On DNA agarose gels we take the position of these two dyes as approx 3500 bp (xylene cyanol) and 300 bp (bromophenol blue). I am curious to know the mobility values (in bps) of these two dyes when run on primer extension gels (6% acrylamide, 8% urea gels).
Firstly, base pairs is not a useful unit to think in when talking about urea gels, as your nucleic acid will (hopefully) be single-stranded. To answer your question, bromophenol will run at ~25 nt (nucleotides) and xylene cyanol 100-110 nt (although it depends whether you're running DNA or RNA as equivalent length molecules run differently owing to the greater mass of RNA).
Firstly, base pairs is not a useful unit to think in when talking about urea gels, as your nucleic acid will (hopefully) be single-stranded. To answer your question, bromophenol will run at ~25 nt (nucleotides) and xylene cyanol 100-110 nt (although it depends whether you're running DNA or RNA as equivalent length molecules run differently owing to the greater mass of RNA).
- Badges
- Science topic
- Similar topics
- Cell Biology
- Methods