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Nucleic Acids Research, 1995, Vol. 23, No. 5 844-848
© 1995

STRUCTURAL BIOLOGY

Determination of the number and location of the manganese binding sites of DNA quadruplexes in solution by EPR and NMR

Ke Yu Wang, Linda Gerena, S. Swaminathan1 and Philip H. Bolton*

Chemistry Department, Wesleyan University Middletown, CT 06459, USA 1Gilead Sciences 346 Lakeside Drive, Foster City, CA 94404, USA

*To whom correspondence should be addressed

Received October 20, 1994. Revised January 5, 1995. Accepted January 5, 1995.

The paramagnetic metal ion Mn2+ has been used to probe the electrostatic potentials of a DNA quadruplex that has two quartets with an overall fold of the chair type. A quadruplex with a basket type structure has also been examined. The binding of the paramagnetic ion manganese to these quadruplex DNAs has been investigated by solution state electron paramagnetic resonance (EPR) and nuclear magnetic resonance (NMR) spectroscoples. The EPR results indicate that theDNA aptamer, d(GGTTGGTGTGGTTGG), binds two manganese ions and that the binding constants for each of these sites is –105 M–1. The NMR results indicate that the binding sites of the manganese are in the narrow grooves of this quadruplex DNA. The binding sites of the DNA quadruplex formed by dimers of d(GGGGTTTTGGGG) which forms a basket structure are also in the narrow groove. These results indicate that the close approach of phosphates in the narrow minor grooves of the quadruplex structures provide strong binding sites for the manganese ions and that EPR and NMR monitoring of manganese binding can be used to distinguish between the different types of quadruplex structures.


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