Abstract
Nucleic acid amplification strategies are often integrated with miniaturized devices including digital microfluidics, microfluidic chips, paper-based fluidic chips, and other open chip without microstructures. In contrast to microdroplet generation on chips with microchannels or on microchambers, recently developed techniques for the generation of droplet arrays (ranging from femtoliter to microliter volumes) on planar substrates have set the stage for the direct manipulation of individual droplets and for image acquisition and quantification. A droplet array on a planar substrate has some advantages over the previous picoliter or nanoliter chambers with solid walls. The integration of nucleic acid amplification into microdroplet array has facilitated the development of nucleic acid-based detection and diagnosis with high assay sensitivity. In this section, we highlight recent progress made on the characterization of open-access microdroplet array, focusing particularly on design, fabrication, and clinical application.
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Arrabito G, Galati C, Castellano S et al (2013) Luminometric sub-nanoliter droplet-to-droplet array (LUMDA) and its application to drug screening by phase I metabolism enzymes. Lab Chip 13:68–72
Baner J, Nilsson M, Mendel-Hartvig M et al (1998) Signal amplification of padlock probes by rolling circle replication. Nucleic Acids Res 26:5073–5078
Baret JC (2012) Surfactants in droplet-based microfluidics. Lab chip 12:422–433
Beer NR, Wheeler EK, Lee-Houghton L et al (2008) On-chip single-copy real-time reverse-transcription PCR in isolated picolater droplets. Anal Chem 80:1854–1858
Berthier E, Warrick J, Yu H et al (2008) Managing evaporation for more robust microscale assays Part 1. volume loss in high throughput assays. Lab Chip 8:852–859
Cao A, Zhang CY (2012) Sensitive and label-free DNA methylation detection by ligation-mediated hyperbranched rolling circle amplification. Anal Chem 84:6199–6205
Chen F, Lin Z, Zheng Y et al (2012) Development of an automatic multi-channel ink-jet ejection chemiluminescence system and its application to the determination of horseradish peroxidase. Anal Chim Acta 739:77–82
Chen F, Mao S, Zeng H et al (2013a) Inkjet nanoinjection for high-thoughput chemiluminescence immunoassay on multicapillary glass plate. Anal Chem 85:7413–7418
Chen F, Zhang Y, Nakagawa Y et al (2013b) A piezoelectric drop-on-demand generator for accurate samples in capillary electrophoresis. Talanta 107:111–117
Clausell-Tormos J, Lieber D, Baret JC (2008) Droplet-based microfluidic platforms for the encapsulation and screening of mammalian cells and multicellular organisms. Chem Biol 15:427–437
Dalerba P, Kalisky T, Sahoo D et al (2011) Single-cell dissection of transcriptional heterogeneity in human colon tumors. Nat Biotechnol 29:1111–1112
Du WB, Fang Q, Fang ZL (2006) Microfluidic sequential injection analysis in a short capillary. Anal Chem 78:6404–6410
Du WB, Sun M, Gu SQ et al (2010) Automated microfluidic screening assay platform based on DropLab. Anal Chem 82:9941–9947
Du GS, Pan JZ, Zhao SP et al (2013) Cell-based drug combination screening with a microfluidic droplet array system. Anal Chem 85:6740–6747
Du XH, Li WM, Du GS et al (2018) Droplet array-based 3D coculture system for high-throughput tumor angiogenesis assay. Anal Chem 90:3253–3261
Efremov AN, Stanganello E, Welle A et al (2013) Micropatterned superhydrophobic structures for the simultaneous culture of multiple cell types and the study of cell-cell communication. Biomaterials 34:1757–1763
Feng W, Li L, Ueda E et al (2014) Surface patterning via thiol-yne click chemistry: an extremely fast and versatile approach to superhydrophilic-super-hydrophobic micropatterns. Adv Mater Interfaces 1:1400269
Ferraro P, Coppola S, Grilli S et al (2010) Dispensing nano-pico droplets and liquid patterning by pyro-electrodynamic shooting. Nat Nanotechnol 5:429–435
