Fast Screening of Single-Nucleotide Polymorphisms Using Chip-Based Temperature Gradient Capillary Electrophoresis

Abstract

Recently, the analysis of single-nucleotide polymorphisms (SNPs) has attracted much attention. Although many techniques have been reported, new methods with high resolving power, low-cost, and fast speed are still required to meet the great demand of analyzing and detecting large amount of SNPs in the human genome. Capillary electrophoresis (CE) in the microchip format is a powerful separation technique, and has been applied to many fields in recent years, including SNPs detection. In this work, we present a fast SNPs detection scheme based on chip-based temperature gradient capillary electrophoresis. The cross-channel CE chip is made of poly- (dimethylsiloxane) (PDMS). A temporal temperature gradient with a precision of 0.1°C per step was applied on the chip during the separation process. The Cy5-labeled PCR products which contain one and two SNP sites were separated and detected. The homoduplexes and heteroduplexes were successfully base-line resolved and the total time of a single run was only 8 min. The separation was also confirmed by DHPLC. This work indicates that chip-based temperature gradient capillary electrophoresis is a fast and convenient screening approach for recognizing the presence of SNPs prior to further characterization. This method can be used for detecting both known and unknown mutations.

Keywords:

• Single-nucleotide polymorphisms
• Temperature gradient
• Chip-based capillary electrophoresis

Acknowledgments

This work was supported by National Natural Science Foundation of China (Contract number: 39825108, 30000040), National Key Fundamental Science Development Program (Contract number: G19990116), and National High-Tech Program (Contract number: 2002AA2Z2011).