GO:0000404 ! loop DNA binding uses loop DNA to mean a ssDNA loop formed by a heteroduplex involving a deletion or insertion. In other contexts, DNA loop refers to a dsDNA loop formed by juxtaposition of binding sites that are separated on a DNA, as in loop formation by enhancer binding proteins, or looping by lac or lambda repressors in bacteria.
suggestions: rename to
GO:0000404 ! heteroduplex DNA loop binding
Edited as suggested.