Enzyme-Powered Three-Dimensional DNA Nanomachine for DNA Walking, Payload Release, and Biosensing

ACS Nano

Volumn 10, Issue 2, 2016, Pages 2324-2330

  Yang, Xiaolong ^a   Tang, Yanan ^a   Mason, Sean D ^a   Chen, Junbo ^b   Li, Feng ^a  

^a BROCK UNIVERSITY   (Canada)

^b SICHUAN UNIVERSITY   (China)

Author keywords

DNA nanotechnology; nanomachine; nanosensors; nicking endonuclease; nucleic acid analysis

Indexed keywords

DNA; NANOSENSORS; NANOTECHNOLOGY; NUCLEIC ACIDS;

DNA NANOTECHNOLOGY; DNA-FUNCTIONALIZED GOLD NANOPARTICLES; EFFECTIVE CONCENTRATION; NANOMACHINES; NICKING ENDONUCLEASE; NUCLEIC ACID ANALYSIS; SIGNAL AMPLIFICATIONS; THREEDIMENSIONAL (3-D);

DNA SEQUENCES;

DEOXYRIBONUCLEASE I; DNA; GOLD; METAL NANOPARTICLE;

CHEMISTRY; GENETIC PROCEDURES; MOTION; PROCEDURES;

BIOSENSING TECHNIQUES; DEOXYRIBONUCLEASE I; DNA; GOLD; METAL NANOPARTICLES; MOTION;

EID: 84960116235     PISSN: 19360851     EISSN: 1936086X     Source Type: Journal    
DOI: 10.1021/acsnano.5b07102     Document Type: Article

References (36)

