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).