Recently I conducted an experiment to conjugate amine-modified oligonucleotides with hydrogel particles having carboxyl groups. However, the fluorescence (from hybridized FAM-DNA) only appears on a small area of the particle and its shape is this ill-defined, like in the image below.
My advisor said that "DNA is negative charge and carboxyl group also have negative charge so there is no possibility of conjugation, conjugation of streptavidin to particle, attaching biotinylated DNA and proceed with hybridization".
However, conjugation using NHS / EDC requires both an amine group and a carboxyl group. Does streptavidin have the requisite chemical groups to do such a conjugation? Streptavidin is Sigma Aldrich's 85878 (Streptavidin of Streptomyces avidinii, affinity purified, 10 mM potassium phosphate, lyophilized product of ≧ 13 U / mg protein).
PS: Please tell me if there is a secret to make it conjugate evenly on the surface.
PPS: We use 5 μM anime modified oligonucleotide and 100 nM FAM-DNA.