Over the past 30 years DNA has been assembled into a plethora of structures by design, based on its reliable base pairing properties. As a result, many applications of DNA nanotechnology are emerging. Here, we review recent advances in the use of self-assembled DNA nanostructures as sensors. In particular, we focus on how defined nanostructures, such as rigid DNA tetrahedra, provide an advantage over traditional nanosensors consisting of arrays of single-stranded DNA. We also explore advances in DNA origami that have resulted in consistent detection of single molecules.
Karina M. M. Carneiro,
Andrea A. Greschner,
Recent Advances in Self-Assembled DNA Nanosensors, American Journal of Nano Research and Applications. Special Issue: Nanomaterials and Nanosensors for Chemical and Biological Detection.
Vol. 3, No. 1-1,
2015, pp. 1-7.
K.M. Carneiro, N. Avakyan, H.F. Sleiman, "Long-range assembly of DNA into nanofibers and highly ordered networks", Wiley interdisciplinary reviews. Nanomedicine and nanobiotechnology, 2013, pp.
J. Liu, Z. Cao, Y. Lu, "Functional nucleic acid sensors", Chemical Reviews, 109, 2009, pp. 1948-1998.
K. Wang, Z. Tang, C.J. Yang, Y. Kim, X. Fang, W. Li, Y. Wu, C.D. Medley, Z. Cao, J. Li, P. Colon, H. Lin, W. Tan, "Molecular engineering of DNA: Molecular beacons", Angewandte Chemie International Edition, 48, 2009, pp. 856-870.
C. Tuerk, L. Gold, "Systematic evolution of ligands by exponential enrichment: Rna ligands to bacteriophage t4 DNA polymerase", Science, 249, 1990, pp. 505-510.
S.D. Jayasena, "Aptamers: An emerging class of molecules that rival antibodies in diagnostics", Clinical Chemistry, 45, 1999, pp. 1628-1650.
K. Robison, A.M. McGuire, G.M. Church, "A comprehensive library of DNA-binding site matrices for 55 proteins applied to the complete escherichia coli k-12 genome", Journal of Molecular Biology, 284, 1998, pp. 241-254.
S. Tyagi, F.R. Kramer, "Molecular beacons: Probes that fluoresce upon hybridization", Nat Biotech, 14, 1996, pp. 303-308.
R.P. Goodman, R.M. Berry, A.J. Turberfield, "The single-step synthesis of a DNA tetrahedron", Chemical Communications, 2004, pp. 1372-1373.
J.-W. Keum, H. Bermudez, "Enhanced resistance of dnananostructures to enzymatic digestion", Chemical Communications, 2009, pp. 7036-7038.
N. Mitchell, R. Schlapak, M. Kastner, D. Armitage, W. Chrzanowski, J. Riener, P. Hinterdorfer, A. Ebner, S. Howorka, "A DNA nanostructure for the functional assembly of chemical groups with tunable stoichiometry and defined nanoscale geometry", Angewandte Chemie International Edition, 48, 2009, pp. 525-527.
M. Leitner, N. Mitchell, M. Kastner, R. Schlapak, H.J. Gruber, P. Hinterdorfer, S. Howorka, A. Ebner, "Single-molecule afm characterization of individual chemically tagged DNA tetrahedra", ACS Nano, 5, 2011, pp. 7048-7054.
D.Y. Petrovykh, V. Pérez-Dieste, A. Opdahl, H. Kimura-Suda, J.M. Sullivan, M.J. Tarlov, F.J. Himpsel, L.J. Whitman, "Nucleobase orientation and ordering in films of single-stranded DNA on gold", Journal of the American Chemical Society, 128, 2005, pp. 2-3.
H. Pei, X. Zuo, D. Pan, J. Shi, Q. Huang, C. Fan, "Scaffolded biosensors with designed DNA nanostructures", NPG Asia Mater, 5, 2013, pp. e51.
H. Pei, N. Lu, Y. Wen, S. Song, Y. Liu, H. Yan, C. Fan, "A DNA nanostructure-based biomolecular probe carrier platform for electrochemical biosensing", Advanced Materials, 22, 2010, pp. 4754-4758.
H. Pei, L. Liang, G. Yao, J. Li, Q. Huang, C. Fan, "Reconfigurable three-dimensional DNA nanostructures for the construction of intracellular logic sensors", Angewandte Chemie International Edition, 51, 2012, pp. 9020-9024.
