Filling the spaces between boards in hardwood floors.

I am getting ready to reseal the hardwood flooring in a 100 year old house. There are some pretty big spaces in between many of the boards that create a dust trap... I would like to fill these spaces with some kind of (preferably clear and flexible) caulk or filler... I was warned against this because the boards need room to expand with the weather... any ideas? It seems to me that a material that remained rubbery would be ok... Not concerned with how it looks in the end... I just want the surface to be sealed.