What is the difference (especially in enzymatic incorporation and/or after incorporation as a template for PCR) between Biotin-AA-dCTP (N-5002) and N4-Biotin-OBEA-dCTP (N-5004)? I want to incorporate biotin in a primer extension reaction (Klenow), pull down with streptavidin, and then use the biotinylated template for PCR. – Jen

A. We have documented Biotin-AA-dCTP (N-5002) incorporating at a very high percent substitution for dCTP, up to 97%, in our white paper: PCR incorporation of modified dNTPs: the substrate properties of biotinylated dNTPs. We do not have analagous PCR data on the efficiency of the N4-Biotin-OBEA-dCTP (N-5004), but since the modification is to the N4 nitrogen, it may interfere with Watson-Crick base pairing. Therefore, while this dCTP analog can be incorporated in PCR, the percent substitution for dCTP may not be as high as for Biotin-AA-dCTP.
As you eluded to, different analogs will incorporate in PCR with varying efficiency and some optimization may be needed. We recommend performing some initial PCR experiments using natural:modified dNTPs in ratios such as 1:0, 3:1, 1:1, 1:3 and 0:1 to identify the best conditions for modified nucleotide incorporation with robust amplicon yield.