Please wait a minute...

中国生物工程杂志

CHINA BIOTECHNOLOGY
中国生物工程杂志
中国生物工程杂志  2022, Vol. 42 Issue (9): 67-82    DOI: 10.13523/j.cb.2203060
综述     
核糖核酸调节子的构建与即时检测中的应用*
梁书瑞,李娇娇,齐浩**()
天津大学化工学院 系统生物工程教育部重点实验室 天津化学化工协同创新中心合成生物学平台 天津 300072
Construction of Riboregulator in the Application of Point-of-care Testing
LIANG Shu-rui,LI Jiao-jiao,QI Hao**()
Synthetic Biology Research Platform, Tianjin Collaborative Innovation Center of Chemical Science and Engineering,Key Laboratory of Systems Bioengineering of Ministry of Education, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
 全文: PDF(5464 KB)   HTML
摘要：

合成生物学专注于可重复利用模块和元件的工程化设计,并在生物系统中表现出良好的行为和功能。在无细胞蛋白表达系统中,核糖核酸调节子作为即时检测中的重要传感元件,通过靶标分子的诱导使其自身结构发生变化,进而调控下游基因的表达。系统介绍不同类型的核糖核酸调节子及其作用原理,包括一代核糖核酸调节子、toehold开关、功能拓展的核糖核酸调节子和核糖开关。详细阐明构建核糖核酸调节子的设计-测试-分析过程:计算机辅助设计、基因表达测试和结构功能化分析。汇总基于核糖核酸调节子的体外即时检测应用,重点总结toehold开关介导的病原菌核酸检测和核糖开关参与的小分子检测。讨论当前无细胞即时检测的特点、挑战和发展趋势,为开发新型核糖核酸调节子和即时检测工具提供思路和参考。
关键词： 核糖核酸调节子;  Toehold 开关;  核糖开关;  无细胞蛋白表达;  即时检测    
Abstract:

Ongoing efforts in synthetic biology are focused on the design of reusable and modular fragments that demonstrate well-characterized behaviors and functionalities in biological systems. In the cell-free protein expression system, riboregulators are developed as an important sensing element in point-of-care testing, which can change their structure through the induction of target molecules, thereby regulating the expression of downstream genes. Different types of riboregulators and their action mechanisms are systematically introduced, including traditional riboregulators, toehold switch, toehold repressor, three-way junction repressor, small transcription activating RNA, and riboswitch. The main processes of constructing riboregulators are described in detail: designing with computers, testing gene expression, and analyzing the functional structure. Finally, the applications of in vitro point-of-care testing (POCT) based on riboregulators are summarized, mainly including pathogen nucleic acid detection based on toehold switch and small molecule detection mediated by riboswitch. The characteristics, challenges, and development tendencies of POCT in the cell-free system are discussed and summarized. In conclusion, the construction and application of riboregulators have opened up a new direction in the biosensing field. This article is expected to provide some helpful insight into the development of new riboregulators and POCT tools.
Key words: Riboregulator    Toehold switch    Riboswitch    Cell-free protein synthesis    Point-of-care testing (POCT)
收稿日期: 2022-03-26 出版日期: 2022-10-10
ZTFLH:  Q78  
基金资助: * 国家自然科学基金(21778039);国家自然科学基金(21621004);国家重点研发计划(2019YFA0904103)
通讯作者: 齐浩     E-mail: haoq@tju.edu.cn
服务　　
把本文推荐给朋友
加入引用管理器
E-mail Alert
RSS
作者相关文章　　
梁书瑞
李娇娇
齐浩

引用本文:

梁书瑞,李娇娇,齐浩. 核糖核酸调节子的构建与即时检测中的应用*[J]. 中国生物工程杂志, 2022, 42(9): 67-82.

LIANG Shu-rui,LI Jiao-jiao,QI Hao. Construction of Riboregulator in the Application of Point-of-care Testing. China Biotechnology, 2022, 42(9): 67-82.