1. Abendroth, J. M.; Bushuyev, O. S.; Weiss, P. S.; Barrett, C. J. Controlling Motion at the Nanoscale: Rise of the Molecular Machines ACS Nano 2015, 9, 7746-7768 10.1021/acsnano.5b03367
2. Bath, J.; Turberfield, A. J. DNA Nanomachines Nat. Nanotechnol. 2007, 2, 275-284 10.1038/nnano.2007.104
3. Zhang, D. Y.; Seelig, G. Dynamic DNA Nanotechnology Using Strand-Displacement Reactions Nat. Chem. 2011, 3, 103-113 10.1038/nchem.957
4. von Delius, M.; Leigh, D. A. Walking Molecules Chem. Soc. Rev. 2011, 40, 3656-3676 10.1039/c1cs15005g
5. Pan, J.; Li, F.; Cha, T.-G.; Chen, H.; Choi, J. H. Recent Progress on DNA Based Walkers Curr. Opin. Biotechnol. 2015, 34, 56-64 10.1016/j.copbio.2014.11.017
6. Sherman, W. B.; Seeman, N. C. A Precisely Controlled DNA Biped Walking Device Nano Lett. 2004, 4, 1203-1207 10.1021/nl049527q
7. Shin, J.-S.; Pierce, N. A. A Synthetic DNA Walker for Molecular Transport J. Am. Chem. Soc. 2004, 126, 10834-10835 10.1021/ja047543j
8. Omabegho, T.; Sha, R.; Seeman, N. C. A Bipedal DNA Brownian Motor with Coordinated Legs Science 2009, 324, 67-71 10.1126/science.1170336
9. Yin, P.; Yan, H.; Daniell, X. G.; Turberfield, A. J.; Reif, J. H. A Unidirectional DNA Walker That Moves Autonomously Along a Track Angew. Chem., Int. Ed. 2004, 43, 4906-4911 10.1002/anie.200460522
10. Bath, J.; Green, S. J.; Turberfield, A. J. A Free-Running DNA Motor Powered by a Nicking Enzyme Angew. Chem., Int. Ed. 2005, 44, 4358-4361 10.1002/anie.200501262
11. Cha, T.-G.; Pan, J.; Chen, H.; Salgado, J.; Li, X.; Mao, C.; Choi, J. H. A Synthetic DNA Motor That Transports Nanoparticles Along Carbon Nanotubes Nat. Nanotechnol. 2013, 9, 39-43 10.1038/nnano.2013.257
12. You, M.; Chen, Y.; Zhang, X.; Liu, H.; Wang, R.; Wang, K.; Williams, K. R.; Tan, W. An Autonomous and Controllable Light-Driven DNA Walking Device Angew. Chem., Int. Ed. 2012, 51, 2457-2460 10.1002/anie.201107733
13. Yang, Y.; Goetzfried, M. A.; Hidaka, K.; You, M.; Tan, W.; Sugiyama, H.; Endo, M. Direct Visualization of Walking Motions of Photocontrolled Nanomachine on the DNA Nanostructure Nano Lett. 2015, 15, 6672-6676 10.1021/acs.nanolett.5b02502
14. Wickham, S. F. J.; Endo, M.; Katsuda, Y.; Hidaka, K.; Bath, J.; Sugiyama, H.; Turberfield, A. J. Direct Observation of Stepwise Movement of a Synthetic Molecular Transporter Nat. Nanotechnol. 2011, 6, 166-169 10.1038/nnano.2010.284
15. 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. 2012, 7, 169-173 10.1038/nnano.2011.253
16. Zhou, C.; Duan, X.; Liu, N. A Plasmonic Nanorod That Walks on DNA Origami Nat. Commun. 2015, 6, 8102 10.1038/ncomms9102
17. Tian, Y.; Mao, C. Molecular Gears: A Pair of DNA Circles Continuously Rolls against Each Other J. Am. Chem. Soc. 2004, 126, 11410-11411 10.1021/ja046507h
18. 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. 2006, 128, 12693-12699 10.1021/ja058394n
19. 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 2010, 465, 206-209 10.1038/nature09012
20. Zhang, H.; Lai, M.; Zuehlke, A.; Peng, H.; Li, X.-F.; Le, X. C. Binding-Induced DNA Nanomachines Triggered by Proteins and Nucleic Acids Angew. Chem., Int. Ed. 2015, 54, 14326-14330 10.1002/anie.201506312
21. Jung, C.; Allen, P. B.; Ellington, A. D. A Stochastic DNA Walker That Traverses a Microparticle Surface Nat. Nanotechnol. 2015, 10.1038/nnano.2015.246
22. 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. 2012, 51, 9317-9320 10.1002/anie.201202677
23. Li, F.; Zhang, H.; Wang, Z.; Li, X.-F.; Le, X. C. Dynamic DNA Assemblies Mediated by Binding-Induced DNA Strand Displacement J. Am. Chem. Soc. 2013, 135, 2443-2446 10.1021/ja311990w
24. Li, F.; Lin, Y.; Le, X. C. Binding-Induced Formation of DNA Three-Way Junctions and Its Application in Real-Time Protein Detection and DNA Strand Displacement Anal. Chem. 2013, 85, 10835-10841 10.1021/ac402179a
25. 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. 2015, 6, 5729-5733 10.1039/C5SC01870F
26. Hinsch, B.; Kula, M. R. Physical and Kinetic Properties of the Site Specific Endonuclease Bam HI from Bacillus Amylolique-Faciens Nucleic Acids Res. 1980, 8, 623-633 10.1093/nar/8.3.623
27. Pingoud, A.; Jeltsch, A. Recognition and Cleavage of DNA by Type-II Restriction Endonuclease Eur. J. Biochem. 1997, 246, 1-22 10.1111/j.1432-1033.1997.t01-6-00001.x
28. Li, S.; Chen, N.; Zhang, Z.; Wang, Y. Endonuclease-Responsive Aptamer-Functionalized Hydrogel Coating for Sequential Catch and Release of Cancer Cells Biomaterials 2013, 34, 460-469 10.1016/j.biomaterials.2012.09.040
29. Hill, H. D.; Millstone, J. E.; Banholzer, M. J.; Mirkin, C. A. The Role Radius of Curvature Plays in Thiolated Oligonucleotide Loading on Gold Nanoparticles ACS Nano 2009, 3, 418-424 10.1021/nn800726e
30. Li, J. J.; Chu, Y.; Lee, B. Y.-H.; Xie, X. S. Enzymatic Signal Amplification of Molecular Beacons for Sensitive DNA Detection Nucleic Acids Res. 2008, 36, e36 10.1093/nar/gkn033
31. Zhang, D. Y.; Winfree, E. Control of DNA Strand Displacement Kinetics Using Tehold Exchange J. Am. Chem. Soc. 2009, 131, 17303-17314 10.1021/ja906987s
32. Zhang, D. Y.; Chen, S. X.; Yin, P. Optimizing the Specificity of Nucleic Acid Hybridization Nat. Chem. 2012, 4, 208-214 10.1038/nchem.1246
33. Zhang, H.; Li, F.; Dever, B.; Li, X.-F.; Le, X. C. DNA-Mediated Homogeneous Binding Assays for Nucleic Acids and Proteins Chem. Rev. 2013, 113, 2812-2841 10.1021/cr300340p
34. Li, F.; Zhang, H.; Dever, B.; Li, X.-F.; Le, X. C. Thermal Stability of DNA Functionalized Gold Nanoparticles Bioconjugate Chem. 2013, 24, 1790-1797 10.1021/bc300687z
35. Hurst, S. J.; Lytton-Jean, A. K.; Mirkin, C. A. Maximizing DNA Loading on a Range of Gold Nanoparticle Sizes Anal. Chem. 2006, 78, 8313-8318 10.1021/ac0613582
36. Demers, L. M.; Mirkin, C. A.; Mucic, R. C.; Reynolds, R. A.; Letsinger, R. L.; Elghanian, R.; Viswanadham, G. A Fluorescence-Based Method for Determining the Surface Coverage and Hybridization Efficiency of Thiol-Capped Oligonucleotides Bound to Gold Thin Films and Nanoparticles Anal. Chem. 2000, 72, 5535-5541 10.1021/ac0006627