Green Chemical Analysis

Biomedical applications of synthetic nucleic acid engineering

  • Mengyao CAO ,
  • Li LI ,
  • Hao PEI
Expand
  • Shanghai Key Laboratory of Green Chemistry and Chemical Processes, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai 200062, China

Received date: 2022-06-29

  Accepted date: 2022-09-09

  Online published: 2023-01-07

Abstract

The simple rule of base-pairing of nucleic acids enables nucleic acid structures to be designed via powerful energy-based prediction tools. Thus, nucleic acid structures have attracted considerable attention owing to their ability to fold into a variety of synthetic structures. However, the lack of chemical diversity of nucleic acid bases makes nucleic acid structures less functionally diverse than proteins, thereby limiting their practical applications. This review focuses on the underlying technology of nucleic acid molecular engineering, especially on the studies of nucleic acid structures and their molecular interactions. As nucleic acid structures are fully spatially addressable, a diversity of particles could be linked to designated positions on the surface of nucleic acid structures. Additionally, the intermolecular reaction kinetics of nucleic acids could be continuously fine-tuned by rational design of nucleic acid sequences. This review also summarizes the development of synthetic molecular networks, dynamic molecular machines, and nucleic acid-based biomaterials, as well as the application of these as green biomedical devices in biomolecular recognition, cell surface engineering, and biocatalysis.

Cite this article

Mengyao CAO , Li LI , Hao PEI . Biomedical applications of synthetic nucleic acid engineering[J]. Journal of East China Normal University(Natural Science), 2023 , 2023(1) : 177 -185 . DOI: 10.3969/j.issn.1000-5641.2023.01.018

