PDF
Abstract
DNA is a biological macromolecule that carries genetic information in organisms. It provides a series of predominant biological advantages, such as sequence programmability, high biocompatibility, and low biotoxicity. As such, it is a unique polymer material that shows great potential for application in biological and medical fields. DNA aptamers are short DNA sequences with a specific ability of molecular recognition. With its discovery, the application prospect of DNA materials has broadened, especially for the separation and analysis of biological particles. In this review, the functions and characteristics of DNA aptamers are introduced, and the applications of DNA materials in cell/exosome separation and cancer detection are summarized. The application prospect and possible challenges of DNA materials are predicted.
Keywords
DNA materials
/
DNA aptamer
/
Biological particle separation
/
Disease analysis
Cite this article
Download citation ▾
Chenxu Zhu, Chi Yao, Dayong Yang.
Aptamer-Based DNA Materials for the Separation and Analysis of Biological Particles.
Transactions of Tianjin University, 2021, 27(6): 450-459 DOI:10.1007/s12209-021-00301-y
| [1] |
Seeman NC, Sleiman HF DNA nanotechnology. Nat Rev Mater, 2017, 3(1): 1-23.
|
| [2] |
Lv J, Dong Y, Gu Z, et al. Programmable DNA nanoflowers for biosensing, bioimaging, and therapeutics. Chemistry, 2020, 26(64): 14512-14524.
|
| [3] |
Tian TR, Xiao DX, Zhang T, et al. A framework nucleic acid based robotic nanobee for active targeting therapy. Adv Funct Mater, 2021, 31(5): 2007342.
|
| [4] |
Castro CE, Kilchherr F, Kim DN, et al. A primer to scaffolded DNA origami. Nat Methods, 2011, 8(3): 221-229.
|
| [5] |
Tang J, Yao C, Gu Z, et al. Super-soft and super-elastic DNA robot with magnetically driven navigational locomotion for cell delivery in confined space. Angew Chem Int Ed Engl, 2020, 59(6): 2490-2495.
|
| [6] |
Zhou T, Chen P, Niu L, et al. pH-responsive size-tunable self-assembled DNA dendrimers. Angew Chem Int Ed, 2012, 51(45): 11271-11274.
|
| [7] |
Mukundan VT, Phan AT Bulges in G-quadruplexes: broadening the definition of G-quadruplex-forming sequences. J Am Chem Soc, 2013, 135(13): 5017-5028.
|
| [8] |
Yin P, Choi HM, Calvert CR, et al. Programming biomolecular self-assembly pathways. Nature, 2008, 451(7176): 318-322.
|
| [9] |
Yüce M, Ullah N, Budak H Trends in aptamer selection methods and applications. Analyst, 2015, 140(16): 5379-5399.
|
| [10] |
Röthlisberger P, Hollenstein M Aptamer chemistry. Adv Drug Deliv Rev, 2018, 134: 3-21.
|
| [11] |
Zhou J, Rossi J Aptamers as targeted therapeutics: current potential and challenges. Nat Rev Drug Discov, 2017, 16(3): 181-202.
|
| [12] |
Li L, Xu S, Yan H, et al. Nucleic acid aptamers for molecular diagnostics and therapeutics: advances and perspectives. Angew Chem Int Ed Engl, 2021, 60(5): 2221-2231.
|
| [13] |
Sun S, Wang R, Huang Y, et al. Design of hierarchical beads for efficient label-free cell capture. Small, 2019, 15(34): e1902441.
|
| [14] |
Yao C, Tang H, Wu WJ, et al. Double rolling circle amplification generates physically cross-linked DNA network for stem cell fishing. J Am Chem Soc, 2020, 142(7): 3422-3429.
|
| [15] |
Oh S, Jung SH, Seo H, et al. Magnetic activated cell sorting (MACS) pipette tip for immunomagnetic bacteria separation. Sensor Actuat B Chem, 2018, 272: 324-330.
