Systematic bio-fabrication of aptamers and their applications in engineering biology

Abstract

Aptamers are single-stranded DNA or RNA molecules that have high affinity and selectivity to bind to specific targets. Compared to antibodies, aptamers are easy to in vitro synthesize with low cost, and exhibit excellent thermal stability and programmability. With these features, aptamers have been widely used in biology and medicine-related fields. In the meantime, a variety of systematic evolution of ligands by exponential enrichment (SELEX) technologies have been developed to screen aptamers for various targets. According to the characteristics of targets, customizing appropriate SELEX technology and post-SELEX optimization helps to obtain ideal aptamers with high affinity and specificity. In this review, we first summarize the latest research on the systematic bio-fabrication of aptamers, including various SELEX technologies, post-SELEX optimization, and aptamer modification technology. These procedures not only help to gain the aptamer sequences but also provide insights into the relationship between structure and function of the aptamers. The latter provides a new perspective for the systems bio-fabrication of aptamers. Furthermore, on this basis, we review the applications of aptamers, particularly in the fields of engineering biology, including industrial biotechnology, medical and health engineering, and environmental and food safety monitoring. And the encountered challenges and prospects are discussed, providing an outlook for the future development of aptamers.

Keywords

Aptamer / SELEX / Engineering biology / Biosensors

References

[1] MackelprangR, AurandER, BovenbergRAL, et al. . Guiding ethical principles in engineering biology research. ACS Synth Biol, 2021, 10: 907-910.

[2] PatraP, DasM, KunduP, et al. . Recent advances in systems and synthetic biology approaches for developing novel cell-factories in non-conventional yeasts. Biotechnol Adv, 2021, 47. 107695

[3] HuaZ, YuT, LiuD, et al. . Recent advances in gold nanoparticles-based biosensors for food safety detection. Biosens Bioelectron, 2021, 179. 113076

[4] LiY, DengJ, HanZ, et al. . Molecular identification of tumor-derived extracellular vesicles using thermophoresis-mediated DNA computation. J Am Chem Soc, 2021, 143: 1290-1295.

[5] YuS, ZhouY, SunY, et al. . Endogenous mRNA triggered DNA-Au nanomachine for in situ imaging and targeted multimodal synergistic cancer therapy. Angew Chem Int Ed, 2021, 60: 5948-5958.

[6] KaushalS, PinnakaAK, SoniS, et al. . Antibody assisted graphene oxide coated gold nanoparticles for rapid bacterial detection and near infrared light enhanced antibacterial activity. Sens Actuat B Chem, 2021, 329. 129141

[7] WeiJ, LiuS, QilengA, et al. . A photoelectrochemical/colorimetric immunosensor for broad-spectrum detection of ochratoxins using bifunctional copper oxide nanoflowers. Senso Actuat B Chem, 2021, 330. 129380

[8] GuC, BaiL, PuL, et al. . Highly sensitive and stable self-powered biosensing for exosomes based on dual metal-organic frameworks nanocarriers. Biosens Bioelectron, 2021, 176. 112907

[9] PerweinMK, SmestadJA, WarringtonAE, et al. . A comparison of human natural monoclonal antibodies and aptamer conjugates for promotion of CNS remyelination: Where are we now and what comes next?. Expert Opin Biol Th, 2018, 18: 545-560.

[10] PiroB, ShiS, ReisbergS, et al. . Comparison of electrochemical immunosensors and aptasensors for detection of small organic molecules in environment, food safety, clinical and public security. Biosensors (Basel), 2016, 6: 7.

[11] GuptaV, LassmanME, McAvoyT, et al. . An evaluation of an aptamer for use as an affinity reagent with MS: PCSK9 as an example protein. Bioanalysis, 2016, 8: 1557-1564.

[12] ȘtefanG, HosuO, De WaelK, et al. . Aptamers in biomedicine: selection strategies and recent advances. Electrochim Acta, 2021, 376. 137994

[13] NiS, ZhuoZ, PanY, et al. . Recent progress in aptamer discoveries and modifications for therapeutic applications. ACS Appl Mater Interfaces, 2021, 13: 9500-9519.

[14] VandghanooniS, EskandaniM, BararJ, et al. . Bispecific therapeutic aptamers for targeted therapy of cancer: a review on cellular perspective. J Mol Med, 2018, 96: 885-902.

