Presumably as long as there is a way for everyone to access whatever information you are supplying, then yes. If you are relying entirely on JavaScript to provide said information, then I would guess no, since not everyone has JavaScript enabled. Section 508 requires <noscript>
tags that provide the ability to get the information in by other means because not all assistive technology can access the same. That seems to be the general way these things work (the W3 Accessibility guidelines emphasize that, and the 508 standards, specifically those on equivalency, seem to say much the same).
So the presentation doesn't have to be the same, as long as the experience is "comparable", according to the 508 standards. But I would think that if the presentation relies on JavaScript (and dynamic DOM building requires JavaScript), the experience would not be comparable, and thus you would have to provide an alternative HTML-only version of the site.