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I would like to crosslink an amino-modified DNA strand with an APTES monolayer (which also has a $\ce{NH2}$ end group) using a glutaraldehyde linker. After the formation of Schiff base linkages between the aldehyde and the amino groups, I would like to reduce the bonds using sodium cyanoborohydride to form secondary amine bonds.
Does the cyanoborohydride also affect the $\ce{C=N}$ bonds in the DNA bases or not?
Sodium cyanoborohydride is a very selective reducing agent. Another (safer) alternative would be sodium triacetoxyborohydride. But this doesn't really matter as far as $\ce{C=N}$ bonds of DNA bases are concerned since they are very stable.