References

1 LIU S, JIANG Q, WANG Y, et al. Biomedical applications of DNA-based molecular devices. Advanced Healthcare Materials, 2019, 8 (10): e1801658.
2 CHEN J, LUO Z, SUN C, et al. Research progress of DNA walker and its recent applications in biosensor. TrAC Trends in Analytical Chemistry, 2019, 120, 115626.
3 PAYNE R J, WINSSINGER N. Editorial overview: Synthetic biomolecules. Current Opinion in Chemical Biology, 2018, 46, A3- A4.
4 ZHANG D Y, SEELIG G. Dynamic DNA nanotechnology using strand-displacement reactions. Nature Chemistry, 2011, 3 (2): 103- 113.
5 SEEMAN N C, SLEIMAN H F. DNA nanotechnology. Nature Reviews Materials, 2017, 3 (1): 1- 23.
6 HUANG P, WANG J, JIAO L, et al. A “time-frozen” technique in microchannel used for the thermodynamic studies of DNA origami. Biosensors and Bioelectronics, 2019, 131, 224- 231.
7 DELUCA M, SHI Z, CASTRO C E, et al. Dynamic DNA nanotechnology: Toward functional nanoscale devices. Nanoscale Horizons, 2020, 5 (2): 182- 201.
8 MAN T, JI W, LIU X, et al. Chiral metamolecules with active plasmonic transition. ACS Nano, 2019, 13 (4): 4826- 4833.
9 ZHU D, SONG P, SHEN J, et al. Polya-mediated DNA assembly on gold nanoparticles for thermodynamically favorable and rapid hybridization analysis. Analytical Chemistry, 2016, 88 (9): 4949- 4954.
10 SUN W, JI W, HALL J M, et al. Self-assembled DNA nanoclews for the efficient delivery of CRISPR–Cas9 for genome editing. Angewandte Chemie-International Edition, 2015, 54 (41): 12029- 12033.
11 CAO M, SUN Y, XIAO M, et al. Multivalent aptamer-modified DNA origami as drug delivery system for targeted cancer therapy. Chemical Research in Chinese Universities, 2019, 36 (2): 254- 260.
12 WANG P, XIAO M, PEI H, et al. Biomineralized DNA nanospheres by metal organic framework for enhanced chemodynamic therapy. Chemical Engineering Journal, 2021, 415, 129036.
13 XIAO M, LAI W, WANG F, et al. Programming drug delivery kinetics for active burst release with DNA toehold switches. Journal of the American Chemical Society, 2019, 141 (51): 20354- 20364.
14 JI W, LI X, XIAO M, et al. DNA-scaffolded disulfide redox network for programming drug-delivery kinetics. Chemistry-A European Journal, 2021, 27 (34): 8745- 8752.
15 LOPEZ R, WANG R, SEELIG G. A molecular multi-gene classifier for disease diagnostics. Nature Chemistry, 2018, 10 (7): 746- 754.
16 ZHANG C, ZHAO Y, XU X, et al. Cancer diagnosis with DNA molecular computation. Nature Nanotechnology, 2020, 15 (8): 709- 715.
17 张浩千, 娄春波. 合成生物学的发展、挑战及应对. 科学与社会, 2014, 4 (4): 26- 33.
18 KALLENBACH N R, MA R I, SEEMAN N C. An immobile nucleic acid junction constructed from oligonucleotides. Nature, 1983, 305 (5937): 829- 831.
19 ROTHEMUND P W. Folding DNA to create nanoscale shapes and patterns. Nature, 2006, 440 (7082): 297- 302.
20 TIKHOMIROV G, PETERSEN P, QIAN L. Fractal assembly of micrometre-scale DNA origami arrays with arbitrary patterns. Nature, 2017, 552 (7683): 67- 71.
21 ANDERSEN E S, DONG M, NIELSEN M M, et al. Self-assembly of a nanoscale DNA box with a controllable lid. Nature, 2009, 459 (7243): 73- 76.
22 DIETZ H, DOUGLAS S M, SHIH W M. Folding DNA into twisted and curved nanoscale shapes. Science, 2009, 325 (5941): 725- 730.
23 LIEDL T, HOGBERG B, TYTELL J, et al. Self-assembly of three-dimensional prestressed tensegrity structures from DNA. Nature Nanotechnology, 2010, 5 (7): 520- 524.
24 HAN D, PAL S, NANGREAVE J, et al. DNA origami with complex curvatures in three-dimensional space. Science, 2011, 332 (6027): 342- 346.
25 GERLING T, WAGENBAUER K F, NEUNER A M, et al. Dynamic DNA devices and assemblies formed by shape-complementary, non–base pairing 3D components. Science, 2015, 347 (6229): 1446- 1452.
26 余紫荆, 肖明书, 裴昊, 等. 基于DNA折纸的酶级联催化用于低密度脂蛋白的电化学检测. 分析化学, 2022, 50 (6): 850- 858.
27 YU H, MAN T, JI W, et al. Controllable self-assembly of parallel gold nanorod clusters by DNA origami. Chinese Chemical Letters, 2019, 30 (1): 175- 178.
28 LAI W, REN L, TANG Q, et al. Programming chemical reaction networks using intramolecular conformational motions of DNA. ACS Nano, 2018, 12 (7): 7093- 7099.
