. Chem. Res. 50:503–7
    [Google Scholar]
  2. 2.  Labib M, Sargent EH, Kelley SO 2016. Electrochemical methods for the analysis of clinically relevant biomolecules. Chem. Rev. 116:9001–90
    [Google Scholar]
  3. 3.  Lin MH, Song P, Zhou GB, Zuo XL, Aldalbahi A et al. 2016. Electrochemical detection of nucleic acids, proteins, small molecules and cells using a DNA nanostructure-based universal biosensing platform. Nat. . Protoc 11:1244–63
    [Google Scholar]
  4. 4.  Kelley SO 2017. What are clinically relevant levels of cellular and biomolecular analytes?. ACS Sens 2:193–97
    [Google Scholar]
  5. 5.  Kelley SO, Mirkin CA, Walt DR, Ismagilov RF, Toner M, Sargent EH 2014. Advancing the speed, sensitivity and accuracy of biomolecular detection using multi-length-scale engineering. Nat. Nanotechnol. 9:969–80
    [Google Scholar]
  6. 6.  Fan CH, Plaxco KW, Heeger AJ 2003. Electrochemical interrogation of conformational changes as a reagentless method for the sequence-specific detection of DNA. PNAS 100:9134–37
    [Google Scholar]
  7. 7.  Sage AT, Besant JD, Lam B, Sargent EH, Kelley SO 2014. Ultrasensitive electrochemical biomolecular detection using nanostructured microelectrodes. Acc. Chem. Res. 47:2417–25
    [Google Scholar]
  8. 8.  Lu CH, Willner B, Willner I 2013. DNA nanotechnology: from sensing and DNA machines to drug-delivery systems. ACS Nano 7:8320–32
    [Google Scholar]
  9. 9.  Soleymani L, Fang ZC, Sargent EH, Kelley SO 2009. Programming the detection limits of biosensors through controlled nanostructuring. Nat. Nanotechnol. 4:844–48
    [Google Scholar]
  10. 10.  Levicky R, Horgan A 2005. Physicochemical perspectives on DNA microarray and biosensor technologies. Trends Biotechnol 23:143–49
    [Google Scholar]
  11. 11.  Lin MH, Wang JJ, Zhou GB, Wang JB, Wu N et al. 2015. Programmable engineering of a biosensing interface with tetrahedral DNA nanostructures for ultrasensitive DNA detection. Angew. Chem. Int. Ed. 54:2151–55
    [Google Scholar]
  12. 12.  Wang SP, Cai XQ, Wang LH, Li J, Li Q et al. 2016. DNA orientation-specific adhesion and patterning of living mammalian cells on self-assembled DNA monolayers. Chem. Sci. 7:2722–27
    [Google Scholar]
  13. 13.  Ke YG, Lindsay S, Chang Y, Liu Y, Yan H 2008. Self-assembled water-soluble nucleic acid probe tiles for label-free RNA hybridization assays. Science 319:180–83
    [Google Scholar]
  14. 14.  Kilchherr F, Wachauf C, Pelz B, Rief M, Zacharias M, Dietz H 2016. Single-molecule dissection of stacking forces in DNA. Science 353:aaf5508
    [Google Scholar]
  15. 15.  Veneziano R, Ratanalert S, Zhang KM, Zhang F, Yan H et al. 2016. Designer nanoscale DNA assemblies programmed from the top down. Science 352:aaf4388
    [Google Scholar]
  16. 16.  Chen YJ, Groves B, Muscat RA, Seelig G 2015. DNA nanotechnology from the test tube to the cell. Nat. Nanotechnol. 10:748–60
    [Google Scholar]
  17. 17.  Bell NA, Keyser UF 2016. Digitally encoded DNA nanostructures for multiplexed, single-molecule protein sensing with nanopores. Nat. Nanotechnol. 11:645–51
    [Google Scholar]
  18. 18.  Modi S, Nizak C, Surana S, Halder S, Krishnan Y 2013. Two DNA nanomachines map pH changes along intersecting endocytic pathways inside the same cell. Nat. Nanotechnol. 8:459–67
    [Google Scholar]
  19. 19.  Surana S, Shenoy AR, Krishnan Y 2015. Designing DNA nanodevices for compatibility with the immune system of higher organisms. Nat. Nanotechnol. 10:741–47
    [Google Scholar]
  20. 20.  Southern E, Mir K, Shchepinov M 1999. Molecular interactions on microarrays. Nat. Genet. 21:5–9
    [Google Scholar]
