Coupling 2-Aminopurine with DNA Copper Nanoparticles as a Rapid and Enzyme-Free System for Operating DNA Contrary Logic Pairs
Abstract
1. Introduction
2. Discussion and Results
2.1. Experimental Section
2.1.1. Materials and Reagents
2.1.2. Synthesis of CuNPs and Characterization
2.1.3. Apparatus
2.1.4. Native Polyacrylamide Gel Electrophoresis (PAGE)
2.1.5. Operation of YES/NOT Gate
2.1.6. Operation of OR/NOR Gate
2.1.7. Ratiometric Fluorescent Detection of A25
2.2. Mechanism and Verification Experiments
2.2.1. Construction of YES/NOT Logic Pair
2.2.2. Operation of OR/NOR Logic Pair
2.2.3. Ratiometric Fluorescent Detection of Poly-A Strand
3. Conclusions
Supplementary Materials
Author Contributions
Funding
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
- De Silva, A.P.; Gunaratne, H.Q.N.; McCoy, C.P. A molecular photoionic and gate based on fluorescent signaling. Nature 1993, 364, 42–44. [Google Scholar] [CrossRef]
- Feng, C.; Chen, T.S.; Mao, D.S.; Zhang, F.; Tian, B.; Zhu, X.L. Construction of a Ternary Complex Based DNA Logic Nanomachine for a Highly Accurate Imaging Analysis of Cancer Cells. ACS Sens. 2020, 5, 3116–3123. [Google Scholar] [CrossRef] [PubMed]
- Merkx, M.; Janssen, B.; van Rosmalen, M.; van Beek, L. Antibody Activation using DNA-Based Logic Gates. Protein Sci. 2015, 24, 35. [Google Scholar]
- Shin, T.H.; Choi, J.S.; Yun, S.; Kim, I.S.; Song, H.T.; Kim, Y.; Park, K.I.; Cheon, J. T-1 and T-2 Dual-Mode MRI Contrast Agent for Enhancing Accuracy by Engineered Nanomaterials. ACS Nano 2014, 8, 3393–3401. [Google Scholar] [CrossRef]
- Strack, G.; Ornatska, M.; Pita, M.; Katz, E. Biocomputing security system: Concatenated enzyme-based logic gates operating as a biomolecular keypad lock. J. Am. Chem. Soc. 2008, 130, 4234. [Google Scholar] [CrossRef]
- Mailloux, S.; Gerasimova, Y.V.; Guz, N.; Kolpashchikov, D.M.; Katz, E. Bridging the Two Worlds: A Universal Interface between Enzymatic and DNA Computing Systems. Angew. Chem. Int. Edit. 2015, 54, 6562–6566. [Google Scholar] [CrossRef]
- Prokup, A.; Deiters, A. Interfacing Synthetic DNA Logic Operations with Protein Outputs. Angew. Chem. Int. Edit. 2014, 53, 13192–13195. [Google Scholar] [CrossRef] [PubMed]
- Fan, D.Q.; Wang, J.; Wang, E.K.; Dong, S.J. Propelling DNA Computing with Materials’ Power: Recent Advancements in Innovative DNA Logic Computing Systems and Smart Bio-Applications. Adv. Sci. 2020, 7, 25. [Google Scholar] [CrossRef]
- Jiao, K.; Au, B.; Guo, L.J.; Zhou, H.B.; Wang, F.; Zhang, X.L.; Shi, J.Y.; Li, Q.; Wang, L.H.; Li, J.; et al. Programming Switchable Transcription of Topologically Constrained DNA. J. Am. Chem. Soc. 2020, 142, 10739–10746. [Google Scholar] [CrossRef]
- Prokup, A.; Hemphill, J.; Deiters, A. DNA Computation: A Photochemically Controlled AND Gate. J. Am. Chem. Soc. 2012, 134, 3810–3815. [Google Scholar] [CrossRef]
- Wilkins, M.H.F.; Stokes, A.R.; Wilson, H.R. Molecular structure of deoxypentose nucleic acids. Nature 1953, 171, 738–740. [Google Scholar] [CrossRef] [PubMed]
- Zhang, C.; Ma, X.Y.; Zheng, X.D.; Ke, Y.G.; Chen, K.T.; Liu, D.S.; Lu, Z.H.; Yang, J.; Yan, H. Programmable allosteric DNA regulations for molecular networks and nanomachines. Sci. Adv. 2022, 8, eabl4589. [Google Scholar] [CrossRef] [PubMed]
