...Sometimes I will even get noise at 400. ...
All digital images always have noise, period. Whether your brain notices the noise is affected, in part, by the detail in the image. In images with large middle-toned areas that lack detail (e.g. medium blue skies, ...) the noise is more noticeable. When there is a lot of fine sharp detail (e.g. the squirrel's fur in the pic in one of the other replies) you brain doesn't "see" the noise even when its rather significant.
Also, any image processing to correct for white balance, other than "daylight", or underexposure is the equivalent of using a higher ISO and results in increased noise. A shot under common tungsten light requires a 2-3 stop amplification of the blue channel to accomplish WB. If shot at ISO 400, the blue channel would be effectively working as ISO 1600-3200 and would have the accompanying increased noise.
Also, when doing HDR, how I can aviod getting noisy photographs as my end result?
Use only the lowest ISO available and, of course frame your pictures properly when shot so that there is no need to do any cropping other than to alter the aspect ratio to fit the composition.
If you are using HDR techniques to produce true High Dynamic Range images you should
NEVER use anything other than your camera's lowest ISO.
Any increase in ISO will always reduce the dynamic range of the individual shots in the stack and is thus working against your goal.
Using anything other than the lowest ISO when doing HDR should be for only those times that true HDR is not your goal, for times when you are using HDR techniques for solely its Tone Mapping to create exaggerated colors and tones.