A. Abi, M. Lin, H. Pei, C. Fan, E.E. Ferapontova, X. Zuo, "Electrochemical switching with 3d DNA tetrahedral nanostructures self-assembled at gold electrodes", ACS Applied Materials & Interfaces, 6, 2014, pp. 8928-8931.
L. Yuan, M. Giovanni, J. Xie, C. Fan, D.T. Leong, "Ultrasensitive igg quantification using DNA nano-pyramids", NPG Asia Mater, 6, 2014, pp. e112.
X. Chen, G. Zhou, P. Song, J. Wang, J. Gao, J. Lu, C. Fan, X. Zuo, "Ultrasensitive electrochemical detection of prostate-specific antigen by using antibodies anchored on a DNA nanostructural scaffold", Analytical Chemistry, 86, 2014, pp. 7337-7342.
Z. Li, B. Zhao, D. Wang, Y. Wen, G. Liu, H. Dong, S. Song, C. Fan, "DNA nanostructure-based universal microarray platform for high-efficiency multiplex bioanalysis in biofluids", ACS Applied Materials & Interfaces, 6, 2014, pp. 17944-17953.
M. Zhang, B.-C. Ye, "Label-free fluorescent detection of copper (ii) using DNA-templated highly luminescent silver nanoclusters", Analyst, 136, 2011, pp. 5139-5142.
M. Zhang, S.-M. Guo, Y.-R. Li, P. Zuo, B.-C. Ye, "A label-free fluorescent molecular beacon based on DNA-templated silver nanoclusters for detection of adenosine and adenosine deaminase", Chemical Communications, 48, 2012, pp. 5488-5490.
T. Do, F. Ho, B. Heidecker, K. Witte, L. Chang, L. Lerner, "A rapid method for determining dynamic binding capacity of resins for the purification of proteins", Protein Expression and Purification, 60, 2008, pp. 147-150.
M. Zhang, X.-Q. Jiang, H.-N. Le, P. Wang, B.-C. Ye, "Dip-and-read method for label-free renewable sensing enhanced using complex DNA structures", ACS Applied Materials & Interfaces, 5, 2013, pp. 473-478.
P.W.K. Rothemund, "Folding DNA to create nanoscale shapes and patterns", Nature, 440, 2006, pp. 297-302.
E.S. Andersen, M. Dong, M.M. Nielsen, K. Jahn, A. Lind-Thomsen, W. Mamdouh, K.V. Gothelf, F. Besenbacher, J. Kjems, "DNA origami design of dolphin-shaped structures with flexible tails", ACS nano, 2, 2008, pp. 1213-1218.
E.S. Andersen, M. Dong, M.M. Nielsen, K. Jahn, R. Subramani, W. Mamdouh, M.M. Golas, B. Sander, H. Stark, C.L.P. Oliveira, J.S. Pedersen, V. Birkedal, F. Besenbacher, K.V. Gothelf, J. Kjems, "Self-assembly of a nanoscale DNA box with a controllable lid", Nature, 459, 2009, pp. 73-U75.
Y. Ke, S. Lindsay, Y. Chang, Y. Liu, H. Yan, "Self-assembled water-soluble nucleic acid probe tiles for label-free rna hybridization assays", Science, 319, 2008, pp. 180-183.
Z. Zhang, Y. Wang, C. Fan, C. Li, Y. Li, L. Qian, Y. Fu, Y. Shi, J. Hu, L. He, "Asymmetric DNA origami for spatially addressable and index-free solution-phase DNA chips", Advanced Materials, 22, 2010, pp. 2672-2675.
Z. Zhang, D. Zeng, H. Ma, G. Feng, J. Hu, L. He, C. Li, C. Fan, "A DNA-origami chip platform for label-free snp genotyping using toehold-mediated strand displacement", Small, 6, 2010, pp. 1854-1858.
H.K.K. Subramanian, B. Chakraborty, R. Sha, N.C. Seeman, "The label-free unambiguous detection and symbolic display of single nucleotide polymorphisms on DNA origami", Nano Letters, 11, 2011, pp. 910-913.
A. Kuzuya, Y. Sakai, T. Yamazaki, Y. Xu, M. Komiyama, "Nanomechanical DNA origami 'single-molecule beacons' directly imaged by atomic force microscopy", Nat Commun, 2, 2011, pp. 449.
A. Kuzuya, R. Watanabe, Y. Yamanaka, T. Tamaki, M. Kaino, Y. Ohya, "Nanomechanical DNA origami ph sensors", Sensors, 14, 2014, pp. 19329-19335.