  21. 21.  De Luna P Mahshid SS, Das J, Luan BQ, Sargent EH et al. 2017. High-curvature nanostructuring enhances probe display for biomolecular detection. Nano Lett 17:1289–95
    [Google Scholar]
  22. 22.  Zhao Z, Fu JL, Dhakal S, Johnson-Buck A, Liu MH et al. 2016. Nanocaged enzymes with enhanced catalytic activity and increased stability against protease digestion. Nat. Commun. 7:10619
    [Google Scholar]
  23. 23.  Fu JL, Yang YR, Johnson-Buck A, Liu MH, Liu Y et al. 2014. Multi-enzyme complexes on DNA scaffolds capable of substrate channelling with an artificial swinging arm. Nat. Nanotechnol. 9:531–36
    [Google Scholar]
  24. 24.  Bracha D, Karzbrun E, Shemer G, Pincus PA, Bar-Ziv RH 2013. Entropy-driven collective interactions in DNA brushes on a biochip. PNAS 110:4534–38
    [Google Scholar]
  25. 25.  Gong P, Levicky R 2008. DNA surface hybridization regimes. PNAS 105:5301–6
    [Google Scholar]
  26. 26.  Opdahl A, Petrovykh DY, Kimura-Suda H, Tarlov MJ, Whitman LJ 2007. Independent control of grafting density and conformation of single-stranded DNA brushes. PNAS 104:9–14
    [Google Scholar]
  27. 27.  Hanssen BL, Siraj S, Wong DKY 2016. Recent strategies to minimise fouling in electrochemical detection systems. Rev. Anal. Chem. 35: https://doi.org/10.1515/revac-2015-0008
    [Crossref] [Google Scholar]
  28. 28.  Watkins HM, Simon AJ, Ricci F, Plaxco KW 2014. Effects of crowding on the stability of a surface-tethered biopolymer: an experimental study of folding in a highly crowded regime. J. Am. Chem. Soc. 136:8923–27
    [Google Scholar]
  29. 29.  Pei H, Zuo XL, Zhu D, Huang Q, Fan CH 2014. Functional DNA nanostructures for theranostic applications. Acc. Chem. Res. 47:550–59
    [Google Scholar]
  30. 30.  Belozerova I, Levicky R 2012. Melting thermodynamics of reversible DNA/ligand complexes at interfaces. J. Am. Chem. Soc. 134:18667–76
    [Google Scholar]
  31. 31.  Irving D, Gong P, Levicky R 2010. DNA surface hybridization: comparison of theory and experiment. J. Phys. Chem. B 114:7631–40
    [Google Scholar]
  32. 32.  Ge DB, Wang X, Williams K, Levicky R 2012. Thermostable DNA immobilization and temperature effects on surface hybridization. Langmuir 28:8446–55
    [Google Scholar]
  33. 33.  Bin XM, Sargent EH, Kelley SO 2010. Nanostructuring of sensors determines the efficiency of biomolecular capture. Anal. Chem. 82:5928–31
    [Google Scholar]
  34. 34.  Ye DK, Zuo XL, Fan CH 2017. DNA nanostructure-based engineering of the biosensing interface for biomolecular detection. Prog. Chem. 29:36–46
    [Google Scholar]
  35. 35.  Klebe G 2015. Applying thermodynamic profiling in lead finding and optimization. Nat. Rev. Drug Discov. 14:95–110
    [Google Scholar]
  36. 36.  Jones MR, Seeman NC, Mirkin CA 2015. Programmable materials and the nature of the DNA bond. Science 347:1260901
    [Google Scholar]
  37. 37.  Dong YC, Yang ZQ, Liu DS 2014. DNA nanotechnology based on i-motif structures. Acc. Chem. Res. 47:1853–60
    [Google Scholar]
  38. 38.  Tsukanov R, Tomov TE, Liber M, Berger Y, Nir E 2014. Developing DNA nanotechnology using single-molecule fluorescence. Acc. Chem. Res. 47:1789–98
    [Google Scholar]
  39. 39.  Chandrasekaran AR, Anderson N, Kizer M, Halvorsen K, Wang X 2016. Beyond the fold: emerging biological applications of DNA origami. ChemBioChem 17:1081–89
    [Google Scholar]
  40. 40.  Linko V, Dietz H 2013. The enabled state of DNA nanotechnology. Curr. Opin. Biotechnol. 24:555–61
    [Google Scholar]
  41. 41.  Zakeri B, Lu TK 2015. DNA nanotechnology: new adventures for an old warhorse. Curr. Opin. Chem. Biol. 28:9–14
