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Aptamers as Functional Modules for DNA Nanostructures

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DNA and RNA Origami

Part of the book series: Methods in Molecular Biology ((MIMB,volume 2639))

Abstract

Watson-Crick base-pairing of DNA allows the nanoscale fabrication of biocompatible synthetic nanostructures for diagnostic and therapeutic biomedical purposes. DNA nanostructure design elicits exquisite control of shape and conformation compared to other nanoparticles. Furthermore, nucleic acid aptamers can be coupled to DNA nanostructures to allow interaction and response to a plethora of biomolecules beyond nucleic acids. When compared to the better-known approach of using protein antibodies for molecular recognition, nucleic acid aptamers are bespoke with the underlying DNA nanostructure backbone and have various other stability, synthesis, and cost advantages. Here, we provide detailed methodologies to synthesize and characterize aptamer-enabled DNA nanostructures. The methods described can be generally applied to various designs of aptamer-enabled DNA nanostructures with a wide range of applications both within and beyond biomedical nanotechnology.

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References

  1. Seeman NC (1982) Nucleic acid junctions and lattices. J Theor Biol 99(2):237–247

    Article  CAS  PubMed  Google Scholar 

  2. Kallenbach NR, Ma R-I, Seeman NC (1983) An immobile nucleic acid junction constructed from oligonucleotides. Nature 305(5937):829–831

    Article  CAS  Google Scholar 

  3. Seeman NC (2003) DNA in a material world. Nature 421(6921):427–431

    Article  PubMed  Google Scholar 

  4. Ellington AD, Szostak JW (1990) In vitro selection of RNA molecules that bind specific ligands. Nature 346(6287):818–822

    Article  CAS  PubMed  Google Scholar 

  5. Tuerk C, Gold L (1990) Systematic evolution of ligands by exponential enrichment: RNA ligands to bacteriophage T4 DNA polymerase. Science 249(4968):505

    Article  CAS  PubMed  Google Scholar 

  6. Cheung YW, Kwok J, Law AW, Watt RM, Kotaka M, Tanner JA (2013) Structural basis for discriminatory recognition of Plasmodium lactate dehydrogenase by a DNA aptamer. Proc Natl Acad Sci U S A 110(40):15967–15972

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  7. Shiu SC-C, Cheung Y-W, Dirkzwager RM, Liang S, Kinghorn AB, Fraser LA, Tang MSL, Tanner JA (2017) Aptamer-mediated protein molecular recognition driving a DNA tweezer nanomachine. Adv Biosyst 1(1–2):1600006

    Article  Google Scholar 

  8. Tang MSL, Shiu SC-C, Godonoga M, Cheung Y-W, Liang S, Dirkzwager RM, Kinghorn AB, Fraser LA, Heddle JG, Tanner JA (2018) An aptamer-enabled DNA nanobox for protein sensing. Nanomed Nanotechnol 14(4):1161–1168

    Article  CAS  Google Scholar 

  9. Shiu CS, Fraser AL, Ding Y, Tanner AJ (2018) Aptamer display on diverse DNA polyhedron supports. Molecules 23(7)

    Google Scholar 

  10. Fraser AL, Kinghorn BA, Tang SLM, Cheung Y-W, Lim B, Liang S, Dirkzwager MR, Tanner AJ (2015) Oligonucleotide functionalised microbeads: indispensable tools for high-throughput aptamer selection. Molecules 20(12)

    Google Scholar 

  11. Li Y, Lee J-S (2019) Recent developments in affinity-based selection of aptamers for binding disease-related protein targets. Chem Pap 73(11):2637–2653

    Article  CAS  Google Scholar 

  12. Chao Y, Shum HC (2020) Emerging aqueous two-phase systems: from fundamentals of interfaces to biomedical applications. Chem Soc Rev 49:114

    Article  CAS  PubMed  Google Scholar 

  13. Tawfik DS, Griffiths AD (1998) Man-made cell-like compartments for molecular evolution. Nat Biotechnol 16(7):652–656

    Article  CAS  PubMed  Google Scholar 

  14. Ryckelynck M, Baudrey S, Rick C, Marin A, Coldren F, Westhof E, Griffiths AD (2015) Using droplet-based microfluidics to improve the catalytic properties of RNA under multiple-turnover conditions. RNA 21(3):458–469

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  15. Teh S-Y, Lin R, Hung L-H, Lee AP (2008) Droplet microfluidics. Lab Chip 8(2):198–220

