A novel approach to produce DNA molecular size marker

Determining the length of nucleic acid in molecular laboratories is necessary. The DNA molecular ladder consists of DNA fragments with different lengths but known sizes to estimate the size of unknown DNA molecules on the agarose gel electrophoresis. Therefore, DNA size indicators are essential tools in molecular biology, genetics, biotechnology, and the related-laboratories. Producing DNA molecular ladders encounters some limitations due to inflexibility, complexity, time-consuming, and costly methods. In this study, using bioinformatics and the combination of PCR and restriction enzyme, a simple and cost-effective method for production of DNA ladders is introduced. A house-keeping gene from the Saccharomyces cerevisiae was considered as the template gene. ۱۷ pairs of primers and ۲ restriction enzymes Eco۷۲I and Bsp۶۸I were also used to design the DNA molecular ladder. Two bioinformatics software Snap gene (version ۳.۲.۱) and Gene runner (version ۶.۵.۴۶ x۶۴ Beta) were used in the primer design and PCR reaction and other related processes. Finally, ۲۶ fragments with different lengths were obtained in a wide range from ۵۰ to ۱۰,۰۰۰ bp with high accuracy. The designed fragments include ۵۰ bp, sizes ranging from۱۰۰ to۱۰۰۰ in ۱۰۰ bp increments, ۱۲۵۰-۱۷۵۰ in ۲۵۰ bp, ۲۰۰۰-۴۰۰۰ with a distance of ۱۰۰۰ bp, ۴۵۰۰-۶۵۰۰ with a distance of ۵۰۰ bp, ۶۵۰۰-۹۵۰۰ with a distance of ۱۰۰۰ bp and ۱۰,۰۰۰ bp.

کلیدواژه ها:

Bioinformatics ، DNA molecular ladder ، PCR simulation ، Enzymatic digestion