Biotechnology Bulletin ›› 2020, Vol. 36 ›› Issue (1): 182-192.doi: 10.13560/j.cnki.biotech.bull.1985.2019-0568
Previous Articles Next Articles
WANG Xin1,2, ZHU Long-jiao1, XU Wen-tao1,3, ZHAI Chen4, WANG Shu-ya4, HUANG Wei-xia4
Received:
2019-06-22
Online:
2020-01-26
Published:
2020-01-08
WANG Xin, ZHU Long-jiao, XU Wen-tao, ZHAI Chen, WANG Shu-ya, HUANG Wei-xia. Research Progress on RNA-cleaving DNAzyme in the Detection of Pathogens[J]. Biotechnology Bulletin, 2020, 36(1): 182-192.
[1] Nayak M, Kotian A, Marathe S, et al.Detection of microorganisms using biosensors—A smarter way towards detection techniques[J]. Biosensors and Bioelectronics, 2009, 25(4):661-667. [2] Abubakar I, Irvine L, Aldus CF, et al.A systematic review of the clinical, public health and cost-effectiveness of rapid diagnostic tests for the detection and identification of bacterial intestinal pathogens in faeces and food[J]. Health Technology Assessment(Winchester, England), 2007, 11(36):1-216. [3] Principles of bacterial detection:biosensors, recognition receptors and microsystems[M]. Springer Science & Business Media, 2008. [4] Call DR.Challenges and opportunities for pathogen detection using DNA microarrays[J]. Crit Rev Microbiol, 2005, 31(2):91-99. [5] Lazcka O, Del Campo FJ, Munoz FX.Pathogen detection:A perspective of traditional methods and biosensors[J]. Biosensors and Bioelectronics, 2007, 22(7):1205-1217. [6] Velusamy V, Arshak K, Korostynska O, et al.An overview of foodb-orne pathogen detection:In the perspective of biosensors[J]. Biotechnology Advances, 2010, 28(2):232-254. [7] Yang L, Bashir R.Electrical/electrochemical impedance for rapid detection of foodborne pathogenic bacteria[J]. Biotechnology Advances, 2008, 26(2):135-150. [8] Arlett JL, Myers EB, Roukes ML.Comparative advantages of mechanical biosensors[J]. Nat Nanotechnol, 2011, 6(4):203. [9] Skottrup PD, Nicolaisen M, Justesen AF.Towards on-site pathogen detection using antibody-based sensors[J]. Biosensors and Bioelectronics, 2008, 24(3):339-348. [10] 董文娟, 王保亚, 彭文雯, 等. 索氏梭菌在艰难梭菌感染实验室检测中的影响分析[J]. 北京医学, 2019(3):202-205. [11] 孙淑娟. Development of FICA and UPLC-MS/MS for Simultaneous Determination of Aflatoxin B1 and Zearalenone in Chinese herbal medicines[D]. 北京:中国农业大学, 2018. [12] Brandon DL, Adams LM.Milk matrix effects on antibody binding analyzed by enzyme-linked immunosorbent assay and biolayer interferometry[J]. J Agric Food Chem, 2015, 63(13):3593-3598. [13] 梁华丽, 方毅. 简析食品微生物检测技术进展[J]. 食品工程, 2015(1):22-24. [14] Ali MM, Aguirre SD, Lazim H, et al.Fluorogenic DNAzyme probes as bacterial indicators[J]. Angew Chem Int Ed Engl, 2011, 50(16):3751-3754. [15] Li D, Song S, Fan C.Target-responsive structural switching for nucleic acid-based sensors[J]. Accounts of Chemical Research, 2010, 43(5):631-641. [16] Ellington AD, Szostak JW.In vitro selection of RNA molecules that bind specific ligands[J]. Nature, 1990, 346(6287):818. [17] Qi L, Zhao Y, Yuan H, et al.Amplified fluorescence detection of mercury(II)ions(Hg2+)using target-induced DNAzyme cascade with catalytic and molecular beacons[J]. Analyst, 2012, 137(12):2799-2805. [18] Gotrik MR, Feagin TA, Csordas AT, et al.Advancements in aptamer discovery technologies[J]. Accounts of Chemical Research, 2016, 49(9):1903-1910. [19] Hui CY, Liu M, Li Y, et al.A paper sensor printed with multifunctional bio/nano materials[J]. Angew Chem Int Ed Engl, 2018, 57(17):4549-4553. [20] 马芬, 张成孝. 