Create a PHP file where you have all the code to interact with the database.
Then from your JS file make an AJAX call using POST or GET method.
Example:
This can be in your JS code
parameters = "url=" + yourJSObject;
    request = new XMLHttpRequest();
    request.open("POST", "yourPHPFile.php", true)
    request.setRequestHeader("Content-type","application/x-www-form-urlencoded")
    request.setRequestHeader("Content-length", params.length)
    request.setRequestHeader("Connection", "close")
    request.onreadystatechange = function()
        {   
            if (this.readyState == 4)
            {
                 if (this.status == 200)
                    {
                     if (this.responseText != null)
                        {
                            ///You can use this responseText from your PHP file
                        }                       
                    else alert("Ajax error: No data received")
                    }
                else alert( "Ajax error: " + this.statusText)
             }
        }
 request.send(parameter)
And this is yourPHPFile code:
<?php 
 if (isset($_POST['url']))
 {
    $js_object = $_POST['url']
     /*use this object as you want */
 }
?>
EDIT: please refer to this example I wrote here