Fluorescent d(CGCGAATTCGCG): characterization of major groove polarity and study of minor groove interactions through a major groove semantophore conjugate.

The major and minor groove in duplex DNA are sites of specific molecular recognition by DNA-binding agents such as proteins, drugs and metal complexes and have functional significance. In view of this, understanding of the inherent differences in their environment and the allosteric information transfer between them induced by DNA-binding agents assumes importance. Site-specific incorporation of 5-aminodansyl-dU, (U*) in oligonucleotides d(CGCGAAU*TCGCG) and d(CGCGAATU*CGCG) leads to fluorogenic nucleic acids, in which the reporter group resides in the major groove. The fluorescent observables from such a probe are used to estimate the dielectric constant of the major groove to be approximately 55D, in comparison to the reported non polar environment of the minor groove (approximately 20D) in poly d[AT]-poly d[AT]. An exclusive minor groove event such as DNA-netropsin association can be quantitatively monitored by fluorescence of the dansyl moiety located in the major groove. This suggests existence of an information network among the two grooves. The fluorescent DNA probes as reported here may have potential applications in the study of structural polymorphisms in DNA, DNA-ligand interactions and triple helix structure.