[jwfoley]

I misunderstood the question. Yes, as long each molecule's outer sequences are still the two distinct P5 and P7 adapters, not identical, the innermost sequence can match. (The innermost dozen bases match on the original Solexa adapters too, not just Nextera, because that's the complementary portion of the Y-linker.)

But because of the Tm issue, it'll need to be a longer primer than that. On the other hand, because the inner sequences of the Illumina adapters match, it might still be the same primer for both ends.

Don't try this unless you really know what you're doing.

[bilyl]

This can probably work, as long as you have the P5 and P7 sequences surrounding the sequencing primer. That is, it's not exactly an inverted repeat.

The only issue you will have is competition for hybridization from the reverse complement that exists in cis on the library that's on the flow cell versus your incoming sequencing primer. But if you flood it in at 0.5uM you should still be able to get a large number of clusters.

[aaron_tao]

Thanks so much. It help me a lot. I would design a longer adapter according illumina's guideline.