DNA from Oral Rinse- A Comparison of Three Protocols for Amplification of VDR, FTO and Beta-Globin Genes

Aims: The aim of the study was to evaluate the efficacy of three different protocols for DNA extraction from oral rinse on the basis of their quantity and quality of DNA, simplicity, cost effectiveness and rapidity, as well as its efficiency for amplification of vitamin D receptor (VDR), Fat mass and obesity (FTO) and β-globin genes.

Methodologies: The three methods included; Method 1 (organic solvent extraction), Method 2 (spin column) and Method 3 (ion-exchange extraction). DNA extracted from oral rinse was used for PCR amplification of β-globin, VDR-FOK1 and FTO gene.

Results: The amplified products of 268bp (β-globin), 265bp (VDR-Fok1) and 182bp (FTO) were observed on HeroLab Gel doc system (Germany). Method 2 provided the average highest DNA yield (9.54±1.85 ng/µl) compared to 6.66±1.14 ng/µl and 7.57±0.96 ng/µl by method 1 and 3. Method 2 was found to have a better performance in terms of DNA quantity and quality, however, method 3 was the fastest and method 1 was the most cost effective methods but the PCR amplification from DNA from all three methods was the same.

Conclusion: Oral rinse was found one of the alternative non-invasive sources for DNA extraction and is sufficient for good quality and quantity of DNA extracted by three different methods. It may be concluded that method 1 can be employed for large scale epidemiological and molecular biological studies.