Single and Double flux DNS activity detection and prevention

What are the mechanisms to prevent users from visiting malware sites
even when Single/Double flux methods are used?  I am using snort
inline IPS.

I had gone through http://www.honeynet.org/papers/ff/fast-flux.html
and http://netsecinfo.blogspot.com/2008/04/botnets-using-fast-flux-and-double-flux.html.

One of the mitigation technique mentioned is to apply domain block
list.  I feel that domain name based block list is CPU intensive.  Are
there any other simple methods?

Thanks
Ravi

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