链接本文:

https://manu60.magtech.com.cn/biotech/CN/10.13523/j.cb.2203060    或    https://manu60.magtech.com.cn/biotech/CN/Y2022/V42/I9/67

图1  位于5'-非翻译区的核糖核酸调节子
图2  一代核糖核酸调节子的作用机制
图3  不同作用原理的核糖核酸调节子
图4  核糖开关的调控机制
分类 名称 调节类型 动态范围
(激活/抑制倍数)		 设计来源 参考文献
一代核糖核酸调节子 RR10、RR12 翻译激活 8~19 从头设计 [9]
RAJ11、RAJ12 翻译激活 11.2~26.7 细菌sRNA、人工结构 [32]
RR42、RR12y 翻译激活 70~200 RR10、RR12 [33]
二代核糖核酸调节子 Toehold switch 翻译激活 >400 从头设计 [10]
功能拓展的调节子 STARs 转录激活 94~9 000 转录衰减 [19,21]
3WJ repressor 翻译抑制 43 从头设计 [16]
Toehold repressor 翻译抑制 122 从头设计 [16]
表1  核糖核酸调节子的特点
图5  工程化核糖核酸调节子的设计-测试-分析循环
图6  纸上无细胞传感装置
图7  基于toehold开关的即时检测
图8  SNIPR设计原理
图9  基于核糖开关的即时检测
无细胞系统 开关类型 检测对象 报告蛋白 检测限 检测时间 参考文献
PURE Toehold switch Zika virus LacZ 2.8 fmol/L 3 h [60]
PURE Toehold switch Dengue virus LacZ 5.23 nmol/L 3 h [61]
PURE Toehold switch Norovirus LacZα/LacZω 270 zmol/L 3~6 h [62]
E. coli Toehold switch RSV LacZ 91 amol/L 2.5 h [63]
N. Tabassum leaf STAR Plant pathogen C23DO 4.4 pmol/L 2.5 h [64]
E. coli Toehold switch Shiga toxin gene LacZ 5 nmol/L 1 h [65]
PURE Riboswitch Theophylline LacZ 1 mmol/L 35 min [73]
PURE Toehold switch SARS-CoV-2 GFP 1 800 copies 2 h [75]
E. coli Toehold switch SARS-CoV-2 NanoLuc 10 nmol/L 0.5 h [76]
PURE Toehold switch Gut bacteria GFP 30 amol/L 3~5 h [78]
PURE SNIPR SNV LacZ 10 fmol/L 1 h [79]
E. coli Riboswitch Fluoride C23DO 2 ppm 1 h [81]
表2  核糖核酸调节子介导的无细胞生物传感器
[1] Patel S, Panchasara H, Braddick D, et al. Synthetic small RNAs: current status, challenges, and opportunities. Journal of Cellular Biochemistry, 2018, 119(12): 9619-9639.
doi: 10.1002/jcb.27252 pmid: 30010218
[2] Rossetti M, del Grosso E, Ranallo S, et al. Programmable RNA-based systems for sensing and diagnostic applications. Analytical and Bioanalytical Chemistry, 2019, 411(19): 4293-4302.
doi: 10.1007/s00216-019-01622-7 pmid: 30734852
[3] Tietze L, Lale R. Importance of the 5' regulatory region to bacterial synthetic biology applications. Microbial Biotechnology, 2021, 14(6): 2291-2315.
doi: 10.1111/1751-7915.13868 pmid: 34171170
[4] Steitz J A, Jakes K. How ribosomes select initiator regions in mRNA:base pair formation between the 3' Terminus of 16S rRNA and the mRNA during initiation of protein synthesis in Escherichia coli. Proceedings of the National Academy of Sciences of the United States of America, 1975, 72(12): 4734-4738.
[5] de Smit M H, van Duin J. Control of translation by mRNA secondary structure in Escherichia coli. A quantitative analysis of literature data. Journal of molecular biology, 1994, 244(2): 144-150.
pmid: 7966326
[6] Duval M, Simonetti A, Caldelari I, et al. Multiple ways to regulate translation initiation in bacteria: Mechanisms, regulatory circuits, dynamics. Biochimie, 2015, 114: 18-29.