|
| [16] |
Liu L, Cheung TH, Charville GW, et al. Isolation of skeletal muscle stem cells by fluorescence-activated cell sorting. Nat Protoc, 2015, 10(10): 1612-1624.
|
| [17] |
Li J, Jie HB, Lei Y, et al. PD-1/SHP-2 inhibits Tc1/Th1 phenotypic responses and the activation of T cells in the tumor microenvironment. Cancer Res, 2015, 75(3): 508-518.
|
| [18] |
Guo S, Huang HY, Deng XJ, et al. Programmable DNA-responsive microchip for the capture and release of circulating tumor cells by nucleic acid hybridization. Nano Res, 2018, 11(5): 2592-2604.
|
| [19] |
Kacherovsky N, Cardle II, Cheng EL, et al. Traceless aptamer-mediated isolation of CD8+ T cells for chimeric antigen receptor T-cell therapy. Nat Biomed Eng, 2019, 3(10): 783-795.
|
| [20] |
Kaur H Recent developments in cell-SELEX technology for aptamer selection. Biochim Biophys Acta Gen Subj, 2018, 1862(10): 2323-2329.
|
| [21] |
Song P, Ye D, Zuo X, et al. DNA hydrogel with aptamer-toehold-based recognition, cloaking, and decloaking of circulating tumor cells for live cell analysis. Nano Lett, 2017, 17(9): 5193-5198.
|
| [22] |
Yin F, Li M, Mao X, et al. DNA framework-based topological cell sorters. Angew Chem Int Ed Engl, 2020, 59(26): 10406-10410.
|
| [23] |
Wu LL, Ding HM, Qu X, et al. Fluidic multivalent membrane nanointerface enables synergetic enrichment of circulating tumor cells with high efficiency and viability. J Am Chem Soc, 2020, 142(10): 4800-4806.
|
| [24] |
Zhou GB, Lin MH, Song P, et al. Multivalent capture and detection of cancer cells with DNA nanostructured biosensors and multibranched hybridization chain reaction amplification. Anal Chem, 2014, 86(15): 7843-7848.
|
| [25] |
Shen Q, Xu L, Zhao L, et al. Specific capture and release of circulating tumor cells using aptamer-modified nanosubstrates. Adv Mater, 2013, 25(16): 2368-2373.
|
| [26] |
Poudineh M, Sargent EH, Pantel K, et al. Profiling circulating tumour cells and other biomarkers of invasive cancers. Nat Biomed Eng, 2018, 2(2): 72-84.
|
| [27] |
Li M, Ding H, Lin M, et al. DNA framework-programmed cell capture via topology-engineered receptor-ligand interactions. J Am Chem Soc, 2019, 141(47): 18910-18915.
|
| [28] |
Gao T, Li L, Chen T, et al. DNA-oriented shaping of cell features for the detection of rare disseminated tumor cells. Anal Chem, 2019, 91(1): 1126-1132.
|
| [29] |
Simons M, Raposo G Exosomes: vesicular carriers for intercellular communication. Curr Opin Cell Biol, 2009, 21(4): 575-581.
|
| [30] |
Jeppesen DK, Fenix AM, Franklin JL, et al. Reassessment of exosome composition. Cell, 2019, 177(2): 428-445.e18.
|
| [31] |
Doyle L, Wang M Overview of extracellular vesicles, their origin, composition, purpose, and methods for exosome isolation and analysis. Cells, 2019, 8(7): 727.
|
| [32] |
Théry C, Zitvogel L, Amigorena S Exosomes: composition, biogenesis and function. Nat Rev Immunol, 2002, 2(8): 569-579.
|
| [33] |
Linares R, Tan S, Gounou C, et al. High-speed centrifugation induces aggregation of extracellular vesicles. J Extracell Vesicles, 2015, 4: 29509.
|
| [34] |
Jørgensen M, Bæk R, Pedersen S, et al. Extracellular vesicle (EV) array: microarray capturing of exosomes and other extracellular vesicles for multiplexed phenotyping. J Extracell Vesicles, 2013, 2(1): 20920.