29 LAI W, XIONG X, WANG F, et al. Nonlinear regulation of enzyme-free DNA circuitry with ultrasensitive switches. ACS Synthetic Biology, 2019, 8 (9): 2106- 2112.
30 XIONG X, ZHU T, ZHU Y, et al. Molecular convolutional neural networks with DNA regulatory circuits. Nature Machine Intelligence, 2022, (4): 625- 635.
31 XIONG X, XIAO M, LAI W, et al. Optochemical control of DNA-switching circuits for logic and probabilistic computation. Angewandte Chemie-International Edition, 2021, 60 (7): 3397- 3401.
32 TANG Q, LAI W, WANG P, et al. Multi-mode reconfigurable DNA-based chemical reaction circuits for soft matter computing and control. Angewandte Chemie-International Edition, 2021, 60 (27): 15013- 15019.
33 JI W, LI D, LAI W, et al. pH-operated triplex DNA device on MoS2 nanosheets . Langmuir, 2019, 35 (14): 5050- 5053.
34 DOUGLAS S M, BACHELET I, CHURCH G M J S. A logic-gated nanorobot for targeted transport of molecular payloads. Science, 2012, 335 (6070): 831- 834.
35 CHATTERJEE G, DALCHAU N, MUSCAT R A, et al. A spatially localized architecture for fast and modular DNA computing. Nature Nanotechnology, 2017, 12 (9): 920- 927.
36 THUBAGERE A J, LI W, JOHNSON R F, et al. A cargo-sorting DNA robot. Science, 2017, 357 (6356): 1095- 1096.
37 XIAO M, GAO L, CHANDRASEKARAN A R, et al. Bio-functional G-molecular hydrogels for accelerated wound healing. Materials Science and Engineering: C, 2019, 105, 110067.
38 MAN T, LAI W, ZHU C, et al. Perovskite mediated vibronic coupling of semiconducting SERS for biosensing. Advanced Functional Materials, 2022, 32 (32): 2201799.
39 TANG Q, PLANK T N, ZHU T, et al. Self-assembly of metallo-nucleoside hydrogels for injectable materials that promote wound closure. ACS Applied Materials & Interfaces, 2019, 11 (22): 19743- 19750.
40 WANG X, YAN L, YU Z, et al. Aptamer-functionalized fractal nanoplasmonics-assisted laser desorption/ionization mass spectrometry for metabolite detection. ChemPlusChem, 2022, 87 (1): e202100479.
41 SONG L, XIAO M, LAI W, et al. Intracellular logic computation with framework nucleic acid-based circuits for mRNA imaging. Chinese Journal of Chemistry, 2021, 39 (4): 947- 953.
42 WANG X, XIAO M, ZOU Y, et al. Fractal SERS nanoprobes for multiplexed quantitative gene profiling. Biosensors and Bioelectronics, 2020, 156, 112130.
43 YU H, XIAO M, LAI W, et al. A self-calibrating surface-enhanced Raman scattering-active system for bacterial phenotype detection. Analytical Chemistry, 2020, 92 (6): 4491- 4497.
44 LAI W, XIAO M, YANG H, et al. Circularized blocker-displacement amplification for multiplex detection of rare DNA variants. Chemical Communications, 2020, 56 (82): 12331- 12334.
45 MAN T, LAI W, XIAO M, et al. A versatile biomolecular detection platform based on photo-induced enhanced Raman spectroscopy. Biosensors and Bioelectronics, 2020, 147, 111742.
46 XIAO M, LAI W, MAN T, et al. Rationally engineered nucleic acid architectures for biosensing applications. Chemical Reviews, 2019, 119 (22): 11631- 11717.
47 SHEN J, LIANG L, XIAO M, et al. Fractal nanoplasmonic labels for supermultiplex imaging in single cells. Journal of the American Chemical Society, 2019, 141 (30): 11938- 11946.
48 SU Y, LI D, LIU B, et al. Rational design of framework nucleic acids for bioanalytical applications. ChemPlusChem, 2019, 84 (5): 512- 523.
49 QU X, XIAO M, LI F, et al. Framework nucleic acid-mediated pull-down microRNA detection with hybridization chain reaction amplification. ACS Applied Bio Materials, 2018, 1 (3): 859- 864.
50 王飞, 钟睿博, 唐倩, 等. ATP 触发快速响应的线性DNA凝胶. 高分子学报, 2018, (5): 553- 558.
51 WANG X, LAI W, MAN T, et al. Bio-surface engineering with DNA scaffolds for theranostic applications. Nanofabrication, 2018, 4 (1): 1- 16.
52 ZHONG R, XIAO M, ZHU C, et al. Logic catalytic interconversion of G-molecular hydrogel. ACS Applied Materials & Interfaces, 2018, 10 (5): 4512- 4518.
53 XIAO M, QU X, LI L, et al. Ultrasensitive detection of metal ions with DNA nanostructure. Methods in Molecular Biology, 2018, 1811, 137- 149.