[7] Huang X, Zhang X N, Zhou Y F, et al. Directed evolution of the 5'-untranslated region of the phoA gene in Escherichia coli simultaneously yields a stronger promoter and a stronger Shine-Dalgarno sequence. Biotechnology Journal, 2006, 1(11): 1275-1282.
pmid: 17109483
[8] Bonde M T, Pedersen M, Klausen M S, et al. Predictable tuning of protein expression in bacteria. Nature Methods, 2016, 13(3): 233-236.
doi: 10.1038/nmeth.3727 pmid: 26752768
[9] Isaacs F J, Dwyer D J, Ding C, et al. Engineered riboregulators enable post-transcriptional control of gene expression. Nature Biotechnology, 2004, 22(7): 841-847.
pmid: 15208640
[10] Green A A, Silver P A, Collins J J, et al. Toehold switches: de-novo-designed regulators of gene expression. Cell, 2014, 159(4): 925-939.
doi: 10.1016/j.cell.2014.10.002 pmid: 25417166
[11] Simmel F C, Yurke B, Singh H R. Principles and applications of nucleic acid strand displacement reactions. Chemical Reviews, 2019, 119(10): 6326-6369.
doi: 10.1021/acs.chemrev.8b00580 pmid: 30714375
[12] Chau T H T, Mai D H A, Pham D N, et al. Developments of riboswitches and toehold switches for molecular detection-biosensing and molecular diagnostics. International Journal of Molecular Sciences, 2020, 21(9): 3192.
doi: 10.3390/ijms21093192
[13] Kittle J D, Simons R W, Lee J, et al. Insertion sequence IS10 anti-sense pairing initiates by an interaction between the 5' end of the target RNA and a loop in the anti-sense RNA. Journal of Molecular Biology, 1989, 210(3): 561-572.
pmid: 2482367
[14] Mutalik V K, Qi L, Guimaraes J C, et al. Rationally designed families of orthogonal RNA regulators of translation. Nature Chemical Biology, 2012, 8(5): 447-454.
doi: 10.1038/nchembio.919 pmid: 22446835
[15] Peters G, Maertens J, Lammertyn J, et al. Exploring of the feature space of de novo developed post-transcriptional riboregulators. PLoS Computational Biology, 2018, 14(8): e1006170.
doi: 10.1371/journal.pcbi.1006170
[16] Kim J, Zhou Y, Carlson P D, et al. De novo-designed translation-repressing riboregulators for multi-input cellular logic. Nature Chemical Biology, 2019, 15(12): 1173-1182.
doi: 10.1038/s41589-019-0388-1 pmid: 31686032
[17] Stanton B C, Nielsen A A K, Tamsir A, et al. Genomic mining of prokaryotic repressors for orthogonal logic gates. Nature Chemical Biology, 2014, 10(2): 99-105.
doi: 10.1038/nchembio.1411 pmid: 24316737
[18] Brantl S, Wagner E G H. Antisense RNA-mediated transcriptional attenuation: an in vitro study of plasmid pT181. Molecular Microbiology, 2000, 35(6): 1469-1482.
pmid: 10760147
[19] Chappell J, Takahashi M K, Lucks J B. Creating small transcription activating RNAs. Nature Chemical Biology, 2015, 11(3): 214-220.
doi: 10.1038/nchembio.1737 pmid: 25643173
[20] Meyer S, Chappell J, Sankar S, et al. Improving fold activation of small transcription activating RNAs (STARs) with rational RNA engineering strategies. Biotechnology and Bioengineering, 2016, 113(1): 216-225.
doi: 10.1002/bit.25693 pmid: 26134708
[21] Chappell J, Westbrook A, Verosloff M, et al. Computational design of small transcription activating RNAs for versatile and dynamic gene regulation. Nature Communications, 2017, 8(1): 1051.
doi: 10.1038/s41467-017-01082-6 pmid: 29051490
[22] Hollands K, Proshkin S, Sklyarova S, et al. Riboswitch control of Rho-dependent transcription termination. Proceedings of the National Academy of Sciences of the United States of America, 2012, 109(14): 5376-5381.
[23] Haller A, Rieder U, Aigner M, et al. Conformational capture of the SAM-II riboswitch. Nature Chemical Biology, 2011, 7(6): 393-400.
doi: 10.1038/nchembio.562 pmid: 21532598
[24] Cheah M T, Wachter A, Sudarsan N, et al. Control of alternative RNA splicing and gene expression by eukaryotic riboswitches. Nature, 2007, 447(7143): 497-500.
doi: 10.1038/nature05769
[25] Grundy F J, Henkin T M. tRNA as a positive regulator of transcription antitermination in B. subtilis. Cell, 1993, 74(3): 475-482.
pmid: 8348614
[26] Serganov A, Nudler E. A decade of riboswitches. Cell, 2013, 152(1-2): 17-24.
doi: 10.1016/j.cell.2012.12.024 pmid: 23332744
[27] Kumar D, An C I, Yokobayashi Y. Conditional RNA interference mediated by allosteric ribozyme. Journal of the American Chemical Society, 2009, 131(39): 13906-13907.
doi: 10.1021/ja905596t pmid: 19788322
[28] Jaffrey S R. RNA-based fluorescent biosensors for detecting metabolites in vitro and in living cells. Advances in Pharmacology, 2018, 82: 187-203.
