My Unique Dual Indices with Nextera adapters, dont bind with any library preparation method

[P.B]

Hello everyone!

We designed Unique Dual Indices, with both nextera adapter sequences and truseq so we can see which performs better, in the hopes of sequencing on a NovaSeq.

Every possible library preparation did not work. Ligation, Tagmentation and fragmentation, nothing. The amplicon sequencing commercial kit works with the commercial indices but not with ours.

So question would be why did it not work?

What are some points one needs to pay attention?

How do these adapters bind and what could possibly be the reason for them not to bind?

Can anybody give any insight ?

Thank you !