54 QU X, LI M, ZHANG H, et al. Real-time continuous identification of greenhouse plant pathogens based on recyclable microfluidic bioassay system. ACS Applied Materials & Interfaces, 2017, 9 (37): 31568- 31575.
55 QI L, XIAO M, WANG X, et al. DNA-encoded Raman-active anisotropic nanoparticles for microRNA detection. Analytical Chemistry, 2017, 89 (18): 9850- 9856.
56 QU X, YANG F, CHEN H, et al. Bubble-mediated ultrasensitive multiplex detection of metal ions in three-dimensional DNA nanostructure-encoded microchannels. ACS Applied Materials & Interfaces, 2017, 9 (19): 16026- 16034.
57 QU X, ZHANG H, CHEN H, et al. Convection-driven pull-down assays in nanoliter droplets using scaffolded aptamers. Analytical Chemistry, 2017, 89 (6): 3468- 3473.
58 CHEN L, CHAO J, QU X, et al. Probing cellular molecules with polyA-based engineered aptamer nanobeacon. ACS Applied Materials & Interfaces, 2017, 9 (9): 8014- 8020.
59 QI L, XIAO M, WANG F, et al. Poly-cytosine-mediated nanotags for SERS detection of Hg2+. Nanoscale, 2017, 9 (37): 14184- 14191.
60 闫璐, 李晓丹, 肖明书, 等. 集成DNA分子机器的微针贴片用于细胞外三磷酸腺苷原位监测. 分析化学, 2022, 50 (4): 516- 524.
61 QU X, ZHU D, YAO G, et al. An exonuclease Ⅲ-powered, on-particle stochastic DNA walker. Angewandte Chemie-International Edition, 2017, 56 (7): 1855- 1858.
62 YANG H, XIAO M, LAI W, et al. Stochastic DNA dual-walkers for ultrafast colorimetric bacteria detection. Analytical chemistry, 2020, 92 (7): 4990- 4995.
63 XIAO M, MAN T, ZHU C, et al. MoS2 nanoprobe for microRNA quantification based on duplex-specific nuclease signal amplification . ACS Applied Materials & Interfaces, 2018, 10 (9): 7852- 7858.
64 XIAO M, CHANDRASEKARAN A R, JI W, et al. Affinity-modulated molecular beacons on MoS2 nanosheets for microRNA detection . ACS Applied Materials & Interfaces, 2018, 10 (42): 35794- 35800.
65 XIAO M, WANG X, LI L, et al. Stochastic RNA walkers for intracellular microRNA imaging. Analytical Chemistry, 2019, 91 (17): 11253- 11258.
66 XIAO M, ZOU K, LI L, et al. Stochastic DNA walkers in droplets for super-multiplexed bacterial phenotype detection. Angewandte Chemie International Edition, 2019, 58 (43): 15448- 15454.
67 WU Z, XIAO M, LAI W, et al. Nucleic acid-based cell surface engineering strategies and their applications. ACS Applied Bio Materials, 2022, 5 (5): 1901- 1915.
68 XIAO M, LAI W, WANG X, et al. DNA mediated self-assembly of multicellular microtissues [J]. Microphysiological Systems, 2018, 2(1). DOI: 10.21037/mps.2017.12.01.
69 QU X, WANG S, GE Z, et al. Programming cell adhesion for on-chip sequential boolean logic functions. Journal of the American Chemical Society, 2017, 139 (30): 10176- 10179.
70 XIAO M, LAI W, YU H, et al. Assembly pathway selection with DNA reaction circuits for programming multiple cell-cell interactions. Journal of the American Chemical Society, 2021, 143 (9): 3448- 3454.
71 XIAO M, LAI W, YAO X, et al. Programming receptor clustering with DNA probabilistic circuits for enhanced natural killer cell recognition. Angewandte Chemie-International Edition, 2022, 61 (28): e202203800.
72 LIN M, CHEN Y, ZHAO S, et al. A biomimetic approach for spatially controlled cell membrane engineering using fusogenic spherical nucleic acid. Angewandte Chemie-International Edition, 2022, 61 (1): e202111647.
73 ZHONG R, TANG Q, WANG S, et al. Self-assembly of enzyme-like nanofibrous G-molecular hydrogel for printed flexible electrochemical sensors. Advanced Materials, 2018, 30 (12): e1706887.
74 MAN T, XU C, LIU X Y, et al. Hierarchically encapsulating enzymes with multi-shelled metal-organic frameworks for tandem biocatalytic reactions. Nature Communcation, 2022, 13, 305.
75 ZHONG H, LO W S, MAN T, et al. Stabilizing DNAzymes through encapsulation in a metal-organic framework. Chemistry–A European Journal, 2020, 26 (57): 12931- 12935.
76 ZHOU L, GAO M, FU W, et al. Three-dimensional DNA tweezers serve as modular DNA intelligent machines for detection and regulation of intracellular microRNA. Science Advances, 2020, 6 (22): eabb0695.
77 CHAO J, LIU H, SU S, et al. Structural DNA nanotechnology for intelligent drug delivery. Small, 2014, 10 (22): 4626- 4635.
Outlines

/