增强型铅离子电化学发光传感器的研究[J]. 分析化学, 2009, 37(A02):107. [21] Li J, Lu Y.A highly sensitive and selective catalytic DNA biosensor for lead ions[J]. J Am Chem Soc, 2000, 122(42):10466-10467. [22] Liu J, Lu Y.Improving fluorescent DNAzyme biosensors by combining inter-and intramolecular quenchers[J]. Analytical Chemistry, 2003, 75(23):6666-6672. [23] 戢太云, 徐鲁荣, 周培. 核酸荧光探针检测铅离子的研究[J]. 分析测试学报, 2010(1):51-54. [24] Liu J, Lu Y.A colorimetric lead biosensor using DNAzyme-directed assembly of gold nanoparticles[J]. J Am Chem Soc, 2003, 125(22):6642-6643. [25] Liu D, Daubendiek SL, Zillman MA, et al.Rolling circle DNA synthesis:small circular oligonucleotides as efficient templates for DNA polymerases[J]. J Am Chem Soc, 1996, 118(7):1587-1594. [26] Wei W, Jia LY.Progress in aptamer screening methods[J]. Chinese J Anal Chem, 2009, 37(3):454-460. [27] Pichon V, Brothier F, Combès A.Aptamer-based-sorbents for sample treatment—a review[J]. Analytical and Bioanalytical Chemistry, 2015, 407(3):681-698. [28] Du F, Guo L, Qin Q, et al.Recent advances in aptamer-functionalized materials in sample preparation[J]. TrAC Trends in Analytical Chemistry, 2015, 67:134-146. [29] Gopinath SCB, Awazu K, Fons P, et al.A sensitive multilayered structure suitable for biosensing on the BioDVD platform[J]. Analytical Chemistry, 2009, 81(12):4963-4970. [30] Cao X, Li S, Chen L, et al.Combining use of a panel of ssDNA aptamers in the detection of Staphylococcus aureus[J]. Nucleic Acids Res, 2009, 37(14):4621-4628. [31] Morrison D, Rothenbroker M, Li Y.DNAzymes:selected for applications[J]. Small Methods, 2018, 2(3):1700319. [32] Schlosser K, Li Y.Biologically inspired synthetic enzymes made from DNA[J]. Chemistry & Biology, 2009, 16(3):311-322. [33] Silverman SK.In vitro selection, characterization, and application of deoxyribozymes that cleave RNA[J]. Nucleic Acids Res, 2005, 33(19):6151-6163. [34] Wolfe M, Ali M, Tram K, et al.A DNAzyme-based colorimetric paper sensor for Helicobacter pylori[J]. Angew Chem Int Ed Engl, 2019, 58(29):9907-9911. [35] Schlosser K, Li Y.A versatile endoribonuclease mimic made of DNA:characteristics and applications of the 8-17 RNA cleaving DNAzyme[J]. ChemBioChem, 2010, 11(7):866-879. [36] He S, Qu L, Shen Z, et al.Highly specific recognition of breast tumors by an RNA-cleaving fluorogenic DNAzyme probe[J]. Analytical Chemistry, 2014, 87(1):569-577. [37] Shen Z, Wu Z, Chang D, et al.A catalytic DNA activated by a specific strain of bacterial pathogen[J]. Angew Chem Int Ed Engl, 2016, 55(7):2431-2434. [38] Li Y.Advancements in using reporter DNAzymes for identifying pathogenic bacteria at speed and with convenience[J]. Future Microbiology, 2011, 6(9):973-976. [39] DeStefano JJ, Cristofaro JV. Selection of primer-template sequences that bind human immunodeficiency virus reverse transcriptase with high affinity[J]. Nucleic Acids Res, 2006, 34(1):130-139. [40] Vivekananda J, Kiel JL.Anti-Francisella tularensis DNA aptamers detect tularemia antigen from different subspecies by Aptamer-Linked Immobilized Sorbent Assay[J]. Laboratory Investigation, 2006, 86(6):610. [41] Shen Y, Brennan JD, Li Y.Characterizing the