5-amino-2'-deoxyuridine, a novel thymidine analogue for high-resolution footprinting of protein-DNA complexes

[formula: see text] 5-Amino-2'-deoxyuridine 5'-triphosphate, an analogue of deoxythymidine triphosphate, was synthesized and found to be a substrate of Taq DNA Polymerase. The DNA-borne analogue underwent selective chemical reaction with permanganate. The use of 5-amino-dU as an interference probe was validated using the Ada protein/ada promoter complex. The performance of 5-amino-dU in interference footprints is similar to that of the previously described analogue 5-hydroxy-dU, but the former is incorporated more readily into DNA during enzymatic polymerization.