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Anal Chem. 2017 Mar 21;89(6):3468-3473. doi: 10.1021/acs.analchem.6b04475. Epub 2017 Feb 28.

Convection-Driven Pull-Down Assays in Nanoliter Droplets Using Scaffolded Aptamers.

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Shanghai Key Laboratory of Green Chemistry and Chemical Processes, School of Chemistry and Molecular Engineering, East China Normal University , 500 Dongchuan Road, Shanghai 200241, P. R. China.
Harvard John A. Paulson School of Engineering and Applied Sciences, Harvard University , Cambridge, Massachusetts 02138, United States.
Division of Pharmaceutical Chemistry and Technology, Faculty of Pharmacy, University of Helsinki , FI-00014 Helsinki, Finland.
Pen-Tung Sah Institute of Micro-Nano Science and Technology, Xiamen University , Xiamen 361005, P. R. China.
Chemistry Department, King Saud University , Riyadh 11451, Saudi Arabia.


One of the great challenges in cellular studies is to develop a rapid and biocompatible analytical tool for single-cell analysis. We report a rapid, DNA nanostructure-supported aptamer pull-down (DNaPull) assay under convective flux in a glass capillary for analyzing the contents of droplets with nano- or picoliter volumes. We have demonstrated that the scaffolded aptamer can greatly improve the efficiency of target molecules' pull down. The convective flux allows complete reaction in <5 min, which is an 18-fold improvement compared to purely diffusive flux (traditional model of the stationary case). This established DNaPull assay can serve as a rapid and sensitive analytical platform for analyzing a variety of bioactive molecules, including small molecules [ATP, limit of detecton (LOD) of 1 μM], a drug (cocaine, LOD of 1 μM), and a biomarker (thrombin, LOD of 0.1 nM). Significantly, the designed microfluidic device compartmentalizes live cells into nanoliter-sized droplets to present single-cell samples. As a proof of concept, we demonstrated that cellular molecules (ATP) from a discrete number of HNE1 cells (zero to five cells) lysed inside nanoliter-sized droplets can be analyzed using our DNaPull assay, in which the intracellular ATP level was estimated to be ∼3.4 mM. Given the rapid assay feature and single-cell sample analysis ability, we believe that our analytical platform of convection-driven DNaPull in a glass capillary can provide a new paradigm in biosensor design and will be valuable for single-cell analysis.

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