Below are some Tips to protect the DNS server:-
1. Zone transfer must be secured and target only specific DNS Servers.
2. DNS must always be in DMZ or perimeter network .
3. Install Latest service pack
4. DNS servers should only resolve on internal interface only.
5. Always use Active-Directory Integrated Zone that stores zone data in Active-Directory instead of in files.
6. Always ensure Secure cache against pollution check box is marked.
7. Always use Secure dynamic update so as to prevent IP spoofing attacks.
8. Always use NTFS file system to protect data.
9. Install only that software which is from trusted source.
10. Block all unused or unnecessary ports and applications.
11. Regular monitor DNS log files.
12. Install a second DNS server for fault-tolerance.