secondary structure and identifying functionally essential nucleotides of pH6DZ1, a fluorescence-signaling and RNA-cleaving deoxyribozyme[J]. Biochemistry, 2005, 44(36):12066-12076. [42] Chiuman W, Li Y.Evolution of high-branching deoxyribozymes from a catalytic DNA with a three-way junction[J]. Chemistry & Biology, 2006, 13(10):1061-1069. [43] Chiuman W, Li Y.Revitalization of six abandoned catalytic DNA species reveals a common three-way junction framework and diverse catalytic cores[J]. J Mol Biol, 2006, 357(3):748-754. [44] Liu M, Zhang Q, Li Z, et al.Programming a topologically constrained DNA nanostructure into a sensor[J]. Nature Communications, 2016, 7:12074. [45] Ali MM, Li Y.Colorimetric sensing by using allosteric-DNAzyme-coupled rolling circle amplification and a peptide nucleic acid-organic dye probe[J]. Angewandte Chemie, 2009, 121(19):3564-3567. [46] Xiao SJ, Hu PP, Li YF, et al.Aptamer-mediated turn-on fluorescence assay for prion protein based on guanine quenched fluophor[J]. Talanta, 2009, 79(5):1283-1286. [47] Kuai H, Zhao Z, Mo L, et al.Circular bivalent aptamers enable in vivo stability and recognition[J]. J Am Chem Soc, 2017, 139(27):9128-9131. [48] Dong H, Han L, Wu ZS, et al.Biostable aptamer rings conjugated for targeting two biomarkers on circulating tumor cells in vivo with great precision[J]. Chem Mater, 2017, 29(24):10312-10325. [49] Fire A, Xu SQ.Rolling replication of short DNA circles[J]. Proc Natil Acad Sci USA, 1995, 92(10):4641-4645. [50] Liu M, Hui CY, Zhang Q, et al.Target-induced and equipment-free DNA amplification with a simple paper device[J]. Angew Chem Int Ed Engl, 2016, 55(8):2709-2713. [51] Carrasquilla C, Little JRL, Li Y, et al.Patterned paper sensors printed with long-chain DNA aptamers[J]. Chemistry-A European Journal, 2015, 21(20):7369-7373. [52] Liu M, Zhang Q, Chang D, et al.A DNAzyme feedback amplification strategy for biosensing[J]. Angew Chem Int Ed Engl, 2017, 56(22):6142-6146. [53] Chiuman W, Li Y.Revitalization of six abandoned catalytic DNA species reveals a common three-way junction framework and diverse catalytic cores[J]. J Mol Biol, 2006, 357(3):748-754. [54] Shen Y, Chiuman W, Brennan JD, et al.Catalysis and rational engineering of trans-acting pH6DZ1, an RNA-cleaving and fluorescence-signaling deoxyribozyme with a four-way junction structure[J]. ChemBioChem, 2006, 7(9):1343-1348. [55] Ali MM, Kandadai SA, Li Y.Characterization of pH3DZ1—An RNA-cleaving deoxyribozyme with optimal activity at pH 3[J]. Canadian Journal of Chemistry, 2007, 85(4):261-273. [56] Chiuman W, Li Y.Efficient signaling platforms built from a small catalytic DNA and doubly labeled fluorogenic substrates[J]. Nucleic Acids Res, 2006, 35(2):401-405. [57] Shen Z, Wu Z, Chang D, et al.A catalytic DNA activated by a specific strain of bacterial pathogen[J]. Angew Chem Int Ed Engl, 2016, 55(7):2431-2434. [58] Yousefi H, Ali MM, Su HM, et al.Sentinel wraps:Real-time monitoring of food contamination by printing dnazyme probes on food packaging[J]. ACS Nano, 2018, 12(4):3287-3294. [59] He S, Qu L, Shen Z, et al.Highly specific recognition of breast tumors by an RNA-cleaving fluorogenic DNAzyme probe[J]. Analytical Chemistry, 2014, 87(1):569-577. [60] Di Giusto DA, Wlassoff WA, Gooding JJ, et al.Proximity