    [Google Scholar]
  42. 42.  Chandrasekaran AR, Pushpanathan M, Halvorsen K 2016. Evolution of DNA origami scaffolds. Mater. Lett. 170:221–24
    [Google Scholar]
  43. 43.  Edwardson TGW, Lau KL, Bousmail D, Serpell CJ, Sleiman HF 2016. Transfer of molecular recognition information from DNA nanostructures to gold nanoparticles. Nat. Chem. 8:162–70
    [Google Scholar]
  44. 44.  Yang Y, Wang J, Shigematsu H, Xu WM, Shih WM et al. 2016. Self-assembly of size-controlled liposomes on DNA nanotemplates. Nat. Chem. 8:476–83
    [Google Scholar]
  45. 45.  Elbaz J, Cecconello A, Fan ZY, Govorov AO, Willner I 2013. Powering the programmed nanostructure and function of gold nanoparticles with catenated DNA machines. Nat. Commun. 4:2000
    [Google Scholar]
  46. 46.  Pan KY, Kim DN, Zhang F, Adendorff MR, Yan H, Bathe M 2014. Lattice-free prediction of three-dimensional structure of programmed DNA assemblies. Nat. Commun. 5:5578
    [Google Scholar]
  47. 47.  Zhang DY, Hariadi RF, Choi HMT, Winfree E 2013. Integrating DNA strand-displacement circuitry with DNA tile self-assembly. Nat. Commun. 4:1965
    [Google Scholar]
  48. 48.  Amir Y, Ben-Ishay E, Levner D, Ittah S, Abu-Horowitz A, Bachelet I 2014. Universal computing by DNA origami robots in a living animal. Nat. Nanotechnol. 9:353–57
    [Google Scholar]
  49. 49.  Cha TG, Pan J, Chen HR, Salgado J, Li X et al. 2014. A synthetic DNA motor that transports nanoparticles along carbon nanotubes. Nat. Nanotechnol. 9:39–43
    [Google Scholar]
  50. 50.  Funke JJ, Dietz H 2015. Placing molecules with Bohr radius resolution using DNA origami. Nat. Nanotechnol. 11:47–52
    [Google Scholar]
  51. 51.  Kim J, Lee J, Hamada S, Murata S, Park SH 2015. Self-replication of DNA rings. Nat. Nanotechnol. 10:528–33
    [Google Scholar]
  52. 52.  Lin CX, Yan H 2009. DNA nanotechnology a cascade of activity. Nat. Nanotechnol. 4:211–12
    [Google Scholar]
  53. 53.  Tian Y, Wang T, Liu WY, Xin HL, Li HL et al. 2015. Prescribed nanoparticle cluster architectures and low-dimensional arrays built using octahedral DNA origami frames. Nat. Nanotechnol. 10:637–44
    [Google Scholar]
  54. 54.  Udomprasert A, Bongiovanni MN, Sha RJ, Sherman WB, Wang T et al. 2014. Amyloid fibrils nucleated and organized by DNA origami constructions. Nat. Nanotechnol. 9:537–41
    [Google Scholar]
  55. 55.  Zhang F, Jiang SX, Wu SY, Li YL, Mao CD et al. 2015. Complex wireframe DNA origami nanostructures with multi-arm junction vertices. Nat. Nanotechnol. 10:779–84
    [Google Scholar]
  56. 56.  Benson E, Mohammed A, Gardell J, Masich S, Czeizler E et al. 2015. DNA rendering of polyhedral meshes at the nanoscale. Nature 523:441–45
    [Google Scholar]
  57. 57.  He Y, Ye T, Su M, Zhang C, Ribbe AE et al. 2008. Hierarchical self-assembly of DNA into symmetric supramolecular polyhedra. Nature 452:198–202
    [Google Scholar]
  58. 58.  Wei B, Dai MJ, Yin P 2012. Complex shapes self-assembled from single-stranded DNA tiles. Nature 485:623–26
    [Google Scholar]
  59. 59.  Iinuma R, Ke YG, Jungmann R, Schlichthaerle T, Woehrstein JB, Yin P 2014. Polyhedra self-assembled from DNA tripods and characterized with 3D DNA-PAINT. Science 344:65–69
    [Google Scholar]
  60. 60.  Rogers WB, Manoharan VN 2015. Programming colloidal phase transitions with DNA strand displacement. Science 347:639–42
    [Google Scholar]
  61. 61.  Song J, Li Z, Wang PF, Meyer T, Mao CD, Ke YG 2017. Reconfiguration of DNA molecular arrays driven by information relay. Science 357:aan3377
    [Google Scholar]
