DETERMINATION OF THE NUMBER AND LOCATION OF THE MANGANESE BINDING-SITES OF DNA QUADRUPLEXES IN SOLUTION BY EPR AND NMR

The paramagnetic metal ion Mn2+ has been used to probe the electrostat ic potentials of a DNA quadruplex that has two quartets with an overal l fold of the chair type. A quadruplex with a basket type structure ha s also been examined. The binding of the paramagnetic ion manganese to these quadruplex DNAs has been investigated by solution state electro n paramagnetic resonance (EPR) and nuclear magnetic resonance (NMR) sp ectroscopies. The EPR results indicate that the DNA aptamer, d(GGTTGGT GTGGTTGG), binds two manganese ions and that the binding constants for each of these sites is similar to 10(5) M(-1). The NMR results indica te that the binding sites of the manganese are in the narrow grooves o f this quadruplex DNA. The binding sites of the DNA quadruplex formed by dimers of d(GGGGTTTTGGGG) which forms a basket structure are also i n the narrow groove. These results indicate that the close approach of phosphates in the narrow minor grooves of the quadruplex structures p rovide strong binding sites for the manganese ions and that EPR and NM R monitoring of manganese binding can be used to distinguish between t he different types of quadruplex structures.