extension of circular DNA aptamers with real-time protein detection[J]. Nucleic Acids Res, 2005, 33(6):e64-e64. [61] Yang L, Fung CW, Cho EJ, et al.Real-time rolling circle amplification for protein detection[J]. Analytical Chemistry, 2007, 79(9):3320-3329. [62] Zhou L, Ou LJ, Chu X, et al.Aptamer-based rolling circle amplification:a platform for electrochemical detection of protein[J]. Analytical Chemistry, 2007, 79(19):7492-7500. [63] Cheglakov Z, Weizmann Y, Basnar B, et al.Diagnosing viruses by the rolling circle amplified synthesis of DNAzymes[J]. Organic & Biomolecular Chemistry, 2007, 5(2):223-225. [64] Tian Y, He Y, Mao C.Cascade signal amplification for DNA detection[J]. ChemBioChem, 2006, 7(12):1862-1864. [65] Zhao W, Ali MM, Brook MA, et al.Rolling-circle-amplifikation:anwendungen in der nanotechnologie und in der biodetektion mit funktionellen nucleinsäuren[J]. Angewandte Chemie, 2008, 120(34):6428-6436. [66] Zhao W, Ali MM, Brook MA, et al.Rolling circle amplification:applications in nanotechnology and biodetection with functional nucleic acids[J]. Angew Chem Int Ed Engl, 2008, 47(34):6330-6337. [67] Kushon SA, Jordan JP, Seifert JL, et al.Effect of secondary structure on the thermodynamics and kinetics of PNA hybridization to DNA hairpins[J]. J Am Chem Soc, 2001, 123(44):10805-10813. [68] Komiyama M, Ye S, Liang X, et al.PNA for one-base differentiating protection of DNA from nuclease and its use for SNPs detection[J]. J Am Chem Soc, 2003, 125(13):3758-3762. [69] Dilek I, Madrid M, Singh R, et al.Effect of PNA backbone modifications on cyanine dye binding to PNA-DNA duplexes investigated by optical spectroscopy and molecular dynamics simulations[J]. J Am Chem Soc, 2005, 127(10):3339-3345. [70] Wilhelmsson LM, Nordén B, Mukherjee K, et al.Genetic screening using the colour change of a PNA-DNA hybrid-binding cyanine dye[J]. Nucleic Acids Res, 2002, 30(2):e3-e3. [71] Xiang Y, Lu Y.Using personal glucose meters and functional DNA sensors to quantify a variety of analytical targets[J]. Nature Chemistry, 2011, 3(9):697. [72] Du Y, Pothukuchy A, Gollihar JD, et al.Coupling sensitive nucleic acid amplification with commercial pregnancy test strips[J]. Angew Chem Int Ed Engl, 2017, 56(4):992-996. [73] Liu M, Zhang Q, Kannan B, et al.Self-assembled functional DNA superstructures as high-density and versatile recognition elements for printed paper sensors[J]. Angewandte Chemie, 2018, 130(38):12620-12623. [74] Lv Y, Hu R, Zhu G, et al.Preparation and biomedical applications of programmable and multifunctional DNA nanoflowers[J]. Nature Protocols, 2015, 10(10):1508. [75] Wolfe M, Ali M, Tram K, et al.A DNAzyme-based Colorimetric Paper Sensor for Helicobacter pylori[J]. Angew Chem Int Ed Engl, 2019. [76] Liu M, Yin Q, Chang Y, et al.In vitro selection of circular DNA aptamers for biosensing applications[J]. Angew Chem Int Ed Engl, 2019, 58(24):8013-8017. [77] Carrasquilla C, Kapteyn E, Li Y, et al.Sol-Gel-derived biohybrid materials incorporating long-Chain DNA aptamers[J]. Angew Chem Int Ed Engl, 2017, 56(36):10686-10690. |
[1] | ZHANG Kun, YAN Chang, TIAN Xin-peng. Research Progress in Microbial Single Cell Separation Methods [J]. Biotechnology Bulletin, 2023, 39(9): 1-11. |