  62. 62.  Sun W, Boulais E, Hakobyan Y, Wang WL, Guan A et al. 2014. Casting inorganic structures with DNA molds. Science 346:1258361
    [Google Scholar]
  63. 63.  Chao J, Liu HJ, Su S, Wang LH, Huang W, Fan CH 2014. Structural DNA nanotechnology for intelligent drug delivery. Small 10:4626–35
    [Google Scholar]
  64. 64.  Zhang F, Nangreave J, Liu Y, Yan H 2014. Structural DNA nanotechnology: state of the art and future perspective. J. Am. Chem. Soc. 136:11198–211
    [Google Scholar]
  65. 65.  Lim XZ 2017. The architecture of structured DNA. Nature 546:687–89
    [Google Scholar]
  66. 66.  Qian L, Wang Y, Zhang Z, Zhao J, Pan D et al. 2006. Analogic China map constructed by DNA. Chinese Sci. Bull. 51:2973–76
    [Google Scholar]
  67. 67.  Zhang Z, Zeng DD, Ma HW, Feng GY, Hu J et al. 2010. A DNA-origami chip platform for label-free SNP genotyping using toehold-mediated strand displacement. Small 6:1854–58
    [Google Scholar]
  68. 68.  Marras AE, Zhou LF, Su HJ, Castro CE 2015. Programmable motion of DNA origami mechanisms. PNAS 112:713–18
    [Google Scholar]
  69. 69.  Wollman AJM, Sanchez-Cano C, Carstairs HMJ, Cross RA, Turberfield AJ 2014. Transport and self-organization across different length scales powered by motor proteins and programmed by DNA. Nat. Nanotechnol. 9:44–47
    [Google Scholar]
  70. 70.  Kuzyk A, Schreiber R, Zhang H, Govorov AO, Liedl T, Liu N 2014. Reconfigurable 3D plasmonic metamolecules. Nat. Mater. 13:862–66
    [Google Scholar]
  71. 71.  Elsner M 2013. Membrane channels built from DNA. Nat. Biotechnol. 31:125–25
    [Google Scholar]
  72. 72.  Burns JR, Seifert A, Fertig N, Howorka S 2016. A biomimetic DNA-based channel for the ligand-controlled transport of charged molecular cargo across a biological membrane. Nat. Nanotechnol. 11:152–56
    [Google Scholar]
  73. 73.  Hao CH, Li X, Tian C, Jiang W, Wang GS, Mao CD 2014. Construction of RNA nanocages by re-engineering the packaging RNA of Phi29 bacteriophage. Nat. Commun. 5:3890
    [Google Scholar]
  74. 74.  Geary C, Rothemund PWK, Andersen ES 2014. A single-stranded architecture for cotranscriptional folding of RNA nanostructures. Science 345:799–804
    [Google Scholar]
  75. 75.  Pei H, Lu N, Wen YL, Song SP, Liu Y et al. 2010. A DNA nanostructure-based biomolecular probe carrier platform for electrochemical biosensing. Adv. Mater. 22:4754–58
    [Google Scholar]
  76. 76.  Zhu D, Pei H, Yao GB, Wang LH, Su S et al. 2016. A surface-confined proton-driven DNA pump using a dynamic 3D DNA scaffold. Adv. Mater. 28:6860–65
    [Google Scholar]
  77. 77.  Vainrub A, Pettitt BM 2003. Sensitive quantitative nucleic acid detection using oligonucleotide microarrays. J. Am. Chem. Soc. 125:7798–99
    [Google Scholar]
  78. 78.  Hagan MF, Chakraborty AK 2004. Hybridization dynamics of surface immobilized DNA. J. Chem. Phys. 120:4958–68
    [Google Scholar]
  79. 79.  Herne TM, Tarlov MJ 1997. Characterization of DNA probes immobilized on gold surfaces. J. Am. Chem. Soc. 119:8916–20
    [Google Scholar]
  80. 80.  Levicky R, Herne TM, Tarlov MJ, Satija SK 1998. Using self-assembly to control the structure of DNA monolayers on gold: a neutron reflectivity study. J. Am. Chem. Soc. 120:9787–92
    [Google Scholar]
  81. 81.  Petrovykh DY, Kimura-Suda H, Whitman LJ, Tarlov MJ 2003. Quantitative analysis and characterization of DNA immobilized on gold. J. Am. Chem. Soc. 125:5219–26
    [Google Scholar]
  82. 82.  Petrovykh DY, Perez-Dieste V, Opdahl A, Kimura-Suda H, Sullivan JM et al. 2006. Nucleobase orientation and ordering in films of single-stranded DNA on gold. J. Am. Chem. Soc. 128:2–3
    [Google Scholar]
