As mentioned above you will need to work with the PortalAlias table. I have a full guide that covers this available on my website, but to get you going you can fix things up with a simple insert into your database, and a modification of your web.config.
First you need to add a new portal alias for the new URL to be used for your site. Assuming that you have only one portal the following script should be ok to insert the alias, simply put your own values in for the mysite.com portion.
INSERT INTO PortalAlias (PortalId, HTTPAlias)
VALUES(0, 'mysite.com)
After you do this, add a space to a non-critical part of your web.config and save it. This will trigger a restart of the DotNetNuke application which will update the cache and you should be set to go!