I want to use double stranded DNA linkers to physically bind two "things" together, by grafting ssDNA on each one of them and using DNA hybridization as the locking mechanism.
I do not expect the nature of the two things to be important for this question, but if it is, let's say I want to link a solid surface and a protein.
Let's say that my only constraint is that I want this crosslinking to be stable at 37°C.
There is a gazillion ways I could design the sequences, and pretty much anything above 20bp without massive self complementarities should work, in theory. But I don't like to pick bases randomly. So my question is this: is there anything I can look for, except for the two constraints above, to design a good linker sequence?
For example, if the melting temperature is 50°C vs. 65°C, I would expect the structure to be stable (infinitesimal dissociation constants in both cases). Would there be any reason to choose one over the other, except for maybe oligo synthesis price? For a given melting temerature, is there any difference between a long AT rich sequence and a short GC rich sequence?