    Article  CAS  PubMed  Google Scholar 

  16. Lyu K, Chen S-B, Chan C-Y, Tan J-H, Kwok CK (2019) Structural analysis and cellular visualization of APP RNA G-quadruplex. Chem Sci 10(48):11095–11102

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  17. del Villar-Guerra R, Trent JO, Chaires JB (2018) G-quadruplex secondary structure obtained from circular dichroism spectroscopy. Angew Chem Int Edit 57(24):7171–7175

    Article  Google Scholar 

  18. Pollard TD (2010) A guide to simple and informative binding assays. Mol Biol Cell 21(23):4061–4067

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  19. Siu RHP, Chan KHY, Ridzewski C, Slaugther LS, Wu AR (2019) Single particle analysis of on-bead emulsion polymerase chain reaction (Submitted)

    Google Scholar 

  20. Wang J, Gong Q, Maheshwari N, Eisenstein M, Arcila ML, Kosik KS, Soh HT (2014) Particle display: a quantitative screening method for generating high-affinity aptamers. Angew Chem Int Edit 53(19):4796–4801

    Article  CAS  Google Scholar 

  21. Dirkzwager RM, Kinghorn AB, Richards JS, Tanner JA (2015) APTEC: aptamer-tethered enzyme capture as a novel rapid diagnostic test for malaria. Chem Commun 51(22):4697–4700

    Article  CAS  Google Scholar 

  22. Fraser LA, Kinghorn AB, Dirkzwager RM, Liang S, Cheung Y-W, Lim B, Shiu SC-C, Tang MSL, Andrew D, Manitta J, Richards JS, Tanner JA (2018) A portable microfluidic Aptamer-Tethered Enzyme Capture (APTEC) biosensor for malaria diagnosis. Biosens Bioelectron 100:591–596

    Article  CAS  PubMed  Google Scholar 

  23. Rothemund PW (2006) Folding DNA to create nanoscale shapes and patterns. Nature 440(7082):297–302

    Article  CAS  PubMed  Google Scholar 

  24. Douglas SM, Bachelet I, Church GM (2012) A logic-gated nanorobot for targeted transport of molecular payloads. Science 335(6070):831

    Article  CAS  PubMed  Google Scholar 

  25. Saccà B, Meyer R, Feldkamp U, Schroeder H, Niemeyer CM (2008) High-throughput, real-time monitoring of the self-assembly of DNA nanostructures by FRET spectroscopy. Angew Chem Int Edit 47(11):2135–2137

    Article  Google Scholar 

  26. Tse ECM, Zwang TJ, Bedoya S, Barton JK (2019) Effective distance for DNA-mediated charge transport between repair proteins. ACS Central Sci 5(1):65–72

    Article  CAS  Google Scholar 

  27. Tang MY, Shum HC (2016) One-step immunoassay of C-reactive protein using droplet microfluidics. Lab Chip 16(22):4359–4365

    Article  CAS  PubMed  Google Scholar 

  28. Ji D, Wang H, Ge J, Zhang L, Li J, Bai D, Chen J, Li Z (2017) Label-free and rapid detection of ATP based on structure switching of aptamers. Anal Biochem 526:22–28

    Article  CAS  PubMed  Google Scholar 

  29. Wang J, Yu J, Yang Q, McDermott J, Scott A, Vukovich M, Lagrois R, Gong Q, Greenleaf W, Eisenstein M, Ferguson BS, Soh HT (2017) Multiparameter particle display (MPPD): a quantitative screening method for the discovery of highly specific aptamers. Angew Chem Int Edit 56(3):744–747

    Article  CAS  Google Scholar 

  30. Tse ECM, Zwang TJ, Barton JK (2017) The oxidation state of [4Fe4S] clusters modulates the DNA-binding affinity of DNA repair proteins. J Am Chem Soc 139(36):12784–12792

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  31. Kielar C, Xin Y, Xu X, Zhu S, Gorin N, Grundmeier G, Möser C, Smith DM, Keller A (2019) Effect of staple age on DNA origami nanostructure assembly and stability. Molecules 24(14):2577

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  32. Li L, Tian X, Dong Z, Liu L, Tabata O, Li WJ (2013) Manipulation of DNA origami nanotubes in liquid using programmable tappingmode atomic force microscopy. Micro Nano Lett 8(10):641–645

