Development of a Reference Material of a Single DNA Molecule for the Quality Control of PCR Testing

• Published in: Analytical chemistry (Washington) Vol. 86; no. 17; pp. 8621 - 8627
• Main Authors: Mano, Junichi, Hatano, Shuko, Futo, Satoshi, Yoshii, Junji, Nakae, Hiroki, Naito, Shigehiro, Takabatake, Reona, Kitta, Kazumi
• Format: Journal Article
• Language: English
• Published: United States American Chemical Society 02-09-2014
• Subjects: Biochemistry; Deoxyribonucleic acid; DNA; DNA - analysis; DNA - standards; Enzymes; Gene sequencing; Molecules; Nucleotides; Plants, Genetically Modified - genetics; Polymerase chain reaction; Quality Control; Real time; Real-Time Polymerase Chain Reaction - standards; Reference materials; Wells
• ISSN: 0003-2700; 1520-6882
• DOI: 10.1021/ac501314s

We developed a reference material of a single DNA molecule with a specific nucleotide sequence. The double-strand linear DNA which has PCR target sequences at the both ends was prepared as a reference DNA molecule, and we named the PCR targets on each side as confirmation sequence and standard sequence. The highly diluted solution of the reference molecule was dispensed into 96 wells of a plastic PCR plate to make the average number of molecules in a well below one. Subsequently, the presence or absence of the reference molecule in each well was checked by real-time PCR targeting for the confirmation sequence. After an enzymatic treatment of the reaction mixture in the positive wells for the digestion of PCR products, the resultant solution was used as the reference material of a single DNA molecule with the standard sequence. PCR analyses revealed that the prepared samples included only one reference molecule with high probability. The single-molecule reference material developed in this study will be useful for the absolute evaluation of a detection limit of PCR-based testing methods, the quality control of PCR analyses, performance evaluations of PCR reagents and instruments, and the preparation of an accurate calibration curve for real-time PCR quantitation.