1) Make DNA based on RNA, RNA here is the template
2) Make DNA from RNA fragments (PPT), RNA here is the raw material to make DNA
Question is: How reverse transcriptase behaves differently when the same RNA piece goes through it?
Answer By Zhuang: reverse transcriptase can change its shape in two situation, which is turned on or off by cognate nucleotides and non-nucleoside reverse transcriptase inhibitors.

Fig. 4 Two working modes of reverse transcriptase
Over-doze of these inhibitors will drive reverse transcriptase too crazy to make it right. So it is exactly how HIV drug is working. So Zhuang's work lead people to have a clear vision of working mechanism of the reverse transcriptase, and some new drugs which better target these sites can be developed. Supergirl did a super job again. :-)
Feynman's prediction comes true
Feynman once said that what Biology needs is to see better at the atomic Level:
" We have friends in other fields--in biology, for instance. We physicists often look at them and say, "You know the reason you fellows are making so little progress?" (Actually I don't know any field where they are making more rapid progress than they are in biology today.) "You should use more mathematics, like we do." They could answer us--but they're so polite, so I'll answer for them: "What you should do in order for us to make more rapid progress is to make the electron microscope 100 times better."
What Zhuang Xiaowei excels is exactly what Feynan predicted. If we want to understand the life, or the cell process, we just need to see what's going on for biological molecules at single molecular level.
Reference:
[1] Dynamic binding orientations direct activity of HIV reverse transcriptase, Nature 453, 184-189 (8 May 2008)