[29] Paige J S, Wu K Y, Jaffrey S R. RNA mimics of green fluorescent protein. Science, 2011, 333(6042): 642-646.
doi: 10.1126/science.1207339 pmid: 21798953
[30] Filonov G S, Moon J D, Svensen N, et al. Broccoli: rapid selection of an RNA mimic of green fluorescent protein by fluorescence-based selection and directed evolution. Journal of the American Chemical Society, 2014, 136(46): 16299-16308.
doi: 10.1021/ja508478x pmid: 25337688
[31] Sefah K, Shangguan D H, Xiong X L, et al. Development of DNA aptamers using cell-SELEX. Nature Protocols, 2010, 5(6): 1169-1185.
doi: 10.1038/nprot.2010.66 pmid: 20539292
[32] Rodrigo G, Landrain T E, Jaramillo A. De novo automated design of small RNA circuits for engineering synthetic riboregulation in living cells. Proceedings of the National Academy of Sciences of the United States of America, 2012, 109(38): 15271-15276.
[33] Callura J M, Cantor C R, Collins J J. Genetic switchboard for synthetic biology applications. Proceedings of the National Academy of Sciences of the United States of America, 2012, 109(15): 5850-5855.
[34] Chappell J, Watters K E, Takahashi M K, et al. A renaissance in RNA synthetic biology: new mechanisms, applications and tools for the future. Current Opinion in Chemical Biology, 2015, 28: 47-56.
doi: 10.1016/j.cbpa.2015.05.018 pmid: 26093826
[35] Lee Y J, Moon T S. Design rules of synthetic non-coding RNAs in bacteria. Methods, 2018, 143: 58-69.
doi: S1046-2023(17)30338-9 pmid: 29309838
[36] Zuker M. On finding all suboptimal foldings of an RNA molecule. Science, 1989, 244(4900): 48-52.
pmid: 2468181
[37] Busch A, Richter A S, Backofen R. Intarna: efficient prediction of bacterial sRNA targets incorporating target site accessibility and seed regions. Bioinformatics, 2008, 24(24): 2849-2856.
doi: 10.1093/bioinformatics/btn544 pmid: 18940824
[38] Zadeh J N, Steenberg C D, Bois J S, et al. Nupack: analysis and design of nucleic acid systems. Journal of Computational Chemistry, 2011, 32(1): 170-173.
doi: 10.1002/jcc.21596 pmid: 20645303
[39] Proctor J R, Meyer I M. COFOLD : an RNA secondary structure prediction method that takes co-transcriptional folding into account. Nucleic Acids Research, 2013, 41(9): e102.
doi: 10.1093/nar/gkt174
[40] Rodríguez-Serrano A F, Hsing I M. 110th anniversary: engineered ribonucleic acid control elements as biosensors for in vitro diagnostics. Industrial & Engineering Chemistry Research, 2019, 58(37): 17174-17181.
doi: 10.1021/acs.iecr.9b03963
[41] Wu M J, Andreasson J O L, Kladwang W, et al. Automated design of diverse stand-alone riboswitches. ACS Synthetic Biology, 2019, 8(8): 1838-1846.
doi: 10.1021/acssynbio.9b00142 pmid: 31298841
[42] Valeri J A, Collins K M, Ramesh P, et al. Sequence-to-function deep learning frameworks for engineered riboregulators. Nature Communications, 2020, 11(1): 5058.
doi: 10.1038/s41467-020-18676-2 pmid: 33028819
[43] Angenent-Mari N M, Garruss A S, Soenksen L R, et al. A deep learning approach to programmable RNA switches. Nature Communications, 2020, 11(1): 5057.
doi: 10.1038/s41467-020-18677-1 pmid: 33028812
[44] Findeiβ S, Etzel M, Will S, et al. Design of artificial riboswitches as biosensors. Sensors (Basel, Switzerland), 2017, 17(9): 1990.