  83. 83.  Gillen G, Bennett J, Tarlov MJ, Burgess F 1994. Molecular imaging secondary-ion mass-spectrometry for the characterization of patterned self-assembled monolayers on silver and gold. Anal. Chem. 66:2170–74
    [Google Scholar]
  84. 84.  Arinaga K, Rant U, Tornow M, Fujita S, Abstreiter G, Yokoyama N 2006. The role of surface charging during the coadsorption of mercaptohexanol to DNA layers on gold: direct observation of desorption and layer reorientation. Langmuir 22:5560–62
    [Google Scholar]
  85. 85.  Park S, Brown KA, Hamad-Schifferli K 2004. Changes in oligonucleotide conformation on nanoparticle surfaces by modification with mercaptohexanol. Nano Lett 4:1925–29
    [Google Scholar]
  86. 86.  Henry OYF, Perez JG, Sanchez JLA, O'Sullivan CK 2010. Electrochemcial characterisation and hybridisation efficiency of co-assembled monolayers of PEGylated ssDNA and mercaptohexanol on planar gold electrodes. Biosens. Bioelectron. 25:978–83
    [Google Scholar]
  87. 87.  Zhang LL, Li ZG, Zhou XP, Yang GZ, Yang JM et al. 2015. Hybridization performance of DNA/mercaptohexanol mixed monolayers on electrodeposited nanoAu and rough Au surfaces. J. Electroanal. Chem. 757:203–9
    [Google Scholar]
  88. 88.  Zhang J, Song SP, Zhang LY, Wang LH, Wu HP et al. 2006. Sequence-specific detection of femtomolar DNA via a chronocoulometric DNA sensor (CDS): effects of nanoparticle-mediated amplification and nanoscale control of DNA assembly at electrodes. J. Am. Chem. Soc. 128:8575–80
    [Google Scholar]
  89. 89.  Asav E, Sagiroglu A, Sezginturk MK 2016. Quantitative analysis of a promising cancer biomarker, calretinin, by a biosensing system based on simple and effective immobilization process. Electroanalysis 28:334–42
    [Google Scholar]
  90. 90.  Zhang J, Lao RJ, Song SP, Yan ZY, Fan CH 2008. Design of an oligonucleotide-incorporated nonfouling surface and its application in electrochemical DNA sensors for highly sensitive and sequence-specific detection of target DNA. Anal. Chem. 80:9029–33
    [Google Scholar]
  91. 91.  Wu J, Campuzano S, Halford C, Haake DA, Wang J 2010. Ternary surface monolayers for ultrasensitive (zeptomole) amperometric detection of nucleic acid hybridization without signal amplification. Anal. Chem. 82:8830–37
    [Google Scholar]
  92. 92.  Li Y, Zhao M, Wang H 2017. Label-free peptide aptamer based impedimetric biosensor for highly sensitive detection of TNT with a ternary assembly layer. Anal. Bioanal. Chem. 409:6371–77
    [Google Scholar]
  93. 93.  Dharuman V, Vijayaraj K, Radhakrishnan S, Dinakaran T, Narayanan JS et al. 2011. Sensitive label-free electrochemical DNA hybridization detection in the presence of 11-mercaptoundecanoic acid on the thiolated single strand DNA and mercaptohexanol binary mixed monolayer surface. Electrochim. Acta 56:8147–55
    [Google Scholar]
  94. 94.  Kimura-Suda H, Petrovykh DY, Tarlov MJ, Whitman LJ 2003. Base-dependent competitive adsorption of single-stranded DNA on gold. J. Am. Chem. Soc. 125:9014–15
    [Google Scholar]
  95. 95.  Demers LM, Ostblom M, Zhang H, Jang NH, Liedberg B, Mirkin CA 2002. Thermal desorption behavior and binding properties of DNA bases and nucleosides on gold. J. Am. Chem. Soc. 124:11248–49
    [Google Scholar]
  96. 96.  Storhofff JJ, Elghanian R, Mirkin CA, Letsinger RL 2002. Sequence-dependent stability of DNA-modified gold nanoparticles. Langmuir 18:6666–70
    [Google Scholar]
  97. 97.  Schreiner SM, Shudy DF, Hatch AL, Opdahl A, Whitman LJ, Petrovykh DY 2010. Controlled and efficient hybridization achieved with DNA probes immobilized solely through preferential DNA-substrate interactions. Anal. Chem. 82:2803–10
