Nominating any one novel as the single most significant is a tough call. I'd have to think long and hard before even drawing up a short list. Hmm...
As far as
Dune is concerned, I disagree with many of the previous comments.
Dune was
extremely significant. Why? Because it produced a world, an ecosystem and a society that were incredibly well realised and vividly portrayed; far beyond anything SF had seen before.
If Hal Clement's
Mission of Gravity upped the stakes for SF writers in terms of accurate science (which it did), then
Dune did the same with regard to the realism of the setting and world-building. Before
Dune, planets were just a backdrop against which adventures were set. With
Dune, Herbert gave that backdrop a texture and made it integral to the story. No SF novel had done anything like that before.
Perhaps this is something that's easily missed today, when such things are common place in SF, but they're only common place because of
Dune. Okay, I agree that it probably isn't
the most significant SF novel of all time, but it remains a very important, even a vital one.
Oh, and for the record, I think Frank Herbert's
Dune went way beyond the genre of space opera. It's taken Brian Herbert and Kevin J. Anderson to turn it into that.