[15] YuH, AlkhamisO, CanouraJ, et al. . Advances and challenges in small-molecule DNA aptamer isolation, characterization, and sensor development. Angew Chem Int Ed, 2021, 60: 16800-16823.

[16] LiuR, ZhangF, SangY, et al. . Screening, identification, and application of nucleic acid aptamers applied in food safety biosensing. Trends Food Sci Tech, 2022, 123: 355-375.

[17] QiaoL, WangH, HeJ, et al. . Truncated affinity-improved aptamers for 17β-estradiol determination by AuNPs-based colorimetric aptasensor. Food Chem, 2021, 340. 128181

[18] ZhangN, ChenZ, LiuD, et al. . Structural biology for the molecular insight between aptamers and target proteins. Int J Mol Sci, 2021, 22: 4093.

[19] WangT, ChenC, LarcherLM, et al. . Three decades of nucleic acid aptamer technologies: lessons learned, progress and opportunities on aptamer development. Biotechnol Adv, 2019, 37: 28-50.

[20] PlatellaC, RiccardiC, MontesarchioD, et al. . G-quadruplex-based aptamers against protein targets in therapy and diagnostics. Bba-Gen Subjects, 2017, 1861: 1429-1447.

[21] AgyeiD, AcquahC, TanKX, et al. . Prospects in the use of aptamers for characterizing the structure and stability of bioactive proteins and peptides in food. Chem Rev, 2018, 410: 297-306.

[22] ZhuC, YangG, GhulamM, et al. . Evolution of multi-functional capillary electrophoresis for high-efficiency selection of aptamers. Biotechnol Adv, 2019, 37. 107432

[23] KomarovaN, KuznetsovA. Inside the black box: what makes selex better?. Molecules, 2019, 24: 3598.

[24] KohlbergerM, GadermaierG. Selex: critical factors and optimization strategies for successful aptamer selection. Biotechnol Appl Bioc, 2021.

[25] KamarudinNAAN, SatJNA, ZaidiNFM, et al. . Evolution of specific RNA aptamers via selex targeting recombinant human cd36 protein: a candidate therapeutic target in severe malaria. Asian Pac J Trop Bio, 2020, 10: 23-32.

[26] WangJ, WangQ, LuoY, et al. . In vitro selection of ssDNA aptamers that can specifically recognize and differentiate riboflavin and its derivative fad. Talanta, 2019, 204: 424-430.

[27] KimHK, KimHR, YoonSJ, et al. . Colorimetric aptasensor for detecting bacillus carboniphilus using aptamer isolated with a non-selex-based method. Chemosensors, 2021, 9: 12113.

[28] HanXY, ZhangYH, NieJJ, et al. . Gold nanoparticle based photometric determination of tobramycin by using new specific DNA aptamers. Microchim Acta, 2018.

[29] DuY, LiuD, WangM, et al. . Preparation of DNA aptamer and development of lateral flow aptasensor combining recombinase polymerase amplification for detection of erythromycin. Biosens Bioelectron, 2021, 181. 113157

[30] StoltenburgR, NikolausN, StrehlitzB. Capture-selex: selection of DNA aptamers for aminoglycoside antibiotics. J Anal Methods Chem, 2012, 2012. 415697

[31] ZhangY, LaiBS, JuhasM. Recent advances in aptamer discovery and applications. Molecules, 2019, 24: 941.

[32] LyuC, KhanIM, WangZ. Capture-selex for aptamer selection: a short review. Talanta, 2021, 229. 122274

[33] YueH, ChenJ, ChenX, et al. . Systematic screening and optimization of single-stranded DNA aptamer specific for n-acetylneuraminic acid: a comparative study. Sens Actuat B Chem, 2021, 344. 130270

[34] SattariR, PalizbanA, KhanahmadH. Single-strand DNA-like oligonucleotide aptamer against proprotein convertase subtilisin/kexin 9 using ce-selex: Pcsk9 targeting selection. Cardiovasc Drug Ther, 2020, 34: 475-485.

[35] LeATH, WangTY, KrylovaSM, et al. . Quantitative characterization of partitioning in selection of DNA aptamers for protein targets by capillary electrophoresis. Anal Chem, 2022, 94: 2578-2588.

[36] ZhuC, LiL, YangG, et al. . Online reaction based single-step capillary electrophoresis-systematic evolution of ligands by exponential enrichment for ssDNA aptamers selection. Anal Chim Acta, 2019, 1070: 112-122.