Fodor SP, Read JL, Pirrung MC et al (1991) Light-directed, spatially addressable parallel chemical synthesis. Science 251:767–773
Garcia-Cordero JL, Fan ZH (2017) Sessile droplets for chemical and biological assays. Lab Chip 17:2150–2166
Gonzalez A, Estala L, Gaines M et al (2016) Mixed thread/paper-based microfluidic chips as a platform for glucose assays. Electrophoresis 37:1685–1690
Gorris HH, Walt DR (2010) Analytical chemistry on the femtoliter scale. Angew Chem Int Ed 49: 3880–3895
Gosalia DN, Diamond SL (2003) Printing chemical libraries on microarrays for fluid phase nanoliter reactions. PNAS 100:8721–8726
Gosalia DN, Salisbury CM, Ellman JA et al (2005) High throughput substrate specificity profiling of serine and cysteine proteases using solution-phase fluorogenic peptide microarrays. Mol Cell Proteomics 4:626–636
Gu ZZ, Fujishima A, Sato O (2002) Patterning of a colloidal crystal film on a modified hydrophilic and hydrophobic surface. Angew Chem Int Ed 41:2067–2070
Guo XL, Wei Y, Lou Q et al (2018) Manipulating femtoliter to picoliter droplets by pins for single cell analysis and quantitative biological assay. Anal Chem 90:5810–5817
Han H, Lee JS, Kim H et al (2018) Single-droplet multiplex bioassay on a robust and stretchable extreme wetting substrate through vacuum-based droplet manipulation. ACS Nano 12:932–941
Hatch AC, Fisher JS, Tovar AR et al (2011) 1-Million droplet array with wide-field fluorescence imaging for digital PCR. Lab Chip 11:3838–3845
Heid CA, Stevens J, Livak KJ et al (1996) Real time quantitative PCR. Genome Res 6:986–994
Hu Y, Xu P, Luo J et al (2017) Absolute quantification of H5-subtype avian influenza viruses using droplet digital loop-mediated isothermal amplification. Anal Chem 89:745–750
Huebner A, Sharma S, Demello AJ et al (2008) Microdroplets: a sea of applications. Lab Chip 8:1244–1254
Iino R, Hayama K, Amezawa H et al (2012) A single-cell drug efflux assay in bacteria by using a directly accessible femtoliter droplet array. Lab Chip 12:3923–3929
Jin DQ, Zhu Y, Fang Q (2014) Swan Probe: a nanoliter-scale and high-throughput sampling interface for coupling electrospray ionization mass spectrometry with microfluidic droplet array and multiwell plate. Anal Chem 86:10796–10803
Jose L, Garcia C, Fan ZH (2017) Sessile droplets for chemical and biological assays. Lab Chip 17:2150–2166
Kantlehner M, Kirchner R, Hartmann P et al (2011) Identification of rare DNA variants in mitochondrial disorders with improved array-based sequencing. Nucleic Acids Res 39:44–68
Kim H, Vishniakou S, Faris GW (2009) Petri dish PCR: laser-heated reactions in nanoliter droplet arrays. Lab Chip 9:1230–1235
Kim SH, Iwai S, Araki S et al (2012) Large-scale femtoliter droplet array for digital counting of single biomolecules. Lab Chip 12:4986–4991
Kreutz JE, Munson T, Huynh T et al (2011) Theoretical design and analysis of multivolume digital assays with wide dynamic range validated experimentally with microfluidic digital PCR. Anal Chem 83:8158–8168
Kuan CM, York RL, Cheng CM (2016) Lignocellulose-based analytical devices: bamboo as an analytical platform for chemical detection. Sci Rep 5:18570–18580
Lagos-Quintana M, Rauhut R, Lendeckel W et al (2001) Identification of novel genes coding for small expressed RNAs. Science 294:853–858
Li H, Leulmiab RF, Juncker D (2011) Hydrogel droplet microarrays with trapped antibody-functionalized beads for multiplexed protein analysis. Lab Chip 11:528–534
Li Y, Zeng Y, Ji X et al (2012) Cascade signal amplification for sensitive detection of cancer cell based on self-assembly of DNA scaffold and rolling circle amplification. Sens Actuators B Chem 361–366
Li N, Ma J, Guarnera MA et al (2014) Digital PCR quantification of miRNAs in sputum for diagnosis of lung cancer. J Cancer Res Clin Oncol 140145–140150
Li G, Li MZ, Wang ST et al (2015a) Splitting a droplet for femtoliter liquid patterns and single cell isolation. ACS Appl Mater Interfaces 7:9060–9065
