Comparing Genomic DNA Extraction Methods/ Protocols to obtain High Quality DNA from Ulva lactuca

Abstract

DNA extraction is the process of isolating the nucleic acid (e.g. DNA) from the cells isolated from organism or samples. DNA extraction protocol is crucial for the quality of DNA to be isolated from a sample, it also entails the success of other downstream application like PCR amplification and sequencing. In this study, three (3) extraction protocols were used to extract DNA from the blade of a seaweed, the Ulva lactuca. The protocols that were used in this study were optimized to extract genomic DNA for other organisms, for instance, the sodium dodecyl sulfate (SDS) method was used for insects, the tri-phosphate extraction (TPE) method is used for rice, while cetyltrimethylammonium bromide (CTAB) method is commonly used for plants. Some of the components of the protocols were modified like for instance changing the pH of Tris-HCl. The experiment consists of two trials with two replicates in each trial, the trials ensure the reliability of result, specifically the experiment. For the first trial, the TPE method got the highest DNA concentration of 304.1 ng/ul but it did not pass the purity ratio of A260/280 (1.8-2.0) by only having 1.46, however, two replicates pass the A260/280 ratio and both are the replicates 1 of SDS and CTAB protocol having 1.81 and 1.80 A260/280 ratio and the concentrations of 127 ng/ul and 77.0 ng/ul, respectively. For the second trial, both the replicates using CTAB protocol pass the A260/280 ratio with 1.82 and 1.81, and DNA concentration of 24.2 ng/ul and 1,993.6 ng/ul, respectively. This concludes that, still the conventional genomic DNA extraction protocol for plants, which is the CTAB method can also be used to isolate high quality DNA from a green seaweed, the Ulva lactuca. However, some of the components of CTAB method poses health risks and possible environment hazard, the TPE and SDS method can offer a less harmful way to extract DNA, though further optimization on the components of the two protocol is highly encouraged. This study also shows that CTAB can also be used to isolate DNA from other marine plants.