A fluorescent complex between ethidium bromide and nucleic acids. Physical-chemical characterization.

We have developed a simple and rapid system for the denaturation of nucleic acids and their subsequent analysis by gel electrophoresis. RNA and DNA are denatured in 1 M glyoxal (ethanedial) and 50% (vol/vol) dimethyl sulfoxide, at 50 degrees. The glyoxalated nucleic acids are then subjected to electrophoresis through either acrylamide or agarose gels in a 10 mM sodium phosphate buffer at pH 7.0. When glyoxalated DNA molecules of known molecular weights are used as standards, accurate molecular weights for RNA are obtained. Furthermore, we have employed the metachromatic stain acridine orange for visualization of nucleic acids in gels. This dye interacts differently with double- and single-stranded polynucleotides, fluorescing green and red, respectively. By using these techniques, native and denatured DNA and RNA molecules can be analyzed on the same slab gel.

https://www.pnas.org/content/pnas/74/11/4835.full.pdf

Analysis of single- and double-stranded nucleic acids on polyacrylamide and agarose gels by using glyoxal and acridine orange

The design of small complexes that bind and react at specific sequences of DNA becomes important as we begin to delineate, on a molecular level, how genetic information is expressed. A more complete understanding of how to target DNA sites with specificity will lead not only to novel chemotherapeutics but also to a greatly expanded ability for chemists to probe DNA and to develop highly sensitive diagnostic agents.

Recognition and reaction of metallointercalators with DNA.

Complex formation between ethidium bromide and nucleic acids.

Equilibrium binding studies and viscosity experiments are described that characterize the interaction of delta- and lambda-[Ru(o-phen)3]2+ with calf thymus DNA. The mode of binding of these compounds to DNA is a matter of controversy. Both isomers of [Ru(o-phen)3]2+ were found to bind but weakly to DNA, with binding constants of 4.9 (+/- 0.3) x 10(4) M-1 and 2.8 (+/- 0.2) x 10(4) M-1 determined for the delta and lambda isomers, respectively, at 20 degrees C in a solution containing 5 mM Tris-HCl (pH 7.1) and 10 mM NaCl. We determined that the quantity delta log K/delta log [Na+] equals 1.37 and 1.24 for the delta and lambda isomers, respectively. Application of polyelectrolyte theory allows us to use these values to show quantitatively that both the delta and lambda isomers are essentially electrostatically bound to DNA. Viscosity experiments show that binding the lambda isomer does not alter the relative viscosity of DNA to any appreciable extent, while binding of the delta isomer decreases the relative viscosity of DNA. From these viscosity results, we conclude that neither isomer of [Ru(o-phen)3]2+ binds to DNA by classical intercalation.

Neither delta- nor lambda-tris(phenanthroline)ruthenium(II) binds to DNA by classical intercalation.

Structural considerations in the interaction of DNA and acridines.

The combination in solution of DNA with small amounts of acridine, proflavine, or acridine orange results in markedly enhanced viscosity and a diminution of the sedimentation coefficient of the DNA. These changes are contrary to those expected on the basis of aggregation or simple electrostatic effects. Characteristic changes, which suggest considerable modification of the usual helical structure of DNA, are found in the X-ray diffraction patterns of fibers of the complex with proflavine. It is inferred that these compounds, which are potent mutagens, are intercalated between adjacent nucleotide-pair layers by extension and unwinding of the deoxyribose-phosphate backbone. The hydrodynamic changes are the consequence of the diminished bending between layers, the lengthening of the molecule, and the diminished length-specific mass. The effects are fully reversible at ordinary temperatures. The proposed structural change is compatible with the normal restrictions on bond lengths, angles, and non-bonded contacts, and maintenance of the hydrogen-bonded base pairs perpendicular to the axis of the molecule. Another singly charged dye, pinacyanol, fails to elicit the effects of intercalation, yielding only lowered viscosity and increased sedimentation coefficient.

L.S. Lerman

Papers

Structural considerations in the interaction of DNA and acridines.

Structural Considerations in the Interaction of DNA and Acridines