Transient electric dichroism studies of the structure of the DNA complex with intercalated drugs

Hogan, Michael E.; Dattagupta, Nanibhushan; Crothers, Donald M.

doi:10.1021/bi00569a007

Cited by 117 publications

(85 citation statements)

References 43 publications

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“…The extension of poly(dG-dC) seen with actinomycin D is entirely consistent with its intercalative mode of binding and is larger than found with ethidium, as was also observed with calf thymus DNA [21 ]. The unusual feature of its effect is the apparent decrease in contour length at low binding ratios.…”

Section: Discussionsupporting

confidence: 79%

“…In actual fact, although the extension produced by ethidium falls short of the 'ideal' value of 3.4 h it does lie within the range of values determined for the interaction between other intercalators and natural DNAs [21]. This could mean either that a 3.4 A increase is only an approximation or that the structure of our synthetic DNAs is significantly different from B-DNA.…”

Section: Discussionsupporting

confidence: 54%

See 1 more Smart Citation

Changes in contour length of polydeoxynucleotide fragments

Fox¹,

Harrison²,

Waring³

1981

FEBS Letters

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Section: Discussionsupporting

confidence: 79%

Section: Discussionsupporting

confidence: 54%

Changes in contour length of polydeoxynucleotide fragments

Fox¹,

Harrison²,

Waring³

1981

FEBS Letters

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“…The particular dye that we have chosen (ethidium bromide) binds strongly to double-stranded nucleic acids 17 • 18 by intercalation between adjacent base pairs such that the plane of the phenanthridinium ring (which contains the transition dipole) makes an angle of about 70° with the helix axis. 19 Presumably, the dye is rigidly bound and thus reports local motions of the helix. The double-stranded nucleic acids used in this work are very long (-10 3 -10 4 base pairs) while the duplex structure confers stiffness on the helix, as measured by its persistence length of about 525 A [see Sec.…”

Section: Theoretical Considerationsmentioning

confidence: 99%

“…The dye-tilt angle E: for the ethidium-calf thymus DNA system was taken directly from the transient electric dichroism studies of Hogan et al 19 From the limiting dichroism at high fields, they calculated that the intercalated dye was not perpendicular to the helix axis, but was tilted by about 20° along its long axis (E: = 70° ± 2°). From similar dichroism experiments on the DNA bases, 42 they also estimated that the bases themselves were inclined at an angle of 73° ± 3° to the helix axis, in agreement with the revised model for B-DNA proposed by Levitt 43 on the basis of energy-minimization calculations.…”

Section: B Analysis Of Fluorescence Depolarization Datamentioning

confidence: 99%

Torsion and bending of nucleic acids studied by subnanosecond time-resolved fluorescence depolarization of intercalated dyes

Millar

Robbins

Zewail

1982

The Journal of Chemical Physics

159

109

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Subnanosecond time-resolved fluorescence depolarization has been used to monitor the reorientation of ethidium bromide intercalated in native DNA, synthetic polynucleotide complexes, and in supercoiled plasmid DNA. The fluorescence polarization anisotropy was successfully analyzed with an elastic model of DNA dynamics, including both torsion and bending, which yielded an accurate value for the torsional rigidity of the different DNA samples. The dependence of the torsional rigidity on the base sequence, helical structure, and tertiary structure was experimentally observed. The magnitude of the polyelectrolyte contribution to the torsional rigidity of DNA was measured over a wide range of ionic strength, and compared with polyelectrolyte theories for the persistence length. We also observed a rapid initial reorientation of the intercalated ethidium which had a much smaller amplitude in RNA than in DNA.

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“…In recent years there has been a renewed interest in DNA dynamics (Allison & Schurr, 1979;Hogan et al, 1979;Thomas et al, 1980;Dickman et al, 1982;Schurr, 1984;Fujimoto et al, 1985;Schurr & Fujimoto, 1988;Mohan & Yathindra, 1991;Kumar et al, 1992;Olson et al, 1993;Kahn et al, 1994). The conformational flexibility and dynamics of the DNA polymer is very complex.…”

mentioning

confidence: 99%

Torsional Dynamics and Orientation of DNA−DAPI Complexes

Barcellona

Gratton

1996

Biochemistry

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The flexibility of calf thymus DNA and several polynucleotides was measured using the anisotropy decay of DAPI bound to DNA, a minor groove probe. DNA torsional dynamics were analyzed using the Schurr model [Allison, S. A., & Schurr, J. M. (1979) Chem. Phys. 41, 35-44] in the infinite polymer length approximation. Time-resolved fluorescence depolarization was measured using a frequencydoubled mode-locked dye laser and frequency-domain acquisition methods. At very high P/D ratios, the anisotropy decay is dominated by DNA torsional dynamics. The recovered values of the torsional elastic constant were in good agreement with literature values obtained using other DNA probes. The exact knowledge of the angle between the probe emission dipole transition moment and the helix axis is critical for the determination of the polymer elastic constant. At low P/D ratios, energy transfer between dye molecules strongly contributes to the anisotropy decay. We have developed a statistical model that describes the anisotropy decay, when the correct geometrical factors are included. At low P/D ratios the anisotropy decay is dominated by fluorescence homotransfer. In this regime, it is possible to determine the orientation of the dye molecule with respect to the polymer with accuracy. The values obtained for the distance and orientation of the DAPI molecules in solution using the fluorescence measurements are in excellent agreement with those from the crystal structure of the oligonucleotides-DAPI complex by Dickerson's group [Larsen T.

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Transient electric dichroism studies of the structure of the DNA complex with intercalated drugs

Cited by 117 publications

References 43 publications

Changes in contour length of polydeoxynucleotide fragments

Changes in contour length of polydeoxynucleotide fragments

Torsion and bending of nucleic acids studied by subnanosecond time-resolved fluorescence depolarization of intercalated dyes

Torsional Dynamics and Orientation of DNA−DAPI Complexes

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