- Zhao, J.M.; Chandrasekaran, A.R.; Li, Q.; Li, X.; Sha, R.J.; Seeman, N.C.; Mao, C.D. Post-Assembly Stabilization of Rationally Designed DNA Crystals. Angew. Chem. Int. Edit. 2015, 54, 9936–9939. [Google Scholar] [CrossRef] [PubMed]
- Goodman, R.P.; Schaap, I.A.T.; Tardin, C.F.; Erben, C.M.; Berry, R.M.; Schmidt, C.F.; Turberfield, A.J. Rapid chiral assembly of rigid DNA building blocks for molecular nanofabrication. Science 2005, 310, 1661–1665. [Google Scholar] [CrossRef]
- Hu, Y.; Niemeyer, C.M. From DNA Nanotechnology to Material Systems Engineering. Adv. Mater. 2019, 31, 1806294. [Google Scholar] [CrossRef]
- Li, Q.; Zhao, J.M.; Liu, L.F.; Jonchhe, S.; Rizzuto, F.J.; Mandal, S.; He, H.W.; Wei, S.S.; Sleiman, H.F.; Mao, H.B.; et al. A poly(thymine)-melamine duplex for the assembly of DNA nanomaterials. Nat. Mater. 2020, 19, 1012. [Google Scholar] [CrossRef]
- Pashuck, E.T.; Seeman, N.; Macfarlane, R. Self-assembly of bioinspired and biologically functional materials. MRS Bull. 2020, 45, 832–840. [Google Scholar] [CrossRef]
- Shen, H.J.; Wang, Y.Q.; Wang, J.; Li, Z.H.; Yuan, Q. Emerging Biomimetic Applications of DNA Nanotechnology. ACS Appl. Mater. Interfaces 2019, 11, 13859–13873. [Google Scholar] [CrossRef]
- Zhou, Z.X.; Fan, D.Q.; Winner, I. Modeling Gene Expression Instability by Programmed and Switchable Polymerization/Nicking DNA Nanomachineries. ACS Nano 2020, 14, 5046–5052. [Google Scholar] [CrossRef]
- Du, Y.; Peng, P.; Li, T. DNA Logic Operations in Living Cells Utilizing Lysosome-Recognizing Framework Nucleic Acid Nanodevices for Subcellular Imaging. ACS Nano 2019, 13, 5778–5784. [Google Scholar] [CrossRef]
- Fan, D.Q.; Shang, C.S.; Gu, W.L.; Wang, E.K.; Dong, S.J. Introducing Ratiometric Fluorescence to MnO2 Nanosheet-Based Biosensing: A Simple, Label-Free Ratiometric Fluorescent Sensor Programmed by Cascade Logic Circuit for Ultrasensitive GSH Detection. ACS Appl. Mater. Interfaces 2017, 9, 25870–25877. [Google Scholar] [CrossRef] [PubMed]
- Fan, D.Q.; Zhu, X.Q.; Zhai, Q.F.; Wang, E.K.; Dong, S.J. Polydopamine Nanotubes as an Effective Fluorescent Quencher for Highly Sensitive and Selective Detection of Biomolecules Assisted with Exonuclease III Amplification. Anal. Chem. 2016, 88, 9158–9165. [Google Scholar] [CrossRef]
- Shi, H.; Wang, Y.X.; Zheng, J.; Ning, L.M.; Huang, Y.; Sheng, A.Z.; Chen, T.S.; Xiang, Y.; Zhu, X.L.; Li, G.X. Dual-Responsive DNA Nanodevice for the Available Imaging of an Apoptotic Signaling Pathway in Situ. ACS Nano 2019, 13, 12840–12850. [Google Scholar] [CrossRef]
- Wu, Q.; Liu, C.C.; Liu, Y.; Cui, C.; Ge, J.; Tan, W.H. Multibranched Linear DNA-Controlled Assembly of Silver Nanoclusters and Their Applications in Aptamer-Based Cell Recognition. ACS Appl. Mater. Interfaces 2022, 14, 14953–14960. [Google Scholar] [CrossRef]
- Yan, N.; Lin, L.; Xu, C.N.; Tian, H.Y.; Chen, X.S. A GSH-Gated DNA Nanodevice for Tumor-Specific Signal Amplification of microRNA and MR Imaging-Guided Theranostics. Small 2019, 15, 1903016. [Google Scholar] [CrossRef]
