Spectroscopic Investigation of Metal Ion Binding to DNA Hairpin Loops
Metal ions purportedly bind to and stabilize unique DNA structures such as loops, bulges, hairpins, and base pair mismatches. Spectroscopic techniques are useful for the study of metal ion binding. In our work, the biologically relevant metal ion magnesium (II) is substituted by luminescent lanthanide ions. Direct-excitation europium (III) ion luminescence spectroscopy is used to study europium (III) ion binding to various DNA hairpin loops. New 7Fo to 5Do excitation peaks are observed for sequences containing thymines including 5’-GCG CTT TGC GC-3’. Excitation peak position and intensity is dependent on the closing base pair but not the stem sequence. Other more highly structured loops including GNRA tetraloops do not strongly bind europium (III). Time resolved luminescence spectroscopy experiments show that the europium (III) ion looses at least one water ligand upon binding to the thymidine containing hairpin loops. Thermal melting experiments confirm that the hairpin loops form in the presence of an equivalent (20 micromolar) of europium (III) with very little change in melting temperature.