[2] | JIANG Run-hai, JIANG Ran-ran, ZHU Cheng-qiang, HOU Xiu-li. Research Progress in Mechanisms of Microbial-enhanced Phytoremediation for Lead-contaminated Soil [J]. Biotechnology Bulletin, 2023, 39(8): 114-125. |
[3] | ZHAO Lin-yan, XU Wu-mei, WANG Hao-ji, WANG Kun-yan, WEI Fu-gang, YANG Shao-zhou, GUAN Hui-lin. Effects of Applying Biochar on the Rhizosphere Fungal Community and Survival Rate of Panax notoginseng Under Continuous Cropping [J]. Biotechnology Bulletin, 2023, 39(7): 219-227. |
[4] | ZHANG Jing, ZHANG Hao-rui, CAO Yun, HUANG Hong-ying, QU Ping, ZHANG Zhi-ping. Research Progress in Thermophilic Microorganisms for Cellulose Degradation [J]. Biotechnology Bulletin, 2023, 39(6): 73-87. |
[5] | YU Yang, LIU Tian-hai, LIU Li-xu, TANG Jie, PENG Wei-hong, CHEN Yang, TAN Hao. Study on Aerosol Microbial Community in the Production Workshop of Morel Spawn [J]. Biotechnology Bulletin, 2023, 39(5): 267-275. |
[6] | ZHANG Xue-ping, LU Yu-qing, ZHANG Yue-qian, LI Xiao-juan. Advances in Plant Extracellular Vesicles and Analysis Techniques [J]. Biotechnology Bulletin, 2023, 39(5): 32-43. |
[7] | ZHANG Hua-xiang, XU Xiao-ting, ZHENG Yun-ting, XIAO Chun-qiao. Roles of Phosphate-solubilizing Microorganisms in the Passivation and Phytoremediation of Heavy Metal Contaminated Soil [J]. Biotechnology Bulletin, 2023, 39(3): 52-58. |
[8] | ZHOU Xi-wen, CHENG Ke, ZHU Hong-liang. Research Progress in the Approaches to in vivo RNA Secondary Structure Profiling in Plants [J]. Biotechnology Bulletin, 2023, 39(2): 51-62. |
[9] | LI Xin-yue, ZHOU Ming-hai, FAN Ya-chao, LIAO Sha, ZHANG Feng-li, LIU Chen-guang, SUN Yue, ZHANG Lin, ZHAO Xin-qing. Research Progress in the Improvement of Microbial Strain Tolerance and Efficiency of Biological Manufacturing Based on Transporter Engineering [J]. Biotechnology Bulletin, 2023, 39(11): 123-136. |
[10] | HU Jin-chao, SHEN Wen-qi, XU Chao-ye, FAN Ya-qi, LU Hao-yu, JIANG Wen-jie, LI Shi-long, JIN Hong-chen, LUO Jian-mei, WANG Min. Research Advances in the Enhancement of Microbial Tolerance to Acid Stress [J]. Biotechnology Bulletin, 2023, 39(11): 137-149. |
[11] | WANG Chen-yu, ZHOU Chu-yuan, HE Di, FAN Zi-hao, WANG Meng-meng, YANG Liu-yan. Role and Mechanism of Polyphosphate in the Microbial Response to Environmental Stresses [J]. Biotechnology Bulletin, 2023, 39(11): 168-181. |
[12] | WAN Qi-wu, BAO Xu-dong, DING Ke, MOU Hua-ming, LUO Yang. Research Progress in Microfluidic Technology in the Detection of Pathogenic Microorganisms [J]. Biotechnology Bulletin, 2023, 39(10): 107-114. |
[13] | GUO Wen-bo, LU Yang, SUI Li, ZHAO Yu, ZOU Xiao-wei, ZHANG Zheng-kun, LI Qi-yun. Preparation and Application of Polyclonal Antibodies Against Beauveria bassiana Mycovirus BbPmV-4 Coat Protein [J]. Biotechnology Bulletin, 2023, 39(10): 58-67. |
[14] | LI Hui-jie, DONG Lian-hua, CHEN Gui-fang, LIU Si-yuan, YANG Jia-yi, YANG Jing-ya. Establishment of Droplet Digital PCR Assay for Quantitative Detection of Pseudomonas cocovenenans in Foods [J]. Biotechnology Bulletin, 2023, 39(1): 127-136. |
[15] | CHEN Xiao-lin, LIU Yang-er, XU Wen-tao, GUO Ming-zhang, LIU Hui-lin. Application of Synthetic Biology Based Whole-cell Biosensor Technology in the Rapid Detection of Food Safety [J]. Biotechnology Bulletin, 2023, 39(1): 137-149. |
Viewed | ||||||
Full text |
|
|||||
Abstract |
|
|||||