- Yue, R.Y.; Chen, M.; Ma, N. Dual MicroRNA-Triggered Drug Release System for Combined Chemotherapy and Gene Therapy with Logic Operation. ACS Appl. Mater. Interfaces 2020, 12, 32493–32502. [Google Scholar] [CrossRef] [PubMed]
- Fan, D.Q.; Wang, E.K.; Dong, S.J. An intelligent universal system yields double results with half the effort for engineering a DNA “Contrary Logic Pairs” library and various DNA combinatorial logic circuits. Mater. Horiz. 2017, 4, 924–931. [Google Scholar] [CrossRef]
- Fan, D.Q.; Zhu, J.B.; Zhai, Q.F.; Wang, E.K.; Dong, S.J. Cascade DNA logic device programmed ratiometric DNA analysis and logic devices based on a fluorescent dual-signal probe of a G-quadruplex DNAzyme. Chem. Commun. 2016, 52, 3766–3769. [Google Scholar] [CrossRef]
- Zhu, L.P.; Yu, L.Y.; Yang, X.R. Electrochemical-Based DNA Logic Devices Regulated by the Diffusion and Intercalation of Electroactive Dyes. ACS Appl. Mater. Interfaces 2021, 13, 42250–42257. [Google Scholar] [CrossRef]
- Zhu, L.P.; Yu, L.Y.; Meng, T.; Peng, Y.; Yang, X.R. Contrary Logic Pair Library, Parity Generator/Checker and Various Concatenated Logic Circuits Engineered by a Label-Free and Immobilization-Free Electrochemiluminescence Resonance Energy Transfer System. Small 2021, 17, 2102881. [Google Scholar] [CrossRef]
- Bhasikuttan, A.C.; Mohanty, J. Targeting G-quadruplex structures with extrinsic fluorogenic dyes: Promising fluorescence sensors. Chem. Commun. 2015, 51, 7581–7597. [Google Scholar] [CrossRef] [PubMed]
- Alba, J.J.; Sadurni, A.; Gargallo, R. Nucleic Acid i-Motif Structures in Analytical Chemistry. Crit. Rev. Anal. Chem. 2016, 46, 443–454. [Google Scholar] [CrossRef] [PubMed]
- Dai, H.C.; Shi, Y.; Wang, Y.L.; Sun, Y.J.; Hu, J.T.; Ni, P.J.; Li, Z. Label-free turn-on fluorescent detection of melamine based on the anti-quenching ability of Hg2+ to gold nanoclusters. Biosens. Bioelectron. 2014, 53, 76–81. [Google Scholar] [CrossRef] [PubMed]
- Fan, D.Q.; Wang, E.K.; Dong, S.J. Upconversion-chameleon-driven DNA computing: The DNA-unlocked inner-filter-effect (DU-IFE) for operating a multicolor upconversion luminescent DNA logic library and Its biosensing application. Mater. Horiz. 2019, 6, 375–384. [Google Scholar] [CrossRef]
- Fan, D.Q.; Zhai, Q.F.; Zhou, W.J.; Zhu, X.Q.; Wang, E.K.; Dong, S.J. A label-free colorimetric aptasensor for simple, sensitive and selective detection of Pt (II) based on platinum (II)-oligonucleotide coordination induced gold nanoparticles aggregation. Biosens. Bioelectron. 2016, 85, 771–776. [Google Scholar] [CrossRef] [PubMed]
- Fan, D.Q.; Zhu, J.B.; Liu, Y.Q.; Wang, E.K.; Dong, S.J. Label-free and enzyme-free platform for the construction of advanced DNA logic devices based on the assembly of graphene oxide and DNA-templated AgNCs. Nanoscale 2016, 8, 3834–3840. [Google Scholar] [CrossRef]
- Wu, H.; Zhang, K.; Liu, Y.L.; Wang, H.Y.; Wu, J.; Zhu, F.F.; Zou, P. Binding-induced and label-free colorimetric method for protein detection based on autonomous assembly of hemin/G-quadruplex DNAzyme amplification strategy. Biosens. Bioelectron. 2015, 64, 572–578. [Google Scholar] [CrossRef] [PubMed]
