Minimum size of DNA insertion fragments

[mccullou]

I have small DNA fragments (avg 44 nt) that I would like to sequence but this is out of the recommended range of the GAII. I understand the limits of larger fragments (limited cluster density/large clusters) but, aside from the physical limitation of forming the bridge, what is the real limit to smaller insertions? I have circularized padlock probes from as short at 90 bps meaning the oligo must for a complete circle rather then just a 180° bridge, so the pliability of DNA shouldn't really be a factor.

Has anyone sequences this small of a fragment and if so, what were the limits and what recommendations do you have?

For technical info there will only be ~20 - 30 unique sequences so I anticipate 10K coverage, so if cluster formation efficiency is the issue for smaller fragments, I should still have more than enough coverage.

[elhb]

I recently asked illumina what the minimum supported insert size was and got the following answer:

"The smallest insert size from all the sequencing applications is small RNA. The insert size of the small RNA is between 22nt to 30nt. The small RNA library has to go on single read FC.

The recommend insert size for the gDNA library prep is 150-250bp. You could go 100bp of insert size. There is no problem with the cluster generation. However, if you perform a 2X51 cycle paired end run, or longer run, the two reads could be overlapping. "

So it seems that the bridge amplification isn't limiting the minimum size (I did not check the adapters for the small RNA library, but they are probably not that different from single read gDNA adapters).