Why can I see my phosphorothioate oligo when I stain the gel with ethidium bromide?
RESPONSE:It appears that the sulfur of the phosphorothioate linkage can quench the fluorescence of ethidium bromide. I know researchers who could see their phosphorothioate oligo by UV shadowing but when stained with EtBr, no bands were observed, while on the same gel, normal phosphodiester oligos stained perfectly. FAQs QUESTION: How do you calculate the extinction coefficient of an oligo? RESPONSE:Calculate extinction coefficient of an oligo by either summing up the extinction coefficients of the individual bases times their number of occurrences. Or use a formula that takes into account nearest neighbor effects. algorithm for this calculation can be found on the web (http://www.basic.northwestern.edu/biotools/oligocalc.htmll). Just type in the sequence and the program will calculate the concentration of a 1 A260/ml solution. To calculate the MW of the aminomodified oligo just add 179.16 to the calculated MW of the unmodified oligo.