    [Google Scholar]
  98. 98.  Liu P, Wang DD, Zhou YL, Wang HY, Yin HS, Ai SY 2016. DNA methyltransferase detection based on digestion triggering the combination of poly adenine DNA with gold nanoparticles. Biosens. Bioelectron. 80:74–78
    [Google Scholar]
  99. 99.  Pei H, Li F, Wan Y, Wei M, Liu HJ et al. 2012. Designed diblock oligonucleotide for the synthesis of spatially isolated and highly hybridizable functionalization of DNA-gold nanoparticle nanoconjugates. J. Am. Chem. Soc. 134:11876–79
    [Google Scholar]
  100. 100.  Zhu D, Song P, Shen JW, Su S, Chao J et al. 2016. PolyA-mediated DNA assembly on gold nanoparticles for thermodynamically favorable and rapid hybridization analysis. Anal. Chem. 88:4949–54
    [Google Scholar]
  101. 101.  Guo JX, Chen YL, Jiang YJ, Ju HX 2017. Polyadenine-modulated DNA conformation monitored by surface-enhanced Raman scattering (SERS) on multibranched gold nanoparticles and its sensing application. Chem. Eur. J. 23:9332–37
    [Google Scholar]
  102. 102.  Zhu D, Pei H, Chao J, Su S, Aldalbahi A et al. 2015. Poly-adenine-based programmable engineering of gold nanoparticles for highly regulated spherical DNAzymes. Nanoscale 7:18671–76
    [Google Scholar]
  103. 103.  Wen JL, Chen JH, Zhuang L, Zhou SG 2016. Designed diblock hairpin probes for the nonenzymatic and label-free detection of nucleic acid. Biosens. Bioelectron. 79:656–60
    [Google Scholar]
  104. 104.  Zhu D, Chao J, Pei H, Zuo XL, Huang Q et al. 2015. Coordination-mediated programmable assembly of unmodified oligonucleotides on plasmonic silver nanoparticles. ACS Appl. Mater. Interfaces 7:11047–52
    [Google Scholar]
  105. 105.  Lu C, Huang ZC, Liu BW, Liu YB, Ying YB, Liu JW 2017. Poly-cytosine DNA as a high-affinity ligand for inorganic nanomaterials. Angew. Chem. Int. Ed. 56:6208–12
    [Google Scholar]
  106. 106.  Fang ZC, Soleymani L, Pampalakis G, Yoshimoto M, Squire JA et al. 2009. Direct profiling of cancer biomarkers in tumor tissue using a multiplexed nanostructured microelectrode integrated circuit. ACS Nano 3:3207–13
    [Google Scholar]
  107. 107.  Soleymani L, Fang ZC, Lam B, Bin XM, Vasilyeva E et al. 2011. Hierarchical nanotextured microelectrodes overcome the molecular transport barrier to achieve rapid, direct bacterial detection. ACS Nano 5:3360–66
    [Google Scholar]
  108. 108.  Das J, Kelley SO 2011. Protein detection using arrayed microsensor chips: tuning sensor footprint to achieve ultrasensitive readout of CA-125 in serum and whole blood. Anal. Chem. 83:1167–72
    [Google Scholar]
  109. 109.  Das J, Kelley SO 2013. Tuning the bacterial detection sensitivity of nanostructured microelectrodes. Anal. Chem. 85:7333–38
    [Google Scholar]
  110. 110.  Ivanov I, Stojcic J, Stanimirovic A, Sargent E, Nam RK, Kelley SO 2013. Chip-based nanostructured sensors enable accurate identification and classification of circulating tumor cells in prostate cancer patient blood samples. Anal. Chem. 85:398–403
    [Google Scholar]
  111. 111.  Lam B, Fang ZC, Sargent EH, Kelley SO 2012. Polymerase chain reaction-free, sample-to-answer bacterial detection in 30 minutes with integrated cell lysis. Anal. Chem. 84:21–25
    [Google Scholar]
  112. 112.  Smith SJ, Nemr CR, Kelley SO 2017. Chemistry-driven approaches for ultrasensitive nucleic acid detection. J. Am. Chem. Soc. 139:1020–28
    [Google Scholar]
  113. 113.  Das J, Ivanov I, Montermini L, Rak J, Sargent EH, Kelley SO 2015. An electrochemical clamp assay for direct, rapid analysis of circulating nucleic acids in serum. Nat. Chem. 7:569–75