Li H, Yang Q, Li G et al (2015b) Splitting a droplet for femtoliter liquid patterns and single cell isolation. ACS Appl Mater Interfaces 7:9060–9065
Liang YR, Zhu LN, Gao J et al (2017) 3D-printed high-density droplet array chip for miniaturized protein crystallization screening under vapor diffusion mode. ACS Appl Mater Interfaces 9:11837–11845
Liao S, He Y, Wang D et al (2016) Dynamic interfacial printing for monodisperse droplets and polymeric microparticles. Adv Mater Technol 1:1600021
Liao SL, Tao XL, Ju YJ et al (2017) Multichannel dynamic interfacial printing: an alternative multicomponent droplet generation technique for lab in a drop. ACS Appl Mater Interfaces 9:43545–43552
Liu W, Zhu Y, Feng Y et al (2017) Droplet-based multivolume digital polymerase chain reaction by a surface-assisted multifactor fluid segmentation approach. Anal Chem 89:822–829
Lizardi PM, Huang X, Zhu Z et al (1998) Mutation detection single molecule counting using isothermal rolling circle amplification. Nat Genet 19:225–232
Lo YM, Lun FM, Chan KC et al (2007) Digital PCR for the molecular detection of fetal chromosomal aneuploidy. Proc Natl Acad Sci USA 104:13116–13121
Lorber N, Sarrazin F, Guillot P et al (2011) High-throughput single-cell quantification using simple microwell-based cell docking and programmable time-course live-cell imaging. Lab Chip 11:779–787
Ludlow AT, Robin JD, Sayed M et al (2014) Quantitative telomerase enzyme activity determination using droplet digital PCR with single cell resolution. Nucleic Acids Res 42:e104–e115
Luo C, Ma Y, Li H et al (2013) Generation of picoliter droplets of liquid for electrospray ionization with piezoelectric inkjet. J Mass Spectrom 48:321–328
Ma XD (2016) Development of hydrophilic-hydrophobic-pattern-based microdroplet array and its application in multiplex nucleic acid detection. Southeast University
Ma XD, Xu WW, Chen C et al (2015) A microfabrication-free nanoliter droplet array for nucleic acid detection combined with isothermal amplification. Analyst 140:4370–4373
Marques FZ, Prestes PR, Pinheiro LB et al (2014) Measurement of absolute copy number variation reveals association with essential hypertension. BMC Med Genomics 7:44
Martinez AW, Phillips ST et al (2007) Patterned paper as a platform for inexpensive, low-volume, portable bioassays. Angew Chem Int Ed 46:1318–1320
Martinez AW, Phillips ST, Whitesides GM et al (2010) Diagnostics for the developing world: microfluidic paper-based analytical devices. Anal Chem 82:3–10
May A, May A, Kirchner R et al (2009) Multiplex RT-PCR expression analysis of developmentally important genesin individual mouse preimplantation embryos and blastomeres. Biol Reprod 80:194–202
Mongersun A, Smeenk I, Pratx G et al (2016) Droplet microfluidic platform for the determination of single-cell lactate release. Anal Chem 88:3257–3263
Mugherli L, Burchak ON, Balakireva LA et al (2009) In-situ assembly and screening of enzyme inhibitors with surface tension microarrays. Angew Chem Int Ed 48:7639–7644
Neto AI, Demir K, Popova AA et al (2016a) Fabrication of hydrogel particles of defined shapes using superhydrophobic-hydrophilic micropatterns. Adv Mater 28(35):7613–7619
Neto AI, Demir K, Popova AA et al (2016b) Fabrication of hydrogel particles of defined shapes using superhydrophobic-hydrophilic micropatterns. Adv Mater 28:7613–7619
Nie MY, Zheng M, Li CM et al (2019) Assembled step emulsification device for multiplex droplet digital polymerase chain reaction. Anal Chem 91:1779–1784
Nishimoto S, Sekine H, Zhang X et al (2009) Assembly of self-assembled monolayer-coated Al2O3 on TiO2 thin films for the fabrication of renewable superhydrophobic-superhydrophilic structures. Langmuir 25:7226–7228
Oliveira NM, Reis RL, Mano JF (2013) Superhydrophobic surfaces engineered using diatomaceous earth. ACS Appl Mater Interfaces 5:4202–4208
