Satellite hole investigation of binding mechanism of dipyrrometheneboron difluoride derivative and oligonucleotide in glycerol–water glass

The satellite holes in hole burned (HB) spectra have been used to study the binding modes of chromophore–oligonucleotide interactions. Substantial differences of several distinct satellite holes of 4,4-difluoro-5-(4-phenyl-1,3-butadienyl)-4-bora-3a,4a-diaza-s-indacene-3-propionic acid, succinimidyl ester (BODIPY591) chemically bound to an oligonucleotide of ten bases ofthymidine deoxyribonucleotides, d(T10), doped in glycerol–water (Gl–H2O) glass are observed. Normal mode calculations fordipyrrometheneboron difluoride (BODIPY) and an HB study of the BODIPY591 derivative have been conducted to help with vibrational mode assignments. The lack of appreciable perturbations on the vibrations of the diene chain and the phenyl group implies that these groups are much less perturbed upon interacting with d(T10). However, significant frequency differences for several N2BF2 modes indicate that the geometry of the N2BF2 moiety is dramatically perturbed upon interacting with d(T10). Our results suggest that the central ring of the BODIPY moiety is the main binding site and the electrostatic interaction between the BF2 group of BODIPY591 and the NH group of d(T10), as well as the stacking of the aromatic rings between BODIPY and thymine, are the most probable binding mechanisms.