NHS esters are notoriously tricky, but if you ensure that the NHS group is reactive, and confirm that your resin came with active NHS, it should work. IDT amine-labeled oligos are usually good.

Even in solution I rarely get >70% coupling, at 10x excess of NHS ester (assuming the ester is 100% active and pure).

Check the capacity of the resin, it should be in the specs. 

May be 10% is sufficient for your purpose.

What was the resin stored in? If there was humidity, ithe NHS would hydrolyze during storage. We store all our NHS esters in dessicated jars at -20 or even -80

I sometimes get dead-on-arrival NHS esters from 'reputable' (i.e. big) companies. It's easy to check the activity of the NHS in solution using UVvis, not sure about solid phase.

Depending on the spacer between the NHS ester and the resin, the lifetime of the active compound at pH 8.3 in water can be between

Dear Andrey,

Thank you very much for your reply. I am using a HiTrap sepharose column ordered from GE, and I did not bothered to check its activity, since I trusted it to be active.

As for the spacer, I have a 10 atom spacer linked to the sepharose via epichlorohydrin. The coupling protocol states that I should insert my ligand in the buffer explained above, and to leave it at room temperature for 30 minutes. Would you recommend performing the coupling at 4 degrees to increase the efficiency?

As for the storage, it was delivered in isopropanol which is to be washed out with 1mM HCl directly before inserting your ligand for binding.

Is there yo can direct me towards some better coupling protocols for amino-modified oligos, since the default one I have is optimised for proteins.

In my experience, GE is trustworthy (if expensive). All of their NHSes (dyes etc) lived up to the specs in our hands.

If isopropanol is dry and is not repeatedly exposed to air, should be fine. Warming it to the room temp before opening is key (to prevent condensation)

Wash with the HCl makes sense, b.c. NHS esters are most stable at low pH

I doubt your efficiency will go up with o/n at 4C. In my hands, it never makes a difference. 

I would say, it's a capacity/steric_hindrance/mixing issue. Sonicate during incubation?

Well, I have put around 1mL of 5.3 A260 units of my RNA sample, and when I elute the unbound oligo in 3mL, desalt on G25 Sephadex column  and test the A260, I get result about 1.3, which should point out that I have around 1.5 A260 units of oligo in my column (that's around 35% of coupling efficiency). 

I guess I cannot expect it to go too much higher, since I have heard that people say that amino-modified oligos are not too reactive with solid phase NHS. 

Anyway, thank you for your reply. I will couple a couple of more columns with different oligos, and will let you know how it goes. 

Best