Intercalation of trioxatriangulenium ion in DNA: binding, electron transfer, x-ray crystallography, and electronic structure.
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(+).
Reynisson
Jóhannes
J
Schools of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332, USA.
Schuster
Gary B
GB
Howerton
Sheldon B
SB
Williams
Loren Dean
LD
Barnett
Robert N
RN
Cleveland
Charles L
CL
Landman
Uzi
U
Harrit
Niels
N
Chaires
Jonathan B
JB
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
D004277:DNA, Single-Stranded; D007364:Intercalating Agents; D009692:Nucleic Acid Heteroduplexes; D009841:Oligonucleotides; D011721:Pyrenes; C472757:trioxatriangulenium; D012313:RNA; D004247:DNA