I am trying to determine my drug's target using biotinylated compound. I'm using the shortest version of EZ-link NHS biotin (linker is 13 A). The compound binds to my streptavidin beads, but I am not able to pull out any protein targets. I was wondering if increasing the linker length would help. Thanks.
Carlo Zambonelli
It might help, which is why you have different length linkers at your disposal. But the fact that you are not pulling down anything may suggest that you need to optimize your pull down condition, e.g. start with less stringent conditions and once you can see something pulled down move to more stringent conditions.
Assuming that your protein binds any target: do you have independent evidence of this?
Good luck
Carlo
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