Add "checked' property to checkbox in jquery

So I have no problem actually setting checkboxes as checked, however in my current case I need to actually add the "checked" property to the checkboxes, as the system I'm working in literally grabs the HTML from the DOM.

I can set the checkbox to be checked, however as there's no identifying "checked" property when the HTML gets inserted again it doesn't hold the property so all checkboxes come back unchecked :(

is there a way to add and remove 'checked' as a property so it will be apparent from the raw HTML what boxes are checked? e.g.

unchecked box

<input type="checkbox" value="yes" />

checked box

<input type="checkbox" checked value="yes" />

Appreciate any help!!