Separation-free single-base extension assay with fluorescence resonance energy transfer for rapid and convenient determination of DNA methylation status at specific cytosine and guanine dinucleotide sites

A separation-free single-base extension (SBE) assay utilizing fluorescence resonance energy transfer (FRET) was developed for rapid and convenient interrogation of DNA methylation status at specific cytosine and guanine dinucleotide sites. In this assay, the SBE was performed in a tube using an allele-specific oligonucleotide primer (i.e., extension primer) labeled with Cy3 as a FRET donor fluorophore at the 5'-end, a nucleotide terminator (dideoxynucleotide triphosphate) labeled with Cy5 as a FRET acceptor, a PCR amplicon derived from bisulfite-converted genomic DNA, and a DNA polymerase. A single base-extended primer (i.e., SBE product) that was 5'-Cy3- and 3'-Cy5-tagged was formed by incorporation of the Cy5-labeled terminator into the 3'-end of the extension primer, but only if the terminator added was complementary to the target nucleotide. The resulting SBE product brought the Cy3 donor and the Cy5 acceptor into close proximity. Illumination of the Cy3 donor resulted in successful FRET and excitation of the Cy5 acceptor, generating fluorescence emission from the acceptor. The capacity of the developed assay to discriminate as low as 10% methylation from a mixture of methylated and unmethylated DNA was demonstrated at multiple cytosine and guanine dinucleotide sites.

Microfluidic platforms for DNA methylation analysis

In the field of genetics, epigenetics is the study of changes in gene expression without any change in DNA sequences. Chemical base modification in DNA by DNA methyltransferase, and specifically methylation, has been well studied as the main mechanism of epigenetics. Therefore, the determination of DNA methylation of, for example, 5'-methylcytosine in the CpG sequence in mammals has attracted attention because it should prove valuable in a wide range of research fields including diagnosis, drug discovery, and therapy. Methylated DNA bases and DNA methyltransferase activity are analyzed using conventional methods; however, these methods are time-consuming and require complex multiple operations. Therefore, new methods and devices for DNA methylation analysis are now being actively developed. Furthermore, microfluidic technology has also been applied to DNA methylation analysis because the microfluidic platform offers the promising advantage of making it possible to perform thousands of DNA methylation reactions in small reaction volumes, resulting in a high-throughput analysis with high sensitivity. This review discusses epigenetics and the microfluidic platforms developed for DNA methylation analysis.