    [Google Scholar]
  114. 114.  Besant JD, Das J, Burgess IB, Liu WH, Sargent EH, Kelley SO 2015. Ultrasensitive visual read-out of nucleic acids using electrocatalytic fluid displacement. Nat. Commun. 6:6978
    [Google Scholar]
  115. 115.  Lam B, Das J, Holmes RD, Live L, Sage A et al. 2013. Solution-based circuits enable rapid and multiplexed pathogen detection. Nat. Commun. 4:2001
    [Google Scholar]
  116. 116.  Sage AT, Besant JD, Mahmoudian L, Poudineh M, Bai X et al. 2015. Fractal circuit sensors enable rapid quantification of biomarkers for donor lung assessment for transplantation. Sci. Adv. 1:e1500417
    [Google Scholar]
  117. 117.  Condon A 2006. Designed DNA molecules: principles and applications of molecular nanotechnology. Nat. Rev. Genet. 7:565–75
    [Google Scholar]
  118. 118.  Gopinath A, Rothemund PWK 2014. Optimized assembly and covalent coupling of single-molecule DNA origami nano arrays. ACS Nano 8:12030–40
    [Google Scholar]
  119. 119.  Acuna GP, Bucher M, Stein IH, Steinhauer C, Kuzyk A et al. 2012. Distance dependence of single-fluorophore quenching by gold nanoparticles studied on DNA origami. ACS Nano 6:3189–95
    [Google Scholar]
  120. 120.  Howorka S 2016. Changing of the guard. Science 352:890–91
    [Google Scholar]
  121. 121.  Shen WQ, Bruist MF, Goodman SD, Seeman NC 2004. A protein-driven DNA device that measures the excess binding energy of proteins that distort DNA. Angew. Chem. Int. Ed. 43:4750–52
    [Google Scholar]
  122. 122.  Tintore M, Gallego I, Manning B, Eritja R, Fabrega C 2013. DNA origami as a DNA repair nanosensor at the single-molecule level. Angew. Chem. Int. Ed. 52:7747–50
    [Google Scholar]
  123. 123.  Wang DF, Fu YM, Yan J, Zhao B, Dai B et al. 2014. Molecular logic gates on DNA origami nanostructures for microRNA diagnostics. Anal. Chem. 86:1932–36
    [Google Scholar]
  124. 124.  Chhabra R, Sharma J, Ke Y, Liu Y, Rinker S et al. 2007. Spatially addressable multiprotein nanoarrays templated by aptamer-tagged DNA nanoarchitectures. J. Am. Chem. Soc. 129:10304–5
    [Google Scholar]
  125. 125.  Numajiri K, Yamazaki T, Kimura M, Kuzuya A, Komiyama M 2010. Discrete and active enzyme nanoarrays on DNA origami scaffolds purified by affinity tag separation. J. Am. Chem. Soc. 132:9937–39
    [Google Scholar]
  126. 126.  Wilner OI, Weizmann Y, Gill R, Lioubashevski O, Freeman R, Willner I 2009. Enzyme cascades activated on topologically programmed DNA scaffolds. Nat. Nanotechnol. 4:249–54
    [Google Scholar]
  127. 127.  Fu YM, Zeng DD, Chao J, Jin YQ, Zhang Z et al. 2013. Single-step rapid assembly of DNA origami nanostructures for addressable nanoscale bioreactors. J. Am. Chem. Soc. 135:696–702
    [Google Scholar]
  128. 128.  Li YL, Liu ZY, Yu GM, Jiang W, Mao CD 2015. Self-assembly of molecule-like nanoparticle clusters directed by DNA nanocages. J. Am. Chem. Soc. 137:4320–23
    [Google Scholar]
  129. 129.  Pilo-Pais M, Watson A, Demers S, LaBean TH, Finkelstein G 2014. Surface-enhanced Raman scattering plasmonic enhancement using DNA origami-based complex metallic nanostructures. Nano Lett 14:2099–104
    [Google Scholar]
  130. 130.  Pal S, Deng ZT, Wang HN, Zou SL, Liu Y, Yan H 2011. DNA directed self-assembly of anisotropic plasmonic nanostructures. J. Am. Chem. Soc. 133:17606–9
    [Google Scholar]
  131. 131.  Subramanian HKK, Chakraborty B, Sha R, Seeman NC 2011. The label-free unambiguous detection and symbolic display of single nucleotide polymorphisms on DNA origami. Nano Lett 11:910–13
    [Google Scholar]
