Running a defrag on ntds.dit

I had a question running a defrag on ntds.dit. We currently have 2 domain controllers but are experiencing a weird problem. There is a delay in Active Directory Users and Computers. It seems to be intermittent but sometimes you will be browsing around and get hour glasses when click on objects or OU's. This happens even logged into the local server. I'm at a loss of what it could be and thought I may take a crack at running a defrag on the ntds.dit files. I had a question about the domain controllers. We have 2. AD1 and AD2, is it best practice to take them offline one at a time and run the defrag on each? Since the ntds.dit file is not located in sysvol or netlogon I did not think they were replicated between the two dc's. Any advice or suggestions is greatly appreciated. Thank you