mindboggling ITS

[Menno.Sch...@fungen.el.wau.nl]

Dear molecular malacologists,

I have something very weird. I obtained a PCR-product of ITS from Albinaria
which is 440 bp long on gel (both on agarose and PAGE). But when I sequence it,
either directly or in cloned form, it comes out as only 395 bp long. Suspecting
a stable hairpin, we did the sequencing reaction under denaturing conditions
(DMSO, high annealing temperature), but no improvement. I am at my wit's end how
to explain this. Does this sound familiar to anybody? Could it be that certain
sequences look longer on gel than they actually are? Or is it some post-PCR
modification? Please, help!

Menno Schilthuizen PhD
Lab. of Genetics
Wageningen Agricultural University
Dreijenlaan 2
6703 HA Wageningen
The Netherlands
tel. +31-317-483142
fax. +31-317-483146
Menno.Sch...@fungen.el.wau.nl