Is there any difference for 3' Biotinylation and 5' Biotinylation for the spacer length, binding affinity to streptavdin. Could you label DNA with nanogold particles?

The 3' biotin has one additional oxygen in the spacer, but otherwise the two biotins are the same. The biotin will have the same binding efficiency on either end of the oligo. If you will need to do any sort of extension reaction with the biotinylated oligo you should attach the biotin to the 5' end. A 3' biotin is attached directly to the 3' OH group and will block extension. We do not label oligos with gold nanoparticles, but we can supply the biotinylated or thiol modified oligos which can be used in the coupling reaction.

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