qPCR negative controls

[Gerardine.Persson from gmail.com]

This is a fundamental question about (quantitative realtime) PCR.

Hi group,
I've been using ABI7000 realtime PCR, mostly with SYBR detection. I've
always been wondering why I pick up some amplification eventually.

I get amplification of my samples containing template, so far so good.
They come up at cycle numbers that are around 20-30.

My negative control (PCR with water as "template") also gives
amplification, although as late as CT 35-45, depending on the primer
pairs used. But eventually, they all come up.

My questions:
- What exactly is actually amplified here? I've had many students ask
me, and I grow tired of answering "I don't know, stop asking"

- Why do the CTs vary widely (standard deviation of ca. 3 opposed to
<0,5 for normal triplicates) in the negative controls?

Just so this is clear: I'm not looking for a solution to a problem. I
just want a sound explanation of this phenomenon, which has been
bugging me for a while! And who knows, maybe my students will learn
something, too :)

Cheers,