Manufacturer-provided cut-off figures are actually averages, as anybody who has tried to dialyze a 12 kDa protein using a 10,000 Da cutoff membrane will tell you. Your product is long enough, so I would simply switch to a filter with a larger MWCO.

Thank you, Alejandro. It is good to know as in DNA- related products 100 bp is quite a big deal, so normally I would expect warning that size cut-off is approx value. I am going to check if there is replacement for my application available.