Abstract

The spectral features of satellite holes in nonphotochemical hole burned spectra provide a promising method to identify different conformational structures of chromophore-oligonucleotides. Different hole burned spectra are observed when a 4,4-difluoro-5-(4-phenyl-l,3-butadienyl)-4-bora-3a,4a-diaza-s-indacene-3-propionic acid, succinimidyl ester (BODIPY) molecule is chemically bound to oligonucleotides of different base compositions, implying that different conformational structures exist among them. The study of satellite holes reveals that the conformational structure of BODIPY-oligonucleotide complexes can be described by the degree of intramolecular hydrogen bonding between the BODIPY and oligonucleotides. In addition, the most possible number of the nucleic acid base in the sequence of oligonucleotide to form an intramolecular hydrogen bond with BODIPY can be determined by the study of satellite holes.

© 1996 Optical Society of America