Modification Of Illumina Adapters

Question

[zeropoint1]

Hello,

I need to sequence some DNA that has a small random region flanked by primers. It looks like this:

Primer 1 - N50 - Primer 2

The issue is that the Primer sections are not compatible with the normal adapters used for illumina sequencing. For example:

Snsillumina (TruSeq Universal Adapter) AATGATACGGCGACCACCGA GATCTACACTCTTTCCCTACACGAC GCTCTTCCGATCT

Antillumina#1 CAAGCAGAAGACGGCATACGAGAT CGTGAT GTGACTGGAGTTC AGACGTGTGCTCTTCCGATCT

So, there appears to be two options:

1) Add sections onto the two above adapters which make them compatible with the primer 1 and 2 regions of my DNA.

OR

2) Truncate the rightmost portions of those adapters and replace them with seconds matching my primer 1 and 2.

1 is the safer option but there are some major advantages to 2.

I would like to know if there is any danger in messing with those rightmost regions of the adapters and if this will introduce complications into the sequencing (MiSeq).

Your advice is very appreciated.

Thanks!

Answer 1

[Istvan Albert]

I would be carful with messing with the adapters ;-) both regions are required, this is how the fragment gets those little floppy overhangs that are needed during sequencing.

See also this: Illumina TruSeq DNA Adapters De-Mystified