Highly Parallel Single-Molecule Amplification Approach Based on Agarose Droplet Polymerase Chain Reaction for Efficient and Cost-Effective Aptamer Selection

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• 作者：Wei Yun Zhang ; Wenhua Zhang ; Zhiyuan Liu ; Cong Li ; Zhi Zhu ; Chaoyong James Yang
• 刊名：Analytical Chemistry
• 出版年：2012
• 出版时间：January 3, 2012
• 年：2012
• 卷：84
• 期：1
• 页码：350-355
• 全文大小：818K
• 年卷期：v.84,no.1(January 3, 2012)
• ISSN：1520-6882

文摘

We have developed a novel method for efficiently screening affinity ligands (aptamers) from a complex single-stranded DNA (ssDNA) library by employing single-molecule emulsion polymerase chain reaction (PCR) based on the agarose droplet microfluidic technology. In a typical systematic evolution of ligands by exponential enrichment (SELEX) process, the enriched library is sequenced first, and tens to hundreds of aptamer candidates are analyzed via a bioinformatic approach. Possible candidates are then chemically synthesized, and their binding affinities are measured individually. Such a process is time-consuming, labor-intensive, inefficient, and expensive. To address these problems, we have developed a highly efficient single-molecule approach for aptamer screening using our agarose droplet microfluidic technology. Statistically diluted ssDNA of the pre-enriched library evolved through conventional SELEX against cancer biomarker Shp2 protein was encapsulated into individual uniform agarose droplets for droplet PCR to generate clonal agarose beads. The binding capacity of amplified ssDNA from each clonal bead was then screened via high-throughput fluorescence cytometry. DNA clones with high binding capacity and low K_d were chosen as the aptamer and can be directly used for downstream biomedical applications. We have identified an ssDNA aptamer that selectively recognizes Shp2 with a K_d of 24.9 nM. Compared to a conventional sequencing鈥揷hemical synthesis鈥搒creening work flow, our approach avoids large-scale DNA sequencing and expensive, time-consuming DNA synthesis of large populations of DNA candidates. The agarose droplet microfluidic approach is thus highly efficient and cost-effective for molecular evolution approaches and will find wide application in molecular evolution technologies, including mRNA display, phage display, and so on.