|
| [35] |
Zhou Q, Rahimian A, Son K, et al. Development of an aptasensor for electrochemical detection of exosomes. Methods, 2016, 97: 88-93.
|
| [36] |
Gao ML, He F, Yin BC, et al. A dual signal amplification method for exosome detection based on DNA dendrimer self-assembly. Analyst, 2019, 144(6): 1995-2002.
|
| [37] |
He F, Wang J, Yin BC, et al. Quantification of exosome based on a copper-mediated signal amplification strategy. Anal Chem, 2018, 90(13): 8072-8079.
|
| [38] |
Zhang KX, Yue YL, Wu SX, et al. Rapid capture and nondestructive release of extracellular vesicles using aptamer-based magnetic isolation. ACS Sensor, 2019, 4(5): 1245-1251.
|
| [39] |
Zhang N, Sun N, Deng C Rapid isolation and proteome analysis of urinary exosome based on double interactions of Fe3O4@TiO2-DNA aptamer. Talanta, 2021, 221: 121571.
|
| [40] |
Cheng N, Du D, Wang XX, et al. Recent advances in biosensors for detecting cancer-derived exosomes. Trends Biotechnol, 2019, 37(11): 1236-1254.
|
| [41] |
Melo SA, Luecke LB, Kahlert C, et al. Glypican-1 identifies cancer exosomes and detects early pancreatic cancer. Nature, 2015, 523(7559): 177-182.
|
| [42] |
Pluchino S, Smith JA Explicating exosomes: reclassifying the rising stars of intercellular communication. Cell, 2019, 177(2): 225-227.
|
| [43] |
Zhou Y, Xu HY, Wang H, et al. Detection of breast cancer-derived exosomes using the horseradish peroxidase-mimicking DNAzyme as an aptasensor. Analyst, 2020, 145(1): 107-114.
|
| [44] |
Zhang HX, Wang ZH, Wang F, et al. In situ formation of gold nanoparticles decorated Ti3C2 MXenes nanoprobe for highly sensitive electrogenerated chemiluminescence detection of exosomes and their surface proteins. Anal Chem, 2020, 92(7): 5546-5553.
|
| [45] |
Wang Q, Zou LY, Yang XH, et al. Direct quantification of cancerous exosomes via surface plasmon resonance with dual gold nanoparticle-assisted signal amplification. Biosens Bioelectron, 2019, 135: 129-136.
|
| [46] |
Ning CF, Wang L, Tian YF, et al. Multiple and sensitive SERS detection of cancer-related exosomes based on gold-silver bimetallic nanotrepangs. Analyst, 2020, 145(7): 2795-2804.
|
| [47] |
Yu Q, Zhao Q, Wang S, et al. Development of a lateral flow aptamer assay strip for facile identification of theranostic exosomes isolated from human lung carcinoma cells. Anal Biochem, 2020, 594: 113591.
|
| [48] |
Huang L, Wang DB, Singh N, et al. A dual-signal amplification platform for sensitive fluorescence biosensing of leukemia-derived exosomes. Nanoscale, 2018, 10(43): 20289-20295.
|
| [49] |
Huang R, He L, Xia Y, et al. A sensitive aptasensor based on a hemin/G-quadruplex-assisted signal amplification strategy for electrochemical detection of gastric cancer exosomes. Small, 2019, 15(19): e1900735.
|
| [50] |
An Y, Jin T, Zhu Y, et al. An ultrasensitive electrochemical aptasensor for the determination of tumor exosomes based on click chemistry. Biosens Bioelectron, 2019, 142: 111503.
|
| [51] |
Zhao L, Sun RJ, He P, et al. Ultrasensitive detection of exosomes by target-triggered three-dimensional DNA walking machine and exonuclease III-assisted electrochemical ratiometric biosensing. Anal Chem, 2019, 91(22): 14773-14779.
|
| [52] |
Cao Y, Li L, Han B, et al. A catalytic molecule machine-driven biosensing method for amplified electrochemical detection of exosomes. Biosens Bioelectron, 2019, 141: 111397.
|