Yes, take a look at the following forum post:
http://forums.asp.net/t/1443955.aspx
The RegEx pattern you are looking for would be something similar to the following:
"(?<!<[^>]*)Jon Doe(?<![^>]*<)"
Basically, you're doing a search and replace on anything that lives outside brackets <>.
JavaScript:
phrase = phrase.replace(/"(?<!<[^>]*)Jon Doe(?<![^>]*<)" /i, "is not");