[37] FatimaK, NaqviF, YounasH. A review: Molecular chaperone-mediated folding, unfolding and disaggregation of expressed recombinant proteins. Cell Biochem Biophys, 2021, 79: 153-174.

[38] LiuD, HuB, PengD, et al. . Isolation ssDNA aptamers specific for both live and viable but nonculturable state vibrio vulnificus using whole bacteria-sEILEX technology. Rsc Adv, 2020, 10: 15997-16008.

[39] FellowsT, HoL, FlanaganS, et al. . Gold nanoparticle-streptavidin conjugates for rapid and efficient screening of aptamer function in lateral flow sensors using novel CD4-binding aptamers identified through crossover-selex. Analyst, 2020, 145: 5180-5193.

[40] ZhuH, FohlerovaZ, PekarekJ, et al. . Recent advances in lab-on-a-chip technologies for viral diagnosis. Biosens Bioelectron, 2020, 153. 112041

[41] DembowskiSK, BowserMT. Microfluidic methods for aptamer selection and characterization. Analyst, 2018, 143: 21-32.

[42] HongSL, XiangMQ, TangM, et al. . Ebola virus aptamers: from highly efficient selection to application on magnetism-controlled chips. Anal Chem, 2019, 91: 3367-3373.

[43] YuH, LuoY, AlkhamisO, et al. . Isolation of natural DNA aptamers for challenging small-molecule targets. Cannabinoids Anal Chem, 2021, 93: 3172-3180.

[44] WanJ, YeL, YangX, et al. . Cell-selex based selection and optimization of DNA aptamers for specific recognition of human cholangiocarcinoma qbc-939 cells. Analyst, 2015, 140: 5992-5997.

[45] CaiSD, YanJH, XiongHJ, et al. . Investigations on the interface of nucleic acid aptamers and binding targets. Analyst, 2018, 143: 5317-5338.

[46] SoheiliV, TaghdisiSM, KhayyatMH, et al. . Colorimetric and ratiometric aggregation assay for streptomycin using gold nanoparticles and a new and highly specific aptamer. Microchim Acta, 2016, 183: 1687-1697.

[47] MoghadamM, SankianM, AbnousK, et al. . Cell-selex-based selection and characterization of a G-quadruplex DNA aptamer against mouse dendritic cells. Int Immunopharmacol, 2016, 36: 324-332.

[48] GaoSX, ZhengX, JiaoBH, et al. . Post-selex optimization of aptamers. Anal Bioanal Chem, 2016, 408: 4567-4573.

[49] DongLL, ZhouHX, ZhaoML, et al. . Phosphorothioate-modified AP613-1 specifically targets gpc3 when used for Hepatocellular Carcinoma cell imaging. Mol Ther-Nucl Acids, 2018, 13: 376-386.

[50] GaoSX, ZhengX, TangY, et al. . Development of a fluorescently labeled aptamer structure-switching assay for sensitive and rapid detection of gliotoxin. Anal Chem, 2019, 91: 1610-1618.

[51] HuangCJ, LinHI, ShieshSC, et al. . Integrated microfluidic system for rapid screening of crp aptamers utilizing systematic evolution of ligands by exponential enrichment (selex). Biosens Bioelectron, 2010, 25: 1761-1766.

[52] SongKM, JeongE, JeonW, et al. . Aptasensor for ampicillin using gold nanoparticle based dual fluorescence-colorimetric methods. Anal Bioanal Chem, 2012, 402: 2153-2161.

[53] KaiserL, WeisserJ, KohlM, et al. . Small molecule detection with aptamer based lateral flow assays: applying aptamer-c-reactive protein cross-recognition for ampicillin detection. Sci Rep, 2018, 8: 5628.

[54] AlhadramiHA, ChinnappanR, EissaS, et al. . High affinity truncated DNA aptamers for the development of fluorescence based progesterone biosensors. Anal Biochem, 2017, 525: 78-84.

[55] WuXQ, ZhaoZL, BaiHR, et al. . DNA aptamer selected against pancreatic ductal adenocarcinoma for in vivo imaging and clinical tissue recognition. Theranostics, 2015, 5: 985-994.

[56] ZumrutHE, BatoolS, VanN, et al. . Structural optimization of an aptamer generated from ligand-guided selection (LIGS) resulted in high affinity variant toward migm expressed on burkitt's lymphoma cell lines. Bba-Gen Subjects, 2017, 1861: 1825-1832.

