we are having a problem sequencing a certain region of the genome. Apparently a hairpin loop is built, when the sequence is single-stranded, but it might also already be there under double-stranded conditions. So though we are doing a targeted sequencing of a specific region and have a coverage of over 5000fold, we still get a very low coverage of exactly that region, where we would like to find our results.
Does someone has any idea, as to how to solve this problem? Is there a way of preventing the building of a hairpin loop during the sequencing process, or of denaturing the sequences in the preparations?