Exploring DNA minor groove interactions through a probe conjugate in major groove: fluorescence studies on netropsin complexation with dU-5-aminodansyl-DNA.

The binding of netropsin to 5-Aminodansyl-dU-DNA (2-5) in minor groove is shown to correlate with fluorescence changes of dansyl fluorophore located in major groove. This enables a study of a minor groove binding event through crosstalk with conjugated probe in major groove. The dielectric constant of major groove estimated from fluorescence properties of (2-6) is about 55D in contrast to the literature reported minor groove dielectric constant of 20D in the poly[d(AT)]-poly[d(AT)] duplex.