[57] DavydovaA, VorobyevaM, BashmakovaE, et al. . Development and characterization of novel 2′-f-RNA aptamers specific to human total and glycated hemoglobins. Anal Biochem, 2019, 570: 43-50.

[58] FerreiraD, BarbosaJ, SousaDA, et al. . Selection of aptamers against triple negative breast cancer cells using high throughput sequencing. Sci Rep, 2021, 11: 8614.

[59] LeTT. Determination of minimal sequence for binding of an aptamer. A comparison of truncation and hybridization inhibition methods. Rsc Adv, 2014, 4: 47227-47233.

[60] AzriFA, SelamatJ, SukorR, et al. . Determination of minimal sequence for zearalenone aptamer by computational docking and application on an indirect competitive electrochemical aptasensor. Anal Bioanal Chem, 2021, 413: 3861-3872.

[61] GaoJ, LiuN, ZhangX, et al. . Utilizing the DNA aptamer to determine lethal α-amanitin in mushroom samples and urine by magnetic bead-ELISA (MELISA). Molecules, 2022, 27: 538.

[62] HeilkenbrinkerA, ReinemannC, StoltenburgR, et al. . Identification of the target binding site of ethanolamine-binding aptamers and its exploitation for ethanolamine detection. Anal Chem, 2015, 87: 677-685.

[63] GuoH, SunY, MaP, et al. . Sensitive detection of patulin based on Dnase I-assisted fluorescent aptasensor by using AuNCs-modified truncated aptamer. Food Control, 2022, 131. 108430

[64] EarnestKG, McConnellEM, HassanEM, et al. . Development and characterization of a DNA aptamer for MLL-AF9 expressing acute myeloid leukemia cells using whole cell-selex. Sci Rep, 2021, 11: 19174.

[65] YeH, DuanN, GuHJ, et al. . Fluorometric determination of lipopolysaccharides via changes of the graphene oxide-enhanced fluorescence polarization caused by truncated aptamers. Microchim Acta, 2019.

[66] BaiCJ, LuZW, JiangH, et al. . Aptamer selection and application in multivalent binding-based electrical impedance detection of inactivated H1N1 virus. Biosens Bioelectron, 2018, 110: 162-167.

[67] SoundyJ, DayD. Selection of DNA aptamers specific for live pseudomonas aeruginosa. PLoS ONE, 2017, 12. e0185385

[68] ZhengX, HuB, GaoSX, et al. . A saxitoxin-binding aptamer with higher affinity and inhibitory activity optimized by rational site-directed mutagenesis and truncation. Toxicon, 2015, 101: 41-47.

[69] VuCQ, RotkruaP, TantirungrotechaiY, et al. . Oligonucleotide hybridization combined with competitive antibody binding for the truncation of a high-affinity aptamer. Acs Comb Sci, 2017, 19: 609-617.

[70] XuXJ, DickeyDD, ChenSJ, et al. . Structural computational modeling of rna aptamers. Methods, 2016, 103: 175-179.

[71] WrengerC, ZhangY. Selection of a DNA aptamer against zearalenone and docking analysis for highly sensitive rapid visual detection with label-free aptasensor. Biomolecules, 2018, 66: 12102-12110.

[72] CataldoR, CiriacoF, AlfinitoE. A validation strategy for in silico generated aptamers. Comput Biol Chem, 2018, 77: 123-130.

[73] HaNR, JungIP, LaIJ, et al. . Ultra-sensitive detection of kanamycin for food safety using a reduced graphene oxide-based fluorescent aptasensor. Sci Rep-UK, 2017, 7: 40305.

[74] AlbadaHB, GolubE, WillnerI. Computational docking simulations of a DNA-aptamer for argininamide and related ligands. J Comput Aid Mol Des, 2015, 29: 643-654.

[75] VillaA, WohnertJ, StockG. Molecular dynamics simulation study of the binding of purine bases to the aptamer domain of the guanine sensing riboswitch. Nucleic Acids Res, 2009, 37: 4774-4786.

[76] YamasakiS, AmemiyaT, YabukiY, et al. . Togo-wf: Prediction of rna tertiary structures and rna-rna/protein interactions using the knime workflow. J Comput Aid Mol Des, 2019, 33: 497-507.

[77] NieJJ, YuanLY, HanXY, TianYP, ZhouND. Electrochemical detection of tobramycin based on enzymes-assisted dual signal amplification by using a novel truncated aptamer with high affinity. Biosens Bioelectron, 2018, 122: 254-262.

