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Optica Publishing Group
  • International Quantum Electronics Conference
  • 1996 OSA Technical Digest Series (Optica Publishing Group, 1996),
  • paper TuH4

Intramolecular hydrogen bond of dye- oligonucleotides studied by satellite holes

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Abstract

Satellite holes (SHs) in nonphotochemical hole burned spectra have been used to study the intramolecular hydrogen bond effect of dye- oligonucleotides in polyvinyl alcohol (PVOH) films. Interesting hole burned spectra are observed when a 4,4-difluoro-5-(4-phenyl-1,3-butadienyl)-4-bora-3a,4a-diaza-s-indacene-3-propionic acid, succihimidyl ester (BODIPY) molecule is chemically bound to oligonucleotides of different base compositions. No hole has been found when a BODIPY molecule is bound to an oligomer with ten bases of guanosine deoxyribonucleotide (BODIPY-d(G10)) [1]. However, the hole burned spectra of BODIPY bound to an oligomer with ten bases of cytosine deoxyribonucleotide (BODIPY- d(C10)) are similar to the spectra of free BODIPY. Figures 1a-1b show the hole burned spectra of BODIPY embedded in PVOH films at λB ≈ 590 nm and 560 nm by using pulse energies of ~ 2.5 and ~ 1.5 μJ, respectively and the same burning time of 60 min for each. Figures 1c-1d show the hole burned spectra of BODIPY-d(C10) embedded in PVOH films at λB ≈ 581 nm and 555 nm by using pulse energies of ~ 2.5 and ~ 1.5 μJ and burning times of 20 and 60 min, respectively. Two distinct spectral features of several specific Shs are observed in the hole burned spectra of BODIPY- d(C10). First, the SH linewidth at 435 cm−1 of BODIPY-d(C10) is three times broader than that at 422 cm−1 of free BODIPY. Second, an intense SH at 1135 cm−1 exhibited in the spectra of BODIPY disappears; instead, two intense SHs at 1055 cm−1 and 1095 cm−1 appear in the spectra of BODIPY- d(C10). The BODIPY molecule contains a BF2 functional group, the strong electronegativity of the F atom allows it to form an intermolecular hydrogen bond with PVOH and an intramolecular hydrogen bond with cytosine. The intense SH at 422 cm−1 was assigned to the bending vibration of the B-F bond [2]. The disappearance of the 1135 cm−1 SH and the occurrence of the 1095 cm−1 and 1055 cm−1 SHs suggest that the 1135 cm−1 SH corresponds to the stretching frequency of the BF mode. The observation of hole broadening and line shifting in figure 1 provide convincing evidence for the formation of an intramolecular hydrogen bond between the BF mode of BODIPY and the NH mode of sytosine.

© 1996 Optical Society of America

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