- Xu, L.L.; Zhou, Z.; Gou, X.L.; Shi, W.C.; Gong, Y.; Yi, M.; Cheng, W.; Song, F.Z. Light up multiple protein dimers on cell surface based on proximity-induced fluorescence activation of DNA-templated sliver nanoclusters. Biosens. Bioelectron. 2021, 179, 8. [Google Scholar] [CrossRef]
- Seio, K.; Kanamori, T.; Tokugawa, M.; Ohzeki, H.; Masaki, Y.; Tsunoda, H.; Ohkubo, A.; Sekine, M. Fluorescent properties of oligonucleotides doubly modified with an indole-fused cytosine analog and 2-aminopurine. Bioorgan. Med. Chem. 2013, 21, 3197–3201. [Google Scholar] [CrossRef]
- Jean, J.M.; Hall, K.B. 2-Aminopurine electronic structure and fluorescence properties in DNA. Biochemistry 2002, 41, 13152–13161. [Google Scholar] [CrossRef]
- Peng, P.; Du, Y.; Sun, Y.D.; Liu, S.N.; Mi, L.; Li, T. Probing the propeller-like loops of DNA G-quadruplexes with looped-out 2-aminopurine for label-free switchable molecular sensing. Analyst 2018, 143, 3814–3820. [Google Scholar] [CrossRef]
- Wang, X.L.; Zeng, R.; Chu, S.N.; Tang, W.; Lin, N.; Fu, J.; Yang, J.R.; Gao, B. A quencher-free DNAzyme beacon for fluorescently sensing uranyl ions via embedding 2-aminopurine. Biosens. Bioelectron. 2019, 135, 166–172. [Google Scholar] [CrossRef] [PubMed]
- Xu, Y.J.; Geng, N.N.; Zheng, X.; Luo, X.R.; Wu, M.S.; Zhang, H. DNA logic circuits based amplification system for quencher-free and highly sensitive detection of DNA and adenosine triphosphate. J. Pharmaceut. Biomed. 2018, 161, 393–398. [Google Scholar] [CrossRef] [PubMed]
- Zhao, X.J.; Zhu, Z.C.; Zou, R.; Wang, L.Y.; Gong, H.; Cai, C.Q. An enzyme-free three-dimensional DNA walker powered by catalytic hairpin assembly for H5N1 DNA ratiometric detection. Microchem. J. 2021, 170, 106728. [Google Scholar] [CrossRef]
- Fan, D.Q.; Wang, E.K.; Dong, S.J. Simple, fast, label-free, and nanoquencher-free system for operating multivalued DNA logic gates using poly-thymine templated CuNPs as signal reporters. Nano Res. 2017, 10, 2560–2569. [Google Scholar] [CrossRef]
- Qing, Z.H.; He, X.X.; He, D.G.; Wang, K.M.; Xu, F.Z.; Qing, T.P.; Yang, X. Poly(thymine)-Templated Selective Formation of Fluorescent Copper Nanoparticles. Angew. Chem. Int. Edit. 2013, 2, 9719–9722. [Google Scholar] [CrossRef]
- Fan, D.Q.; Wang, E.K.; Dong, S.J. A DNA-based parity generator/checker for error detection through data transmission with visual readout and an output-correction function. Chem. Sci. 2017, 8, 1888–1895. [Google Scholar] [CrossRef]
- Fan, D.Q.; Wang, J.; Han, J.W.; Wang, E.K.; Dong, S.J. Engineering DNA logic systems with non-canonical DNA-nanostructures: Basic principles, recent developments and bio-applications. Sci. China-Chem. 2022, 65, 284–297. [Google Scholar] [CrossRef]
- Fan, D.Q.; Wang, K.; Zhu, J.B.; Xia, Y.; Han, Y.C.; Liu, Y.Q.; Wang, E.K. DNA-based visual majority logic gate with one-vote veto function. Chem. Sci. 2015, 6, 1973–1978. [Google Scholar] [CrossRef]
- Pan, J.F.; He, Y.; Liu, Z.; Chen, J.H. Tetrahedron-Based Constitutional Dynamic Network for COVID-19 or Other Coronaviruses Diagnostics and Its Logic Gate Applications. Anal. Chem. 2022, 94, 714–722. [Google Scholar] [CrossRef]
- Han, J.W.; Wang, J.; Wang, J.; Fan, D.Q.; Dong, S.J. Recent advancements in coralyne (COR)-based biosensors: Basic principles, various strategies and future perspectives. Biosens. Bioelectron. 2022, 210, 114343. [Google Scholar] [CrossRef] [PubMed]
