DNA Isolation and Purification Protocols for DNA Amplification Enhancement in Monochoria vaginalis PCR Analysis

Kansa Dianti Putri (Horticultural Crop Cultivation Study Program, Rejang Lebong State Community College)
Ramadaniarto Rizqullah (Department of Agronomy and Horticulture, IPB University)

Biota: Jurnal Ilmiah Ilmu-Ilmu Hayati
Vol 11, No 3 (2026): October 2026

Monochoria vaginalis contains phenolic chemicals that can disrupt DNA extraction and downstream molecular processes. Phenolics are known to bind to DNA and hinder enzymatic processes, which affects procedures like PCR.  The goal of this study was to create an effective DNA extraction and purification method for obtaining high-quality genomic DNA from M. vaginalis. The DNA was extracted using a modified CTAB technique and purified with 30 μL sodium acetate and 1,000 μL 70% ethanol. The purification procedure enhanced DNA quality, as seen by less smearing and cleaner bands in electrophoresis, particularly in Sukra, Rawamerta, East Karawang, Patokbeusi, and Ciasem. After purification, DNA concentrations reduced to 6.12-37.45 µg/mL. Spectrophotometric measurements revealed higher purity, with A260/A280 ratios of 1.43-2.31 and A260/A230 ratios of 0.04-0.30. The 1,931 bp MvALS1 gene was successfully amplified across all ecotypes, demonstrating the purification method's efficacy in yielding DNA appropriate for molecular biology applications.