title: Intercalation of trioxatriangulenium ion in DNA: binding, electron transfer, x-ray crystallography, and electronic structure.
abstract: Trioxatriangulenium ion (TOTA(+)) is a flat, somewhat hydrophobic compound that has a low-energy unoccupied molecular orbital. It binds to duplex DNA by intercalation with a preference for G-C base pairs. Irradiation of intercalated TOTA(+) causes charge (radical cation) injection that results in strand cleavage (after piperidine treatment) primarily at GG steps. The X-ray crystal structure of TOTA(+) intercalated in the hexameric duplex d[CGATCG](2) described here reveals that intercalation of TOTA(+) results in an unusually large extension of the helical rise of the DNA and that the orientation of TOTA(+) is sensitive to hydrogen-bonding interactions with backbone atoms of the DNA. Electronic structure calculations reveal no meaningful charge transfer from DNA to TOTA(+) because the lowest unoccupied molecular orbital of TOTA(+), (LUMO)(T), falls in the gap between the highest occupied molecular orbital, (HOMO)(D), and the (LUMO)(D) of the DNA bases. These calculations reveal the importance of backbone, water, and counterion interactions, which shift the energy levels of the bases and the intercalated TOTA(+) orbitals significantly. The calculations also show that the inserted TOTA(+) strongly polarizes the intercalation cavity where a sheet of excess electron density surrounds the TOTA(+).
authors.affiliation: Schools of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332, USA.
authors.forename: Jóhannes
authors.initials: J
authors.lastname: Reynisson
authors.forename: Gary B
authors.initials: GB
authors.lastname: Schuster
authors.forename: Sheldon B
authors.initials: SB
authors.lastname: Howerton
authors.forename: Loren Dean
authors.initials: LD
authors.lastname: Williams
authors.forename: Robert N
authors.initials: RN
authors.lastname: Barnett
authors.forename: Charles L
authors.initials: CL
authors.lastname: Cleveland
authors.forename: Uzi
authors.initials: U
authors.lastname: Landman
authors.forename: Niels
authors.initials: N
authors.lastname: Harrit
authors.forename: Jonathan B
authors.initials: JB
authors.lastname: Chaires
mesh_terms: D002942:Circular Dichroism; D018360:Crystallography, X-Ray; D004247:DNA / Q000737:chemistry*; D004277:DNA, Single-Stranded / Q000737:chemistry; D007364:Intercalating Agents / Q000737:chemistry*; D008958:Models, Molecular; D009690:Nucleic Acid Conformation; D009692:Nucleic Acid Heteroduplexes / Q000737:chemistry; D009841:Oligonucleotides / Q000737:chemistry; D010777:Photochemistry; D011721:Pyrenes / Q000737:chemistry*; D012313:RNA / Q000737:chemistry; D013050:Spectrometry, Fluorescence; D013056:Spectrophotometry, Ultraviolet; D055672:Static Electricity
chemical_list: D004277:DNA, Single-Stranded; D007364:Intercalating Agents; D009692:Nucleic Acid Heteroduplexes; D009841:Oligonucleotides; D011721:Pyrenes; C472757:trioxatriangulenium; D012313:RNA; D004247:DNA