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.
Barawkar
D A
DA
Division of Organic Chemistry, National Chemical Laboratory, Pune, India.
Ganesh
K N
KN
D001483:Base Sequence; D001665:Binding Sites; D004247:DNA / Q000737:chemistry*; D003619:Dansyl Compounds / Q000737:chemistry*; D008969:Molecular Sequence Data; D009429:Netropsin; D009690:Nucleic Acid Conformation; D009691:Nucleic Acid Denaturation; D009838:Oligodeoxyribonucleotides / Q000737:chemistry*; D011067:Poly dA-dT / Q000737:chemistry*; D013050:Spectrometry, Fluorescence; D013329:Structure-Activity Relationship; D013816:Thermodynamics
D003619:Dansyl Compounds; D009838:Oligodeoxyribonucleotides; D011067:Poly dA-dT; D009429:Netropsin; D004247:DNA