doi: 10.3390/s17091990
[45] Senoussi A, Lee Tin Wah J, Shimizu Y, et al. Quantitative characterization of translational riboregulators using an in vitro transcription-translation system. ACS Synthetic Biology, 2018, 7(5): 1269-1278.
doi: 10.1021/acssynbio.7b00387 pmid: 29617125
[46] Perez J G, Stark J C, Jewett M C. Cell-free synthetic biology: engineering beyond the cell. Cold Spring Harbor Perspectives in Biology, 2016, 8(12): a023853.
doi: 10.1101/cshperspect.a023853
[47] Lynch S A, Desai S K, Sajja H K, et al. A high-throughput screen for synthetic riboswitches reveals mechanistic insights into their function. Chemistry & Biology, 2007, 14(2): 173-184.
doi: 10.1016/j.chembiol.2006.12.008
[48] Kirchner M, Schorpp K, Hadian K, et al. An in vivo high-throughput screening for riboswitch ligands using a reverse reporter gene system. Scientific Reports, 2017, 7(1): 7732.
doi: 10.1038/s41598-017-07870-w pmid: 28798404
[49] Silverman A D, Karim A S, Jewett M C. Cell-free gene expression: an expanded repertoire of applications. Nature Reviews Genetics, 2020, 21(3): 151-170.
doi: 10.1038/s41576-019-0186-3 pmid: 31780816
[50] Sun Z Z, Yeung E, Hayes C A, et al. Linear DNA for rapid prototyping of synthetic biological circuits in an Escherichia coli based TX-TL cell-free system. ACS Synthetic Biology, 2014, 3(6): 387-397.
doi: 10.1021/sb400131a
[51] Ayoubi-Joshaghani M H, Dianat-Moghadam H, Seidi K, et al. Cell-free protein synthesis: the transition from batch reactions to minimal cells and microfluidic devices. Biotechnology and Bioengineering, 2020, 117(4): 1204-1229.
doi: 10.1002/bit.27248 pmid: 31840797
[52] Hu C Y, Takahashi M K, Zhang Y, et al. Engineering a functional small RNA negative autoregulation network with model-guided design. ACS Synthetic Biology, 2018, 7(6): 1507-1518.
doi: 10.1021/acssynbio.7b00440 pmid: 29733627
[53] Kim J, Quijano J F, Kim J, et al. Synthetic logic circuits using RNA aptamer against T 7 RNA polymerase. Biotechnology Journal, 2022, 17(3): e2000449.
[54] Dwidar M, Seike Y, Kobori S, et al. Programmable artificial cells using histamine-responsive synthetic riboswitch. Journal of the American Chemical Society, 2019, 141(28): 11103-11114.
doi: 10.1021/jacs.9b03300 pmid: 31241330
[55] Espah Borujeni A, Mishler D M, Wang J Z, et al. Automated physics-based design of synthetic riboswitches from diverse RNA aptamers. Nucleic Acids Research, 2016, 44(1): 1-13.
doi: 10.1093/nar/gkv1289 pmid: 26621913
[56] Tabuchi T, Yokobayashi Y. Cell-free riboswitches. RSC Chemical Biology, 2021, 2(5): 1430-1440.
doi: 10.1039/d1cb00138h pmid: 34704047
[57] Spitale R C, Crisalli P, Flynn R A, et al. RNA SHAPE analysis in living cells. Nature Chemical Biology, 2013, 9(1): 18-20.
doi: 10.1038/nchembio.1131 pmid: 23178934
[58] Aviran S, Pachter L. Rational experiment design for sequencing-based RNA structure mapping. RNA (New York, N Y), 2014, 20(12): 1864-1877.
[59] Watters K E, Abbott T R, Lucks J B. Simultaneous characterization of cellular RNA structure and function with in-cell SHAPE-Seq. Nucleic Acids Research, 2016, 44(2): e12.
doi: 10.1093/nar/gkv879
[60] Pardee K, Green A A, Takahashi M K, et al. Rapid, low-cost detection of zika virus using programmable biomolecular components. Cell, 2016, 165(5): 1255-1266.
doi: S0092-8674(16)30505-0 pmid: 27160350
[61] Suvanasuthi R, Chimnaronk S, Promptmas C. 3D printed hydrophobic barriers in a paper-based biosensor for point-of-care detection of dengue virus serotypes. Talanta, 2022, 237: 122962.
doi: 10.1016/j.talanta.2021.122962
[62] Ma D, Shen L H, Wu K Y, et al. Low-cost detection of norovirus using paper-based cell-free systems and synbody-based viral enrichment. Synthetic Biology (Oxford, England), 2018, 3(1): ysy018.
