Concerted intercalation and minor groove recognition of DNA by a homodimeric thiazole orange dye

The thiazole orange dye TOTO binds to double-stranded DNA (dsDNA) by a sequ ence selective bisintercalation. Each chromophore is sandwiched between two base pairs in a (5'-CpT-3'):(5'-ApG-3') site, and the linker spans two bas e pairs in the minor groove. We have used one- and two-dimensional NMR spec troscopy to examine the dsDNA binding of an analogue of TOTO in which the l inker has been modified to contain a bipyridyl group (viologen) that has mi nor groove binding properties. We have investigated the binding of this ana logue, called TOTOBIPY, to three different dsDNA sequences containing a 5'- CTAG-3', a 5'-CTTAG-3', and a 5'-CTATAG-3' sites, respectively, demonstrati ng that TOTOBIPY prefers to span three base pairs. The many intermolecular NOE connectivities between TOTOBIPY and the d(CGCTTAGCG):d(CGCTAAGCG) oligo nucleotide in the complex shows that the bipyridyl-containing linker is pos itioned in the minor groove and spans three base pairs. Consequently, we ha ve succeeded in designing and synthesizing a ligand that recognizes an exte nded recognition sequence of dsDNA as the result of a concerted intercalati on and minor groove binding mode.