[78] ElleIC, KarlsenKK, TerpMG, et al. . Selection of LNA-containing DNA aptamers against recombinant human CD73. Mol Biosyst, 2015, 11: 1260-1270.

[79] SzameitK, BergK, KruspeS, et al. . Structure and target interaction of a G-quadruplex RNA-aptamer. Rna Biol, 2016, 13: 973-987.

[80] SunQ, SuoZ, PuH, et al. . Studies of the binding properties of the food preservative thiabendazole to DNA by computer simulations and NMR relaxation. Rsc Adv, 2018, 8: 20295-20303.

[81] LaoYH, PhuaKK, LeongKW. Aptamer nanomedicine for cancer therapeutics: barriers and potential for translation. ACS Nano, 2015, 9: 2235-2254.

[82] ZhouJ, RossiJ. Aptamers as targeted therapeutics: current potential and challenges. Nat Rev Drug Discov, 2017, 16: 181-202.

[83] ByunJ. Recent progress and opportunities for nucleic acid aptamers. Life (Basel), 2021, 11: 193.

[84] IsmailSI, AlshaerW. Therapeutic aptamers in discovery, preclinical and clinical stages. Adv Drug Deliv Rev, 2018, 134: 51-64.

[85] LeeCH, LeeSH, KimJH, et al. . Pharmacokinetics of a cholesterol-conjugated aptamer against the hepatitis c virus (hcv) NS5B protein. Mol Ther Nucleic Acids, 2015, 4. e254

[86] WinklerJ. Therapeutic oligonucleotides with polyethylene glycol modifications. Future Med Chem, 2015, 7: 1721-1731.

[87] DaPC, BlackshawE, MissailidisS, et al. . Pegylation and biodistribution of an anti-muc1 aptamer in MCF-7 tumor-bearing mice. Bioconjugate Chem, 2012, 23: 1377-1381.

[88] SeligerH, FröhlichA, MontenarhM, et al. . Oligonucleotide analogues with terminal 3′–3′- and 5′–5′-internucleotidic linkages as antisense inhibitors of viral gene expression. Nucleos Nucleot, 1991, 10: 469-477.

[89] ChakravarthyM, Aung-HtutMT, LeBT, et al. . Novel chemically-modified DNAzyme targeting integrin alpha-4 rna transcript as a potential molecule to reduce inflammation in multiple sclerosis. Sci Rep, 2017, 7: 1613.

[90] StulzE, BürgiHB, LeumannC. Zriv-tetraphenylporphyrinates as nuclease mimics structural, kinetic and mechanistic studies on phosphate diester transesterification. Chemistry, 2000, 6: 523-536.

[91] YangX, ZhuY, WangC, et al. . Alkylation of phosphorothioated thrombin binding aptamers improves the selectivity of inhibition of tumor cell proliferation upon anticoagulation. Biochim Biophys Acta Gen Subj, 2017, 1861: 1864-1869.

[92] NagahamaK, VeeduRN, WengelJ. Nuclease resistant methylphosphonate-DNA/LNA chimeric oligonucleotides. Bioorg Med Chem Lett, 2009, 19: 2707-2709.

[93] WuJ, WangS, LiX, et al. . Selective anti-melanoma effect of phosphothioated aptamer encapsulated by neutral cytidinyl/cationic lipids. Front Cell Dev Biol, 2021, 9. 660233

[94] AbeydeeraND, EgliM, CoxN, et al. . Evoking picomolar binding in RNA by a single phosphorodithioate linkage. Nucleic Acids Res, 2016, 44: 8052-8064.

[95] FlurS, MicuraR. Chemical synthesis of RNA with site-specific methylphosphonate modifications. Methods, 2016, 107: 79-88.

[96] AllemailemKS, AlmatroudiA, AlsahliMA, et al. . Recent advances in understanding oligonucleotide aptamers and their applications as therapeutic agents. 3 Biotech., 2020, 10: 551.

[97] ZhouY, KajinoR, IshiiS, et al. . Synthesis and evaluation of (s)-5′-c-aminopropyl and (s)-5′-c-aminopropyl-2′-arabinofluoro modified DNA oligomers for novel rnase h-dependent antisense oligonucleotides. Rsc Adv, 2020, 10: 41901-41914.