[63] Cao M C, Sun Q L, Zhang X, et al. Detection and differentiation of respiratory syncytial virus subgroups A and B with colorimetric toehold switch sensors in a paper-based cell-free system. Biosensors and Bioelectronics, 2021, 182: 113173.
doi: 10.1016/j.bios.2021.113173
[64] Verosloff M, Chappell J, Perry K L, et al. PLANT-dx: a molecular diagnostic for point-of-use detection of plant pathogens. ACS Synthetic Biology, 2019, 8(4): 902-905.
doi: 10.1021/acssynbio.8b00526 pmid: 30790518
[65] Zhang Y, Steppe P L, Kazman M W, et al. Point-of-care analyte quantification and digital readout via lysate-based cell-free biosensors interfaced with personal glucose monitors. ACS Synthetic Biology, 2021, 10(11): 2862-2869.
doi: 10.1021/acssynbio.1c00282 pmid: 34672518
[66] Chau T H T, Lee E Y. Development of cell-free platform-based toehold switch system for detection of IP-10 mRNA, an indicator for acute kidney allograft rejection diagnosis. Clinica Chimica Acta, 2020, 510: 619-624.
doi: S0009-8981(20)30427-7 pmid: 32860784
[67] Gui Q Y, Lawson T, Shan S Y, et al. The application of whole cell-based biosensors for use in environmental analysis and in medical diagnostics. Sensors (Basel, Switzerland), 2017, 17(7): 1623.
doi: 10.3390/s17071623
[68] Yu L, Wu S S, Hao X W, et al. Rapid detection of COVID-19 coronavirus using a reverse transcriptional loop-mediated isothermal amplification (RT-LAMP) diagnostic platform. Clinical Chemistry, 2020, 66(7): 975-977.
doi: 10.1093/clinchem/hvaa102 pmid: 32315390
[69] Pardee K, Green A A, Ferrante T, et al. Paper-based synthetic gene networks. Cell, 2014, 159(4): 940-954.
doi: 10.1016/j.cell.2014.10.004 pmid: 25417167
[70] Smith M T, Berkheimer S D, Werner C J, et al. Lyophilized Escherichia coli-based cell-free systems for robust, high-density, long-term storage. BioTechniques, 2014, 56(4): 186-193.
doi: 10.2144/000114158
[71] Yang J Z, Cui Y T, Cao Z, et al. Strategy exploration for developing robust lyophilized cell-free systems. Biotechnology Notes, 2021, 2: 44-50.
doi: 10.1016/j.biotno.2021.08.004
[72] Hunt J P, Yang S O, Wilding K M, et al. The growing impact of lyophilized cell-free protein expression systems. Bioengineered, 2017, 8(4): 325-330.
doi: 10.1080/21655979.2016.1241925 pmid: 27791452
[73] Nguyen P Q, Soenksen L R, Donghia N M, et al. Wearable materials with embedded synthetic biology sensors for biomolecule detection. Nature Biotechnology, 2021, 39(11): 1366-1374.
doi: 10.1038/s41587-021-00950-3 pmid: 34183860
[74] de Puig H, Bosch I, Collins J J, et al. Point-of-care devices to detect zika and other emerging viruses. Annual Review of Biomedical Engineering, 2020, 22: 371-386.
doi: 10.1146/annurev-bioeng-060418-052240 pmid: 32501770
[75] Köksaldi I C, Köse S, Ahan R E, et al. SARS-CoV-2 detection with de novo-designed synthetic riboregulators. Analytical Chemistry, 2021, 93(28): 9719-9727.
doi: 10.1021/acs.analchem.1c00886
[76] Hunt J P, Zhao E L, Free T J, et al. Towards detection of SARS-CoV-2 RNA in human saliva: a paper-based cell-free toehold switch biosensor with a visual bioluminescent output. New Biotechnology, 2022, 66: 53-60.
doi: 10.1016/j.nbt.2021.09.002
[77] Park S, Lee J W. Detection of coronaviruses using RNA toehold switch sensors. International Journal of Molecular Sciences, 2021, 22(4): 1772.
