Native d3.js methods to save / store / write data to a database?
This isn't something that you can do with Javascript -- there's no direct access to things like databases. This is not a restriction of d3, but Javascript itself. What you can do is post data to a server which will then add it to a database. There's no support in d3 for that though, only for retrieving data.
There are plenty of other Javascript libraries though that allow you to post data to a server, for example jquery.