[98] ShchurVV, BurankovaYP, ZhauniarovichAI, et al. . 5'-dmt-protected double-stranded DNA: synthesis and competence to enzymatic reactions. Anal Biochem, 2021, 617. 114115

[99] LendellL, CumminsSRO, LisaM, et al. . Characterization of fully 2-modified oligoribonucleotide hetero and homoduplex hybridization and nuclease sensitivity. Nucleic Acids Res, 1995.

[100] NgEW, AdamisAP. Anti-VEGF aptamer (pegaptanib) therapy for ocular vascular diseases. Ann N Y Acad Sci, 2006, 1082: 151-171.

[101] ChenT, HongdilokkulN, LiuZ, et al. . Evolution of thermophilic DNA polymerases for the recognition and amplification of c2'-modified DNA. Nat Chem, 2016, 8: 556-562.

[102] FriedmanAD, KimD, LiuR. Highly stable aptamers selected from a 2'-fully modified fgmh RNA library for targeting biomaterials. Biomaterials, 2015, 36: 110-123.

[103] HoshinoH, KasaharaY, KuwaharaM, et al. . DNA polymerase variants with high processivity and accuracy for encoding and decoding locked nucleic acid sequences. J Am Chem Soc, 2020, 142: 21530-21537.

[104] KotkowiakW, Lisowiec-WachnickaJ, GryndaJ, et al. . Thermodynamic, anticoagulant, and antiproliferative properties of thrombin binding aptamer containing novel UNA derivative. Mol Ther Nucleic Acids, 2018, 10: 304-316.

[105] TeoRD, TeraiK, MiglioreA, et al. . Electron transfer characteristics of 2′-deoxy-2′-fluoro-arabinonucleic acid, a nucleic acid with enhanced chemical stability. Phys Chem Chem Phys, 2018, 20: 26063-26067.

[106] KumarP, TruongL, BakerYR, et al. . Synthesis, affinity for complementary RNA and DNA, and enzymatic stability of triazole-linked locked nucleic acids (t-LNAs). ACS Omega, 2018, 3: 6976-6987.

[107] ForsterC, ZydekM, RothkegelM, et al. . Properties of an LNA-modified ricin RNA aptamer. Biochem Biophys Res Commun, 2012, 419: 60-65.

[108] ShigdarS, SchrandB, GiangrandePH, et al. . Aptamers: cutting edge of cancer therapies. Mol Ther, 2021, 29: 2396-2411.

[109] BouchardPR, HutabaratRM, ThompsonKM. Discovery and development of therapeutic aptamers. Annu Rev Pharmacol Toxicol, 2010, 50: 237-257.

[110] SundaramP, KurniawanH, ByrneME, et al. . Therapeutic RNA aptamers in clinical trials. Eur J Pharm Sci, 2013, 48: 259-271.

[111] Kakiuchi-KiyotaS, WhiteleyLO, RyanAM, et al. . Development of a method for profiling protein interactions with lna-modified antisense oligonucleotides using protein microarrays. Nucleic Acid Ther, 2016, 26: 93-101.

[112] EngelhardtJA. Comparative renal toxicopathology of antisense oligonucleotides. Nucleic Acid Ther, 2016, 26: 199-209.

[113] ZengW, GuoL, XuS, et al. . High-throughput screening technology in industrial biotechnology. Trends Biotechnol, 2020, 38: 888-906.

[114] OuyangCH, ZhangSB, XueC, et al. . Precision-guided missile-like DNA nanostructure containing warhead and guidance control for aptamer-based targeted drug delivery into cancer cells in vitro and in vivo. J Am Chem Soc, 2020, 142: 1265-1277.

[115] LiuB, TangY, YangY, et al. . Design an aptamer-based sensitive lateral flow biosensor for rapid determination of isocarbophos pesticide in foods. Food Control, 2021.

[116] LiuYF, YuanHL, DingDQ, et al. . Establishment of a biosensor-based high-throughput screening platform for tryptophan overproduction. Acs Synth Biol, 2021, 10: 1373-1383.

[117] WuW, DuW, GallegoRP, et al. . Using osmotic stress to stabilize mannitol production in synechocystis sp. PCC6803. Biotechnol Biofuels, 2020, 13: 117.

[118] NaghshbandiMP, TabatabaeiM, AghbashloM, et al. . Progress toward improving ethanol production through decreased glycerol generation in saccharomyces cerevisiae by metabolic and genetic engineering approaches. Renew Sust Energ Rev, 2019, 115. 109353

[119] ElmoreJR, DexterGN, SalvachuaD, et al. . Production of itaconic acid from alkali pretreated lignin by dynamic two stage bioconversion. Nat Commun, 2021, 12: 2261.