doi: 10.3390/ijms22041772
[78] Takahashi M K, Tan X, Dy A J, et al. A low-cost paper-based synthetic biology platform for analyzing gut microbiota and host biomarkers. Nature Communications, 2018, 9(1): 3347.
doi: 10.1038/s41467-018-05864-4 pmid: 30131493
[79] Hong F, Ma D, Wu K Y, et al. Precise and programmable detection of mutations using ultraspecific riboregulators. Cell, 2020, 180(5): 1018-1032, e16.
doi: S0092-8674(20)30155-0 pmid: 32109416
[80] Drachuk I, Harbaugh S, Chávez J L, et al. Improving the activity of DNA-encoded sensing elements through confinement in silk microcapsules. ACS Applied Materials & Interfaces, 2020, 12(43): 48329-48339.
[81] Thavarajah W, Silverman A D, Verosloff M S, et al. Point-of-use detection of environmental fluoride via a cell-free riboswitch-based biosensor. ACS Synthetic Biology, 2020, 9(1): 10-18.
doi: 10.1021/acssynbio.9b00347 pmid: 31829623
[82] Jung J K, Alam K K, Verosloff M S, et al. Cell-free biosensors for rapid detection of water contaminants. Nature Biotechnology, 2020, 38(12): 1451-1459.
doi: 10.1038/s41587-020-0571-7
[83] 盛树悦, 陈悦, 张兴梅, 等. 核糖开关及其在抗菌药物方面的研究进展. 生物技术通报, 2017, 33(1): 114-119.
doi: 10.13560/j.cnki.biotech.bull.1985.2017.01.012
Sheng S Y, Chen Y, Zhang X M, et al. Research progresses on riboswitches and their applications in antimicrobials. Biotechnology Bulletin, 2017, 33(1): 114-119.
doi: 10.13560/j.cnki.biotech.bull.1985.2017.01.012
[84] Panchal V, Brenk R. Riboswitches as drug targets for antibiotics. Antibiotics (Basel, Switzerland), 2021, 10(1): 45.
[85] Cui Z L, Johnston W A, Alexandrov K. Cell-free approach for non-canonical amino acids incorporation into polypeptides. Frontiers in Bioengineering and Biotechnology, 2020, 8: 1031.
doi: 10.3389/fbioe.2020.01031 pmid: 33117774
[86] Sharpes C E, McManus J B, Blum S M, et al. Assessment of colorimetric reporter enzymes in the PURE system. ACS Synthetic Biology, 2021, 10(11): 3205-3208.
doi: 10.1021/acssynbio.1c00360 pmid: 34723497
[87] Zhang L Y, Guo W, Lu Y. Advances in cell-free biosensors: principle, mechanism, and applications. Biotechnology Journal, 2020, 15(9): e2000187.
[88] Wen K Y, Cameron L, Chappell J, et al. A cell-free biosensor for detecting quorum sensing molecules in P. aeruginosa-infected respiratory samples. ACS Synthetic Biology, 2017, 6(12): 2293-2301.
doi: 10.1021/acssynbio.7b00219
[89] Matsuura H, Ujiie K, Duyen T T M, et al. Development of a paper-based luminescence bioassay for therapeutic monitoring of aminoglycosides: a proof-of-concept study. Applied Biochemistry and Biotechnology, 2019, 189(3): 798-809.
doi: 10.1007/s12010-019-03048-4 pmid: 31119530
[90] Carr A R, Dopp J L, Wu K Y, et al. Toward mail-in-sensors for SARS-CoV-2 detection: interfacing gel switch resonators with cell-free toehold switches. ACS Sensors, 2022, 7(3): 806-815.
doi: 10.1021/acssensors.1c02450 pmid: 35254055
[91] Boyd M A, Kamat N P. Designing artificial cells towards a new generation of biosensors. Trends in Biotechnology, 2021, 39(9): 927-939.
doi: 10.1016/j.tibtech.2020.12.002 pmid: 33388162
[1] 王雪, 权春善, 王建华, 范圣第. 不同细胞破碎方法对无细胞蛋白表达系统细胞抽提物活性的影响[J]. 中国生物工程杂志, 2011, 31(01): 46-50.
[2] 黄艳 朱聪 高晓莲. 体外合成组装多元核糖开关[J]. 中国生物工程杂志, 2010, 30(01): 0-.
主管：中国科学院 　主办：中国科学院文献情报中心 　中国生物技术发展中心 　中国生物工程学会