- Zhang, L.L.; Yuan, Y.W.; Wen, X.L.; Li, Y.; Cao, C.; Xiong, Q.H. A coordination and ligand replacement based three-input colorimetric logic gate sensing platform for melamine, mercury ions, and cysteine. RSC Adv. 2015, 5, 59106–59113. [Google Scholar] [CrossRef]
- Han, J.W.; Ding, Y.R.; Lv, X.J.; Zhang, Y.W.; Fan, D.Q. Integration of G-Quadruplex and Pyrene as a Simple and Efficient Ratiometric Fluorescent Platform That Programmed by Contrary Logic Pair for Highly Sensitive and Selective Coralyne (COR) Detection. Biosensors 2023, 13, 489. [Google Scholar] [CrossRef] [PubMed]
- Kuraishi, T.; Mizoguchi, Y.; Sun, Y.; Aoki, F.; Imakawa, K.; Sakai, S. The casein mRNA decay changes in parallel with the poly(A) tail length in the mouse mammary gland. Mol. Cell. Endocrinol 2002, 190, 101–107. [Google Scholar] [CrossRef] [PubMed]
- Zhao, G.G.; Jiao, F.; Liao, Q.; Luo, H.T.; Li, H.; Sun, L.; Bu, D.C.; Yu, K.T.; Zhao, Y.; Chen, R.S. Genome-wide identification of cancer-related polyadenylated and non-polyadenylated RNAs in human breast and lung cell lines. Sci. China-Life Sci. 2013, 56, 503–512. [Google Scholar] [CrossRef]
- Zheng, D.; Tian, B. Sizing up the poly(A) tail: Insights from deep sequencing. Trends Biochem.Sci. 2014, 39, 255–257. [Google Scholar] [CrossRef][Green Version]
- Liao, X.F.; Luo, N.; Li, M.Y.; Fu, H.; Zou, L. Label-free and highly sensitive fluorescent detection of bleomycin based on CRISPR-Cas12a and G-quadruplex-thioflavin T. Sensor. Actuat. B-Chem. 2023, 381, 133459. [Google Scholar] [CrossRef]
Disclaimer/Publisher’s Note: The statements, opinions and data contained in all publications are solely those of the individual author(s) and contributor(s) and not of MDPI and/or the editor(s). MDPI and/or the editor(s) disclaim responsibility for any injury to people or property resulting from any ideas, methods, instructions or products referred to in the content. |
© 2023 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https://creativecommons.org/licenses/by/4.0/).
Share and Cite
Wang, J.; Han, J.; Lv, X.; Hou, J.; Fan, D.; Dong, S. Coupling 2-Aminopurine with DNA Copper Nanoparticles as a Rapid and Enzyme-Free System for Operating DNA Contrary Logic Pairs. Chemistry 2023, 5, 1577-1587. https://doi.org/10.3390/chemistry5030108
Wang J, Han J, Lv X, Hou J, Fan D, Dong S. Coupling 2-Aminopurine with DNA Copper Nanoparticles as a Rapid and Enzyme-Free System for Operating DNA Contrary Logic Pairs. Chemistry. 2023; 5(3):1577-1587. https://doi.org/10.3390/chemistry5030108
Chicago/Turabian StyleWang, Jun, Jiawen Han, Xujuan Lv, Jingyu Hou, Daoqing Fan, and Shaojun Dong. 2023. "Coupling 2-Aminopurine with DNA Copper Nanoparticles as a Rapid and Enzyme-Free System for Operating DNA Contrary Logic Pairs" Chemistry 5, no. 3: 1577-1587. https://doi.org/10.3390/chemistry5030108
APA StyleWang, J., Han, J., Lv, X., Hou, J., Fan, D., & Dong, S. (2023). Coupling 2-Aminopurine with DNA Copper Nanoparticles as a Rapid and Enzyme-Free System for Operating DNA Contrary Logic Pairs. Chemistry, 5(3), 1577-1587. https://doi.org/10.3390/chemistry5030108