[120] DengJ, ChenC, GuY, et al. . Creating an in vivo bifunctional gene expression circuit through an aptamer-based regulatory mechanism for dynamic metabolic engineering in bacillus subtilis. Metab Eng, 2019, 55: 179-190.

[121] JiangH, XuW, DingY, et al. . Quantitative analysis of yeast fermentation process using raman spectroscopy: comparison of cars and vcpa for variable selection. Spectrochim Acta A Mol Biomol Spectrosc, 2020, 228. 117781

[122] CaiR, ZhangZ, ChenH, et al. . A versatile signal-on electrochemical biosensor for staphylococcus aureus based on triple-helix molecular switch. Sens Actuat B Chem, 2021, 326. 128842

[123] WangY, SongW, ZhaoH, et al. . DNA walker-assisted aptasensor for highly sensitive determination of ochratoxin a. Biosens Bioelectron, 2021, 182. 113171

[124] DuH, DingM, LuoN, et al. . Design, synthesis, crystal structure and in vitro antimicrobial activity of novel 1,2,4-triazolo[1,5-a]pyrimidine-containing quinazolinone derivatives. Mol Divers, 2021, 25: 711-722.

[125] Ben AbdallahM, KarrayF, SayadiS. Production of polyhydroxyalkanoates by two halophilic archaeal isolates from chott el jerid using inexpensive carbon sources. Biomolecules, 2020, 10: 109.

[126] Ruiz-GilT, AcunaJJ, FujiyoshiS, et al. . Airborne bacterial communities of outdoor environments and their associated influencing factors. Environ Int, 2020, 145. 106156

[127] AbdelrasoulGN, AnwarA, MacKayS, et al. . DNA aptamer-based non-faradaic impedance biosensor for detecting E. coli. Anal Chim Acta, 2020, 1107: 135-144.

[128] JinCR, KimJY, KimDH, et al. . In vivo monitoring of intracellular metabolite in a microalgal cell using an aptamer/graphene oxide nanosheet complex. ACS Appl Bio Mater, 2021, 4: 5080-5089.

[129] Sonn-SegevA, BelacicK, BodrugT, et al. . Quantifying the heterogeneity of macromolecular machines by mass photometry. Nat Commun, 2020, 11: 1772.

[130] WuS, LiuY, SunH, et al. . An ssDNA aptamer specific for detection and purification of hexahistidine-tagged proteins. Anal Biochem, 2020, 607. 113893

[131] BeloborodovSS, BaoJ, KrylovaSM, et al. . Aptamer facilitated purification of functional proteins. J Chromatogr B Anal Technol Biomed Life Sci, 2018, 1073: 201-206.

[132] NegahdaryM. Aptamers in nanostructure-based electrochemical biosensors for cardiac biomarkers and cancer biomarkers: a review. Biosens Bioelectron, 2020, 152. 112018

[133] DengJ, TianF, LiuC, et al. . Rapid one-step detection of viral particles using an aptamer-based thermophoretic assay. J Am Chem Soc, 2021, 143: 7261-7266.

[134] YangL, YinX, AnB, et al. . Precise capture and direct quantification of tumor exosomes via a highly efficient dual-aptamer recognition-assisted ratiometric immobilization-free electrochemical strategy. Anal Chem, 2021, 93: 1709-1716.

[135] NingY, HuJ, LuF. Aptamers used for biosensors and targeted therapy. Biomed Pharmacother, 2020, 132. 110902

[136] AfrasiabiS, PourhajibagherM, RaoofianR, et al. . Therapeutic applications of nucleic acid aptamers in microbial infections. J Biomed Sci, 2020, 27: 6.

[137] KavrukM, CelikbicakO, OzalpVC, et al. . Antibiotic loaded nanocapsules functionalized with aptamer gates for targeted destruction of pathogens. Chem Commun (Camb), 2015, 51: 8492-8495.

[138] Habibi-YangjehA, Asadzadeh-KhaneghahS, FeizpoorS, et al. . Review on heterogeneous photocatalytic disinfection of waterborne, airborne, and foodborne viruses: can we win against pathogenic viruses?. J Colloid Interface Sci, 2020, 580: 503-514.

