A lot of work has been done using capillary electrophoresis to measure the binding affintiy between aptamers and there respective targets.
ITC could be an better option for the measurement of affinity and binding kinetics.
I would suggest using fluorescence microscale thermophoresis (MST) for determining Kd of aptamers and small molecules, as well as for nanoparticle complexes. (Nanotemper Inc is the supplier for the system I use, if that helps)
Thanks to all for your suggestions. ITC and MST are excellent techniques, I gather, for small molecular interactions, especially since they are not mass dependent. However, fluorescence based studies (including MST) require tagging. SPR is probably a very accurate label free technique, and there are dedicated instruments for small molecule analysis. Hopefully, I shall be able to use one of them for the work.
Could biolayer interferometry be an option?
I would suggest KinExA technology for your measurements. KinExA instruments provide accurate data (with easy to use software) and industry leading sensitivity, ideal for determining Kd.
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