[luc]

It seems unlikely that LNA bases would be used - to my knowledge, LNA in the template inhibits most polymerases.
I assume the phosphorothioate linkage helps predominantly preventing 3’ to 5’ exonuclease activity of the ligase - reducing adapter dimers.
We too, had good experiences with the Bioo adapters though.

[NextGenSeq]

Reduction of non-insert sequence reads by dimer eliminator LNA oligonucleotide for small RNA deep sequencing

Here we describe a method for constructing small RNA libraries for high throughput sequencing in which we have made a significant improvement to commonly available standard protocols. We added a locked nucleic acid (LNA) oligonucleotide—named dimer eliminator—that is complementary to the adapter-dimer ligation products during the reverse transcription reaction. It reduces adapter-dimers, which often contaminate standard libraries and increase the number of non-insert sequence reads.

http://www.biotechniques.com/BiotechniquesJournal/2010/October/Reduction-of-non-insert-sequence-reads-by-dimer-eliminator-LNA-oligonucleotide-for-small-RNA-deep-sequencing/biotechniques-304403.html

Tufts LNA Adapter Protocol

http://www.tucf.org/htseq_protocol_for_illumina_paired.pdf

[M4TTN]

Dear NextGenSeq, (apologies for dragging up an old post!)

I have a DNA enrichment project where our inserts range from only 40bp and up. We'd like to get them all.

We've just done a run and it is clear that we have sequenced a lot of adapter dimers (we expected that to be the case from the bioanalyser trace). My question is how applicable your strategy for dimer removal would be to standard Illumina DNA-DNA adapter dimer junctions? From the % base trace on MiSeq reporter it appears that most of the adapter junctions have gained an A (complementary to the overhanging T).

i.e. the pure adapter dimer junction should be: GCTCTTCCGATC/GATCGGAAGAGC
But we see (I think): GCTCTTCCGATCtaGATCGGAAGAGC

Or rather: in the sequence trace we see: AGATCGGAAGAGC...

And since the read primer ends: ...GCTCTTCCGATCT

This presumably means that the overhanging T is present (for the read primer to work) and an A has been added upstream of the GATCGGAA...

So...questions:
Would an oligo that spans this junction inhibit PCR?
What is the role of the LNA within this oligo?

[nucacidhunter]

i.e. the pure adapter dimer junction should be: GCTCTTCCGATC/GATCGGAAGAGC
But we see (I think): GCTCTTCCGATCtaGATCGGAAGAGC

Or rather: in the sequence trace we see: AGATCGGAAGAGC...

And since the read primer ends: ...GCTCTTCCGATCT

This presumably means that the overhanging T is present (for the read primer to work) and an A has been added upstream of the GATCGGAA...

So...questions:
Would an oligo that spans this junction inhibit PCR?
What is the role of the LNA within this oligo?

I think adapter-dimer formation is more complex. I would suggest analysing a TruSeq Universal and Index adapter for hetero-dimer formation for instance using OligoAnalyzer. You will see that there is more than one way for hetero-dimer formation with relatively low Delta Gs (they will anneal during annealing step) and each of those can be extended and then those products can form new versions of hetero-dimers in the following cycles.

In your target range the best way for getting rid of dimers is preventing or reducing dimer formation by careful titration of adapters or using dimer-free adapter technology.

PS. I have not seen any proof that Illumina uses LNA technology in their adapter oligos but LNA will increase the stability of annealed adapter oligos.