[139] ZhouX, PuH, SunDW. DNA functionalized metal and metal oxide nanoparticles: principles and recent advances in food safety detection. Crit Rev Food Sci Nutr, 2021, 61: 2277-2296.

[140] DanchukAI, KomovaNS, MobarezSN, et al. . Optical sensors for determination of biogenic amines in food. Anal Bioanal Chem, 2020, 412: 4023-4036.

[141] YanSR, ForoughiMM, SafaeiM, et al. . A review: recent advances in ultrasensitive and highly specific recognition aptasensors with various detection strategies. Int J Biol Macromol, 2020, 155: 184-207.

[142] ZhangK, LiH, WangW, et al. . Application of multiplexed aptasensors in food contaminants detection. ACS Sens, 2020, 5: 3721-3738.

[143] AhmedSR, KumarS, OrtegaGA, et al. . Target specific aptamer-induced self-assembly of fluorescent graphene quantum dots on palladium nanoparticles for sensitive detection of tetracycline in raw milk. Food Chem, 2021, 346. 128893

[144] JayanH, PuH, SunD-W. Recent development in rapid detection techniques for microorganism activities in food matrices using bio-recognition: a review. Trends Food Sci Tech, 2020, 95: 233-246.

[145] AbebeE, GugsaG, AhmedM. Review on major food-borne zoonotic bacterial pathogens. J Trop Med, 2020, 2020: 4674235.

[146] SharifiS, VahedSZ, AhmadianE, et al. . Detection of pathogenic bacteria via nanomaterials-modified aptasensors. Biosens Bioelectron, 2020, 150. 111933

[147] McConnellEM, NguyenJ, LiY. Aptamer-based biosensors for environmental monitoring. Front Chem, 2020, 8: 434.

[148] SchmitzFRW, ValerioA, de OliveiraD, et al. . An overview and future prospects on aptamers for food safety. Appl Microbiol Biot, 2020, 104: 6929-6939.

[149] XinJ, WangX, LiN, et al. . Recent applications of covalent organic frameworks and their multifunctional composites for food contaminant analysis. Food Chem, 2020, 330. 127255

[150] SiripongpredaT, SiralertmukulK, RodthongkumN. Colorimetric sensor and LDI-MS detection of biogenic amines in food spoilage based on porous PLA and graphene oxide. Food Chem, 2020, 329. 127165

[151] RifaiL, SalehFA. A review on acrylamide in food: occurrence, toxicity, and mitigation strategies. Int J Toxicol, 2020, 39: 93-102.

[152] DuanN, SongMQ, MiWY, et al. . Effectively selecting aptamers for targeting aromatic biogenic amines and their application in aptasensing establishment. J Agric Food Chem, 2021, 69: 14671-14679.

[153] HuLJ, WangLL, LuWW, et al. . Selection, identification and application of DNA aptamers for the detection of bifidobacterium breve. Rsc Adv, 2017, 7: 11672-11679.

[154] MishraS, WebsterP, DavisME. Pegylation significantly affects cellular uptake and intracellular trafficking of non-viral gene delivery particles. Eur J Cell Biol, 2004, 83: 97-111.

[155] ChenK, LiuJ, TongGX, et al. . Adipo8, a high-affinity DNA aptamer, can differentiate among adipocytes and inhibit intracellular lipid accumulation in vitro. Sci China Chem, 2015, 58: 1612-1620.

[156] LeeKY, KangH, RyuSH, et al. . Bioimaging of nucleolin aptamer-containing 5-(n-benzylcarboxyamide)-2′-deoxyuridine more capable of specific binding to targets in cancer cells. J Biomed Biotechnol, 2010, 2010. 168306

[157] AlShamailehH, VeeduRN. Next-generation nucleic acid aptamers with two-base-modified nucleotides have improved binding affinity and potency. ChemBioChem, 2017, 18: 1565-1567.

[158] ZhangL, YangZ, Le TrinhT, et al. . Aptamers against cells overexpressing glypican 3 from expanded genetic systems combined with cell engineering and laboratory evolution. Angew Chem Int Ed Engl, 2016, 55: 12372-12375.

[159] HiraoI, KimotoM, LeeKH. DNA aptamer generation by Exselex using genetic alphabet expansion with a mini-hairpin DNA stabilization method. Biochimie, 2018, 145: 15-21.

Funding

National Natural Science Foundation of China(42177212)

Fundamental Research Funds for the Central Universities(JUSRP21013)

RIGHTS & PERMISSIONS

Jiangnan University