Oliveira MB, Neto AI, Correia CR et al (2014) Superhydrophobic chips for cell spheroids high-throughput generation and drug screening. ACS Appl Mater Interfaces 6:9488–9495
Park JU, Hardy M, Kang SJ et al (2007) High-resolution electrohydrodynamic jet printing. Nat Mater 6:782–789
Popova AA, Schillo SM, Demir K et al (2015) Droplet-array (DA) sandwich chip: a versatile platform for high-throughput cell screening based on superhydrophobic-superhydrophilic micropatterning. Adv Mater 27:5217–5222
Qin J, Jones RC, Ramakrishnan R (2008) Studying copy number variations using a nanofluidic platform. Nucleic Acids Res 36:e116
Rice D, Kocurek B, Snead CA (2010) Chronic disease management for diabetes: baylor health care system’ s coordinated efforts and the opening of the diabetes health and wellness institute. Proc Bayl Univ Med Cent 23:230–234
Sakakihara S, Araki S, Iinoand R et al (2010) A single-molecule enzymatic assay in a directly accessible femtoliter droplet array. Lab Chip 10:3355–3362
Sanchez-Freire V, Ebert AD, Kalisky T et al (2012) Microfluidic single-cell real-time PCR for comparative analysis of gene expression patterns. Nat Protoc 7:829–838
Schmidt U, Lutz-Bonengel S, Weisser HJ et al (2006) Low-volume amplification on chemically structured chips using the PowerPlex16 DNA amplification kit. Int J Legal Med 120:42–48
Seo J, Lee SK, Lee J et al (2015) Path-programmable water droplet manipulations on an adhesion controlled superhydrophobic surface. Sci Rep 5:12326–12335
Shen F, Sun B, Kreut JE et al (2011) Multiplexed quantification of nucleic acids with large dynamic range using multivolume digital RT-PCR on a rotational slipchip tested with hiv and hepatitis c viral load. J Am Chem Soc 133:17705–17712
Shim J, Cristobal G, Link DR et al (2007) Control and measurement of the phase behavior of aqueous solutions using microfluidics. J Am Chem Soc 129:8825
Sun YN, Zhou XG, Yu YD (2014) A novel picoliter droplet array for parallel real-time polymerase chain reaction based on double-inkjet printing. Lab Chip 14:3603–3610
Sun YN, Chen XD, Zhou XG et al (2015) Droplet-in-oil array for picoliter-scale analysis based on sequential-inkjet printing. Lab Chip 15:2429–2436
Sun YN, Song WH, Sun XH et al (2018) Inkjet-printing patterned chip on sticky superhydrophobic surface for high-efficiency single-cell array trapping and real-time observation of cellular apoptosis. ACS Appl Mater Interfaces 10:31054–31060
Sykes PJ, Neoh SH, Brisco MJ et al (1992) Quantitation of targets for PCR by use of limiting dilution. Biotechniques 13:444–449
Takinoue M, Takeuchi S (2011) Droplet microfluidics for the study of artificial cells. Anal Bioanal Chem 400:1705–1716
Taly V, Kelly BT, Griffiths AD (2007) Droplets as microreactors for high-throughput biology. ChemBioChem 8:263–272
Teh SY, Lin R, Lee AP et al (2008) Droplet microfluidics. Lab Chip 8(2):198–220
Theberge AB, Courtois F, Schaerli Y et al (2010) Microdroplets in microfluidics: an evolving platform for discoveries in chemistry and biology. Angew Chem Int Ed 49:5846–5868
Ueda E, Levkin PA (2013) Emerging applications of superhydrophilic-superhydrophobic micropatterns. Adv Mater 25:1234–1247
Ueda E, Geyer FL, Nedashkivska V et al (2012) Droplet microarray: facile formation of arrays of microdroplets and hydrogel micropads for cell screening applications. Lab Chip 12:5218
Vogelstein B, Kinzler KW (1999) Digital PCR. Proc Natl Acad Sci USA 96:9236–9241
Warren L, Bryder D, Weissman IL et al (2006) Transcription factor profiling in individual hematopoietic progenitors by digital RT-PCR. Proc Natl Acad Sci USA 103:17807–17812
White AK, Heyries KA, Doolin C et al (2013) High-throughput microfluidic single-cell digital polymerase chain reaction. Anal Chem 85:7182–7190
Wu P, Zhang C (2015) Low-cost, high-throughput fabrication of cloth-based microfluidic devices using a photolithographical patterning technique. Lab Chip 15:1598–1608
Wu H, Chen XL, Gao XH et al (2018a) High-throughput generation of durable droplet arrays for single-cell encapsulation, culture, and monitoring. Anal Chem 90:4303–4309