    Article  CAS  Google Scholar 

  33. Andersen ES, Dong M, Nielsen MM, Jahn K, Subramani R, Mamdouh W, Golas MM, Sander B, Stark H, Oliveira CL, Pedersen JS, Birkedal V, Besenbacher F, Gothelf KV, Kjems J (2009) Self-assembly of a nanoscale DNA box with a controllable lid. Nature 459(7243):73–76

    Article  CAS  PubMed  Google Scholar 

  34. Wagenbauer KF, Engelhardt FAS, Stahl E, Hechtl VK, Stommer P, Seebacher F, Meregalli L, Ketterer P, Gerling T, Dietz H (2017) How we make DNA origami. Chembiochem 18(19):1873–1885

    Article  CAS  PubMed  Google Scholar 

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Acknowledgments

J.A.T. acknowledges funding provided by the Hong Kong University Grants Council General Research Fund Grants (17127515, 17163416 and 17102318). L.S.S. acknowledges Professors Angela R. Wu and H. Tom Soh, Dr. Jianpeng Wang, and Kaitlin H.Y. Chan for their support and assistance. L.S.S. is funded by the Hong Kong Innovation and Technology Commission (ITS/350/16) and a Junior Fellowship from the Hong Kong Jockey Club Institute for Advanced Study at the Hong Kong University of Science and Technology. C.K.K. acknowledges support from Shenzhen Basic Research Project [JCYJ20180507181642811]; Research Grants Council of the Hong Kong SAR, China Projects [CityU 11100421, CityU 11101519, CityU 11100218, N_CityU110/17, CityU 21302317]; Croucher Foundation Project [9500030, 9509003]; the State Key Laboratory of Marine Pollution Director Discretionary Fund; and City University of Hong Kong projects [6000711, 7005503, 9667222, 9680261]. E.C.M.T. acknowledges the Croucher Foundation, the HK RGC (HKU JLFS/P-704/18; E-HKU704/19; ECS 27301120), the EU (Horizon 2020: SABYDOMA – 862296), the PRC NSFC (22002132), and the HK ITC (Health@InnoHK Program: Laboratory for Synthetic Chemistry and Chemical Biology).

Author information

Authors and Affiliations

  1. School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong SAR, China

    Simon Chi-Chin Shiu, Andrew B. Kinghorn, Lin Wang, Ngoc Chau Tran & Julian A. Tanner

  2. Microfluidics and Soft Matter Group, Department of Mechanical Engineering, Faculty of Engineering, The University of Hong Kong, Pokfulam, Hong Kong SAR, China

    Wei Guo & Anderson Ho Cheung Shum

  3. Division of Life Science, Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong SAR, China

    Liane S. Slaughter

  4. Department of Chemistry and State Key Laboratory of Marine Pollution, City University of Hong Kong, Kowloon Tong, Hong Kong SAR, China

    Danyang Ji & Chun Kit Kwok

  5. Shenzhen Research Institute of City University of Hong Kong, Shenzhen, China

    Danyang Ji & Chun Kit Kwok

  6. Department of Chemistry, CAS-HKU Joint Laboratory of Metallomics on Health and Environment, The University of Hong Kong, Pokfulam, Hong Kong SAR, China

    Xiaoyong Mo & Edmund Chun Ming Tse

  7. HKU Zhejiang Institute of Research and Innovation, Zhejiang, China

    Edmund Chun Ming Tse

Authors
  1. Simon Chi-Chin Shiu
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  2. Andrew B. Kinghorn
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  3. Wei Guo
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  4. Liane S. Slaughter
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  5. Danyang Ji
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  6. Xiaoyong Mo
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  7. Lin Wang
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  8. Ngoc Chau Tran
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  9. Chun Kit Kwok
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  10. Anderson Ho Cheung Shum
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  11. Edmund Chun Ming Tse
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  12. Julian A. Tanner
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Corresponding author

Correspondence to Julian A. Tanner .

Editor information

Editors and Affiliations

  1. Aarhus university, Interdisciplinary Nanoscience Center (iNANO) and Department of Molecular Biology and Genetics, Aarhus, Denmark

    Julián Valero

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Shiu, S.CC. et al. (2023). Aptamers as Functional Modules for DNA Nanostructures. In: Valero, J. (eds) DNA and RNA Origami. Methods in Molecular Biology, vol 2639. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-3028-0_17

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  • DOI: https://doi.org/10.1007/978-1-0716-3028-0_17

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  • Publisher Name: Humana, New York, NY

  • Print ISBN: 978-1-0716-3027-3

  • Online ISBN: 978-1-0716-3028-0

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