Abstract
Droplet microfluidics combined with the isothermal circular strand displacement polymerization (ICSDP) represents a powerful new technique to detect both single-stranded DNA and microRNA sequences. The method here described helps in overcoming some drawbacks of the lately introduced droplet polymerase chain reaction (PCR) amplification when implemented in microfluidic devices. The method also allows the detection of nanoliter droplets of nucleic acids sequences solutions, with a particular attention to microRNA sequences that are detected at the picomolar level. The integration of the ICSDP amplification protocol in droplet microfluidic devices reduces the time of analysis and the amount of sample required. In addition, there is also the possibility to design parallel analyses to be integrated in portable devices.
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References
Schneider T, Kreutz J, Chiu DT (2013) The potential impact of droplet microfluidics in biology. Anal Chem 85:3476–3482
Spoto G, Corradini R (2012) Detection of non-amplified genomic DNA. Springer, Verlag
Hindson CM, Chevillet JR, Briggs HA, Gallichotte EN, Ruf IK, Hindson BJ, Vessella RL, Tewari M (2013) Absolute quantification by droplet digital PCR versus analog real-time PCR. Nat Methods 10:1003–1005
Pinto AJ, Raskin L (2012) PCR biases distort bacterial and archaeal community structure in pyrosequencing datasets. PLoS One 7:e43093
Craw P, Balachandran W (2012) Isothermal nucleic acid amplification technologies for point-of-care diagnostics: a critical review. Lab Chip 12:2469–2486
Asiello PJ, Baeumner AJ (2011) Miniaturized isothermal nucleic acid amplification, a review. Lab Chip 11:1420–1430
Zanoli LM, Spoto G (2013) Isothermal amplification methods for the detection of nucleic acids in microfluidic devices. Biosensors 3:18–43
Kim J, Easley CJ (2011) Isothermal DNA amplification in bioanalysis: strategies and applications. Bioanalysis 3:227–239
Guo Q, Yang X, Wang K, Tan W, Li W, Tang H, Li H (2009) Sensitive fluorescence detection of nucleic acids based on isothermal circular strand-displacement polymerization reaction. Nucleic Acids Res 37(3):e20
D’Agata R, Corradini R, Ferretti C, Zanoli L, Gatti M, Marchelli R, Spoto G (2010) Ultrasensitive detection of non-amplified genomic DNA by nanoparticle-enhanced surface plasmon resonance imaging. Biosens Bioelectron 25:2095–2100
Giuffrida MC, Zanoli LM, D’Agata R, Finotti A, Gambari R, Spoto G (2015) Isothermal circular-strand-displacement polymerization of DNA and microRNA in digital microfluidic devices. Anal Bioanal Chem 407(6):1533–1543
Nana-Sinkam SP, Croce CM (2013) Clinical applications for microRNAs in cancer. Clin Pharmacol Ther 93:98–104
Dong H, Lei J, Ding L, Wen Y, Ju H, Zhang X (2013) MicroRNA: function, detection, and bioanalysis. Chem Rev 113:6207–6233
Mendell JT, Olson EN (2012) MicroRNAs in stress signaling and human disease. Cell 148:1172–1187
Zampetaki A, Mayr M (2012) MicroRNAs in vascular and metabolic disease. Circ Res 110:508–522
Bartel DP (2009) MicroRNAs: target recognition and regulatory functions. Cell 136:215–233
Tzimagiorgis G, Michailidou EZ, Kritis A, Markopoulos AK, Kouidou S (2011) Recovering circulating extracellular or cell-free RNA from bodily fluids. Cancer Epidemiol 35:580–589
Yan L, Yan Y, Pei L, Wei W, Zhao J (2014) A G-quadruplex DNA-based, label-free and ultrasensitive strategy for microRNA detection. Sci Rep 4:7400
D’Agata R, Breveglieri G, Zanoli LM, Borgatti M, Spoto G, Gambari R (2011) Direct detection of point mutations in non-amplified human genomic DNA. Anal Chem 83:8711–8717
D’Agata R, Spoto G (2013) Surface plasmon resonance imaging for nucleic acid detection. Anal Bioanal Chem 405:573–584
Zanoli LM, D’Agata R, Spoto G (2012) Functionalized gold nanoparticles for the ultrasensitive DNA detection. Anal Bioanal Chem 402:1759–1771
Spoto G, Minunni M (2012) Surface plasmon resonance imaging: what next? J Phys Chem Lett 3:2682–2691
Grasso G, D’Agata R, Zanoli L, Spoto G (2009) Microfluidic networks for surface plasmon resonance imaging real-time kinetics experiments. Microchem J 93:82–86
Acknowledgments
MIUR (PRIN 20093N774P) and Ministry of Health, Italy (n. 098/GR-2009-1596647), are acknowledged for partial financial support.
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Giuffrida, M.C., D’Agata, R., Spoto, G. (2017). Droplet Microfluidic Device Fabrication and Use for Isothermal Amplification and Detection of MicroRNA. In: Dalmay, T. (eds) MicroRNA Detection and Target Identification. Methods in Molecular Biology, vol 1580. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-6866-4_6
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DOI: https://doi.org/10.1007/978-1-4939-6866-4_6
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