Optimization of DNA isolation process and enhancement of RAPD PCR for low quality genomic DNA of Terminalia arjuna

Owing to the presence of higher amount of polyphenolic and polysaccharide compounds, Terminalia arjuna (Roxburgh) is a significant medicinal plant in the Indian primeval medicine system. Polyphenolic and polysaccharide compounds also acts as inhibitors during Genomic DNA isolation from young leaves of T. arjuna, resulting in recovery of low quality genomic DNA, which affects downstream applications like PCR, restriction digestion’s, etc. In this study, nine different methods of genomic DNA isolation were used, out of which two methods were modified CTAB based methods, third one was HEPES based method and remaining six methods was FTA Plant Saver Card based. Out of the six FTA card based methods, in the first method, leaves were directly pressed inside the circle of FTA card. In the second and third methods, the leaves were homogenized with PBS and DNase RNase free water and the sample was applied on the FTA card. In the fourth and fifth methods: finally recovered DNA from two modified CTAB based methods was directly applied to the FTA card. In the sixth method, DNA precipitated after first phenol:chloroform:isoamyl alcohol precipitation of modified CTAB based methods dissolved in DNase RNase free water and applied to FTA Card. To optimize the PCR conditions, BSA (400 ng/μl), formamide (2.5%), DMSO (5% and 10%) and glycerol (5%, 10%, 15%, and 20%) was added into the PCR mix as enhancement agents for amplification of low quality genomic DNA (A260/A280 – 1.27 ± 0.090) of T. arjuna recovered using the HEPES Based method. It was found that the BSA was the best among them followed by 10% glycerol. In addition of BSA to the PCR mixture, it specifically enhances the amplification of the low quality DNA. It reduces the noise in-between the amplified bands and increases the intensity of PCR product.