Ethidium bromide complexes with self-complementary deoxytetranucleotides. Demonstration and discussion of sequence preferences in the intercalative binding of ethidium bromide

Abstract

The binding of ethidium bromide to the self-complementary deoxytetranucleotides containing guanine and cytosine bases has been studied by circular dichroism, visible absorption, and fluorescence spectroscopies. The circular dichroism spectrum of each of the four deoxytetranucleotides was measured and compared to the spectrum calculated by a nearest-neighbor approximation method which utilized the circular dichroism spectra of the deoxydinucleotides as a basis set. Reasonable agreement was obtained between the calculated and experimental spectra for three of the four deoxytetranucleotides; however, pdC-dC-dG-dG exhibited poor agreement between the actual and nearest-neighbor calculated spectra, which suggests that pdC-dC-dG-dG may exist in an unusual conformation. A nearest-neighbor method was also used to calculate the extinction coefficients for each of the deoxytetranucleotides: these values differ substantially from values recently published by Patel and Canuel [(1977), Proc. Natl. Acad. Sci. U.S.A. 74, 2624--2628] in which the method used for the determination of the extinction coefficients was not stated. The magnitude of the extinction coefficients is important in determining the stoichiometry of complex formation as well as the relative sequence preferences for ethidium binding. The visible absorption titrations, the fluorescence titrations, and the circular dichroism titrations with ethidium bromide clearly show that two ethidiums will intercalate into a (pdC-dG-dC-dG).(pdC-dG-dC-dG) double helix presumably at the two (dC-dG).(DC-dG) sequences. Results from the pdG-dC-dG-dC titrations with ethidium bromide are not as definitive. Raising the temperature from approximately 2 to 26 degrees C diminishes the strength of complex formation for the EthBr plus pdC-dG-dC-dG system and makes it more difficult to unequivocally determine the stoichiometry of the complex formation. These data thus confirm and extend our earlier observation that ethidium bromide preferentially binds to pyrimidine-purine sequences as opposed to purine-pyrimidine sequences. Experiments monitoring the binding of ethidium bromide to pdC-dC-dG-dG and pdG-dG-dC-dC indicate that ethidium will bind strongly to the (dG-dG).(dC-dC) sequence. We conclude that the relative ordering of the sequence preferences for the binding of ethidium to the three sequences available in the tetranucleotides studied is (dC-dG).(dC-dG) congruent to (dG-dG).(dC-dC) greater than (dG-dC).(dG-dC).

Geometry of the antitumor drug ditercalinium bisintercalated into d(CpGpCpG)2 by 1H NMR.

“…The rigidity of the chain prevents occupancy of two adjacent binding sites by rings belonging to the same dimer; then only the noncontiguous CpG sites are filled in a bisintercalated d(CpGpCpG)2-Ditercalinium complex. Such a model agrees with the classical pyrimidine-purine sequence preference displayed by intercalators (9,21) and with the similar upfield shifts induced on both the internal and the external base pair protons.…”

The psoralen-DNA photoreaction. Characterization of the monoaddition products from 8-methoxypsoralen and 4,5',8-trimethylpsoralen

“…It is possible that their accompanying diastereomers are present as minor uncharacterized products in our chromatographic system. Also, a .. MOP.-F41 may consist of more than a single diastereomer, but complete Such short range sequence specificity has been observed with other intercalating agents such.as ethidium bromide (Kastrup et al, 1978).…”

On the cooperative and noncooperative binding of ethidium to DNA

“…Although it has been established that ethidium has a preference for binding to pyrimidine(3'-5') purine sequences when compared to purine(3'-5')pyrimidine sequences (9)(10) it has also been shown that the apparent binding affinity of ethidium is not very dependent upon the overall base composition (1-2, 13). The equilibrium binding of ethidium to various native DNAs has been reported (1)(2)(3)(4)(5)(6)(7)(8)(9)(10)(11)(12), with the binding isotherms presented in these papers being well represented by the nearest neighbor exclusion model (14)(15) Volume 10 Number 24 1982 and Young (16) which showed that daunorubicin and adriamycin facilitated the binding of actinomycin D to poly(dA-dT). poly(dA-dT), a polynucleotide to which actinomycin D does not bind.…”