Since the light is gonna change rather quickly you might end up with some flickering, you can fix it to a certain degree in post processing, however I think is better to avoid it at shooting time.

You can read more about it here under advanced techniques.

One trick you can use on your camera is to select the desired aperture using the depth of field button and partially disconnect the lens from the camera body to cut the communication between them, just turn it a tiny bit or you'll end up with the lens falling off, I take no responsibility for it.

Have fun.

BTW the forum at timescapes.org is full of tips and tricks.