I would like to crosslink 10 bp amine terminated DNA probes onto carboxylated microspheres at a controlled density. The carboxyl density on my beads is 2-7 (A^2/carboxyl), however I want to have a final probe density of 19000 (A^2/probe). This equates to ~5000 fold reduction in binding density.
I was wondering if after sulfo-NHS/EDC activation of carboxylated beads, I could link my aminated oligos in a 1:5000 molar ratio with a quencher, for example ethanolamine to achieve desired probe spacing. Does this sound reasonable at all? Are there better alternatives to ethanolamine?
Im sure the difference in mass between ethanolamine and my 10 bp probe will result in favored kinetics for ethanolamine over the probe. If anyone knows any back of the envelope calculations to account for that, that would also be helpful.
You just have to try to find out, use NHS( sulfo-NHS )/EDC chemistry@different condition. You can order probes with various C3 spacers (or other spacers) and NH2 group,. Aminated oligos already have C6 linker, people also use T, TT, TTT,... as spacers.
There should be a lot of protocols out there for conjugation of aminated oligos onto COOH spheres.
Good luck!
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