GETTING THE STAIN IN: A QUANTITATIVE ANALYSIS OF DNA AND RNA STAINING WITH VARIOUS DYES

Rupak Bhuyan, Lauren Dai, Tyler Davenport, Bruce Easop, Arka Mallela, Kenneth Pu, Shireen Rudina, Tina Sankhla, and Margaret Yang

Advisor: Dr. Amber Charlebois
Assistant: Jeremy Tang

ABSTRACT

Staining and other methods of distinguishing between deoxyribonucleic acid and ribonucleic acid in polyacrylamide gels tend to be dangerous or expensive . In addition, retrieving quantitative data from DNA and RNA bands to determine linearity between absorbance and sample size of nucleic acid using fiber optic technology to date has not been established. In an effort to find the dyes that most effectively address these concerns, eight dyes were tested with single stranded DNA and RNA by polyacrylamide gel electrophoresis. The gels were then analyzed with fiber optic spectroscopy to determine which dyes best distinguished between DNA and RNA bands. Of the eight dyes, only Methylene Blue displayed significant differences in absorbency between bands of DNA and RNA. Methylene Blue, Cresyl Violet, Thionin, and Azure B were used to stain gels containing increasing concentrations of nucleic acids to determine if there was a linear relationship between amount of nucleic acid and absorbance. Based on the results of two runs for each stain, Methylene Blue and Azure B showed the greatest linearity in RNA up to 100 pmole. Results for staining of DNA were inconclusive and the other stains lacked clear linear relationships.