696969 Be careful what sealer you use,especially if you plan any paintwork around that area in the future,I would try and avoid silicon based sealers.
Your best bet is to find a butyl based compound it's non setting and non aggressive (it wont hurt your paint)
I'm not sure if it's available your side of the pond but I use a product called
Arbomast ,it's designed specifically for the problems you describe.
Failing that,talk to your local auto glass shop,they might be able to suggest a suitable alternative.