V3 NimbleGen exome kit

[sehrrot]

Dear all,

I am looking forward to use v3 NimbleGen exome kit. But I found that blocking oligos a bit different from v2 NimbleGen exome kit for Illumina TruSeq kit.
It's bit like that a blocking oligos changes the strands .

Does anyone know this issue?

[Rocketknight]

Yeah, they've replaced the blocking oligos with reverse-complemented versions. Additionally, the new versions have extension-blocking modifications.

As far as I'm aware the purpose of those oligos is to stop the adapter sequences on your fragments annealing to each other during the hybridisation step, which means that it shouldn't really matter whether the original or reverse-complement sequence is used.

I presume the reason they changed has something to do with avoiding negative downstream effects of having those oligos in the mix - possibly they were interfering with the later PCR somehow, maybe getting extended and ending up as weird contaminants in the library? Or just annealing to the PCR primers?