Thank you for the response. I am trying to label by DNA attached to an azide with DBCO. But it doesn't get labelled. I am using PBS buffer, 10 pmol 17 mer oligo with an alkoxyamine attached to an abasic site with 300 uM DBCO, react them at RT or 37 overnight. I cant figure out why this happen.

Dear Lakshani Perera  its may be due to steric hindrance when reacting with azide-DNA molecule you should use short spacer molecule such as PEG eg. Extended PEG4 Spacer 

Hi Arvind, 

Thank you for your kind response. 

Yes that is what I am thinking. My Azide is 2 C atoms away from the AP site. This may be not enough to react with DBCO due to the hindrance since it contain a cyclooctyne with 2 benzene rings. Fortunately BCN which is only a cyclooctyne, reacts well. Now I am trying to make a new alkoxyamine 5-6 C chain length. Hopefully it will react with DBCO. 

Hello Lakshani,

I don't think there is something wrong with reaction conditions, not with spacer length. I think the problems is either azide or DBCO, either one is not good any longer. Azides can be easily reduces. How did you put azide onto your oligo? DBCO compounds can go bad quickly under very acidic conditions. 

Hi andrei, 

I made an alkoxyamine with an azide. I attached  this to the abasic site in my oligo (which has an aldehyde group) so it forms an oxime. Now I am trying to tag the azide with DBCO-CY5. I tried it by changing so many conditions such as different buffers, ph , temperature, concentration etc. This reaction doesn't work.  Alkoxyamine reacts with the ap site very well. But I cannot understand why doesn't it get react with DBCO.  Also when I ran DBCO -CY5 on Urea-PAGE it gives me lots of bands too.