  132. 132.  Chen XQ, Zhou GB, Song P, Wang JJ, Gao JM et al. 2014. Ultrasensitive electrochemical detection of prostate-specific antigen by using antibodies anchored on a DNA nanostructural scaffold. Anal. Chem. 86:7337–42
    [Google Scholar]
  133. 133.  Wen YL, Pei H, Wan Y, Su Y, Huang Q et al. 2011. DNA nanostructure-decorated surfaces for enhanced aptamer-target binding and electrochemical cocaine sensors. Anal. Chem. 83:7418–23
    [Google Scholar]
  134. 134.  Liu G, Wan Y, Gau V, Zhang J, Wang LH et al. 2008. An enzyme-based E-DNA sensor for sequence-specific detection of femtomolar DNA targets. J. Am. Chem. Soc. 130:6820–25
    [Google Scholar]
  135. 135.  Wen YL, Pei H, Shen Y, Xi JJ, Lin MH et al. 2012. DNA nanostructure-based interfacial engineering for PCR-free ultrasensitive electrochemical analysis of microRNA. Sci. Rep. 2:867
    [Google Scholar]
  136. 136.  Xiao Y, Lou XH, Uzawa T, Plakos KJI, Plaxco KW, Soh HT 2009. An electrochemical sensor for single nucleotide polymorphism detection in serum based on a triple-stem DNA probe. J. Am. Chem. Soc. 131:15311–16
    [Google Scholar]
  137. 137.  Xiao Y, Qu XG, Plaxco KW, Heeger AJ 2007. Label-free electrochemical detection of DNA in blood serum via target-induced resolution of an electrode-bound DNA pseudoknot. J. Am. Chem. Soc. 129:11896–97
    [Google Scholar]
  138. 138.  Xiao Y, Lai RY, Plaxco KW 2007. Preparation of electrode-immobilized, redox-modified oligonucleotides for electrochemical DNA and aptamer-based sensing. Nat. Protoc. 2:2875–80
    [Google Scholar]
  139. 139.  Lai RY, Lagally ET, Lee SH, Soh HT, Plaxco KW, Heeger AJ 2006. Rapid, sequence-specific detection of unpurified PCR amplicons via a reusable, electrochemical sensor. PNAS 103:4017–21
    [Google Scholar]
  140. 140.  Xiao Y, Lubin AA, Baker BR, Plaxco KW, Heeger AJ 2006. Single-step electronic detection of femtomolar DNA by target-induced strand displacement in an electrode-bound duplex. PNAS 103:16677–80
    [Google Scholar]
  141. 141.  Lu N, Pei H, Ge ZL, Simmons CR, Yan H, Fan CH 2012. Charge transport within a three-dimensional DNA nanostructure framework. J. Am. Chem. Soc. 134:13148–51
    [Google Scholar]
  142. 142.  Ge ZL, Lin MH, Wang P, Pei H, Yan J et al. 2014. Hybridization chain reaction amplification of microRNA detection with a tetrahedral DNA nanostructure-based electrochemical biosensor. Anal. Chem. 86:2124–30
    [Google Scholar]
  143. 143.  Jiang DW, Sun YH, Li J, Li Q, Lv M et al. 2016. Multiple-armed tetrahedral DNA nanostructures for tumor-targeting, dual-modality in vivo imaging. ACS Appl. Mater. Interfaces 8:4378–84
    [Google Scholar]
  144. 144.  Liang L, Li J, Li Q, Huang Q, Shi JY et al. 2014. Single-particle tracking and modulation of cell entry pathways of a tetrahedral DNA nanostructure in live cells. Angew. Chem. Int. Ed. 53:7745–50
    [Google Scholar]
  145. 145.  Walsh AS, Yin HF, Erben CM, Wood MJA, Turberfield AJ 2011. DNA cage delivery to mammalian cells. ACS Nano 5:5427–32
    [Google Scholar]
  146. 146.  Pei H, Liang L, Yao GB, Li J, Huang Q, Fan CH 2012. Reconfigurable three-dimensional DNA nanostructures for the construction of intracellular logic sensors. Angew. Chem. Int. Ed. 51:9020–24
    [Google Scholar]
/content/journals/10.1146/annurev-anchem-061417-010007
Loading
/content/journals/10.1146/annurev-anchem-061417-010007
Loading

Data & Media loading...

  • Article Type: Review Article
This is a required field
Please enter a valid email address
Approval was a Success
Invalid data
An Error Occurred
Approval was partially successful, following selected items could not be processed due to error