Wu WS, Zhou SF, Hu JM et al (2018) A thermosetting oil for droplet-based real-time monitoring of digital PCR and cell culture. Adv Funct Mater 1803559–1803569
Xu LP, Chen Y, Yang G et al (2015) Ultratrace DNA detection based on the condensing-enrichment effect of superwettable microchips. Adv Mater 27:6878–6884
Xu K, Wang X, Ford RM et al (2016a) Self-partitioned droplet array on laser-patterned superhydrophilic glass surface for wall-less cell arrays. Anal Chem 88:2652–2658
Xu P, Zheng X, Tao Y et al (2016b) Cross-interface emulsification for generating size-tunable droplets. Anal Chem 88:3171–3177
Xu TL, Shi WX, Huang JR et al (2017) Superwettable microchips as a platform toward microgravity biosensing. ACS Nano 11:621–626
Yang J, Katagiri D, Mao S et al (2016) Inkjet printing based assembly of thermoresponsive core–shell polymer microcapsules for controlled drug release. Mater Chem B 4:4156–4163
You I, Yun N, Lee H (2013) Surface-tension-confined microfluidics and their applications. ChemPhysChem 14:471–481
Zeng H, Yang J, Katagiri D et al (2015) Investigation of monodisperse droplet generation in liquids by inkjet. Sens Actuators, B 220:958–961
Zeng H, Katagiri D, Ogino T et al (2016) Droplet enhanced fluorescence for ultrasensitive detection using inkjet. Anal Chem 88:6135–6139
Zhang X, Jin M, Liu Z et al (2007) Superhydrophobic TiO2 surfaces: preparation, photocatalytic wettability conversion, and superhydrophobic-superhydrophilic patterning. J Phys Chem C 111:14521–14529
Zhang Y, Zhu Y, Yao B et al (2011) Nanolitre droplet array for real time reverse transcription polymerase chain reaction. Lab Chip 11:1545–1549
Zhang L, Zhu G, Zhang C (2014) Homogeneous and label-free detection of microRNAs using bifunctional strand displacement amplification-mediated hyperbranched rolling circle amplification. Anal Chem 86:6703–6709
Zhang J, Chen F, He Z et al (2016a) A novel approach for precisely controlled multiple cell patterning in microfluidic chip by inkjet printing and the detection of drug metabolism and diffusion. Analyst 141:2940–2947
Zhang W, Mao S, Yang J et al (2016b) The use of an inkjet injection technique in immunoassays by quantitative on-line electrophoretically mediated microanalysis. Chromatogr A 1477:127–131
Zhang W, Li N, Zeng H et al (2017) Inkjet printing based separation of mammalian cells by capillary electrophoresis. Anal Chem 89:8674–8677
Zhang WF, Li N, Koga D et al (2018) Inkjet printing based droplet generation for integrated online digital polymerase chain reaction. Anal Chem 90:5329–5334
Zhao H, Ma XD, Li ML et al (2011) Analysis of CpG island methylation using rolling circle amplification (RCA) product microarry. J Biomed Nanoteclmol 7:292
Zhu Y, Zhang YX, Cai LF et al (2013a) Sequential operation droplet array: an automated microfluidic platform for picoliter-scale liquid handling, analysis and screening. Anal Chem 85:6723–6731
Zhu X, Xu H, Zheng H et al (2013b) An ultrasensitive aptameric sensor for proteins based on hyperbranched rolling circle amplification. Chem Comm 49:10115–10117
Zhu Y, Zhu LN, Guo R et al (2014) Nanoliter-scale protein crystallization and screening with a microfluidic droplet robot. Scientific Report 4:5046
Zhu Y, Zhang YX, Liu WW et al (2015) Printing 2-dimentional droplet array for single-cell reverse transcription quantitative PCR assay with a microfluidic robot. Sci Rep 5:9551
Zhu P, Kong T, Zhou C et al (2018) Engineering microstructure with evaporation-induced self-assembly of microdroplets. Small Methods 2:1800017
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Sun, Y. (2019). Microdroplet Array for Nucleic Acid Amplification Strategies. In: Zhang, S., Bi, S., Song, X. (eds) Nucleic Acid Amplification Strategies for Biosensing, Bioimaging and Biomedicine. Springer, Singapore. https://doi.org/10.1007/978-981-13-7044-1_15
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