Different binding structures of a covalently linked bodipy-493/503 dye to an oligonucleotide investigated by satellite hole spectroscopy

Abstract

Distinct non-resonant holes in the satellite hole (SH) spectra as a function of burning wavelength have been used to distinguish two major complexes of 4,4-difluoro-1,3,5,7-tetramethyl-4-bora-3a,4a-diaza-s-indacene-8-propionic acid, succinimidyl ester (BP493) covalently bound to an oligonucleotide of ten bases of thymidine deoxyribonucleotides, d(T₁₀), when these two adducts cannot be separated in sample preparation. Our SH results further suggest that different sites of the BP493 interact with the d(T₁₀) in these adducts. In addition, the lack of photochemical antihole implies no interconversion between these two adducts. By comparison with the significant effect on the N₂BF₂ moiety of 4,4-difluoro-5-(4-phenyl-1,3-butadienyl)-4-bora-3a,4a-diaza-s-indacene-3-propionic acid, succinimidyl ester (BP591) upon covalent attachment to the d(T₁₀), we anticipated that the four methyl groups in BP493 can interfere with the π–π interaction of the aromatic rings stacked between the BP493 and d(T₁₀).