Structure of A-DNA in Solution

• Published in: Proceedings of the National Academy of Sciences - PNAS 1987-03, Vol.84 (6), p.1546-1549
• Main Authors: Charney, Elliot, Chen, Holly Ho
• Format: Article
• Language: English
• Subjects: A form DNA; Alcoholism; Aqueous solutions; Base Composition; Biological and medical sciences; Circular Dichroism; Crystals; Dichroism; DNA; Electric fields; Electricity; Ethanol; Fundamental and applied biological sciences. Psychology; Molecular biophysics; Nucleic Acid Conformation; Oligomers; Phosphates; Solutions; Structure in molecular biology; Tridimensional structure
• ISSN: 0027-8424; 1091-6490
• DOI: 10.1073/pnas.84.6.1546

The structure of DNA in aqueous trifluoroethanol solutions containing more than 70% (vol/vol) trifluoroethanol, where it has been proposed to have the A-conformation, has been studied by the technique of electric linear dichroism. The data demonstrate that both linear φ X174 DNA [5386 base pairs (bp) long] and a 172-bp fragment of sea urchin 5S RNA gene are in the double-helical A-form in the alcoholic solution and that two of the important structural parameters, the base tilt and the base-pair translation along the helical axis, are the same as in the A-form structure of crystalline double-helical d(GGTATACC). Despite its molecular length, the limiting reduced dichroism (-1.41) of the φ X174 DNA in low-salt aqueous solution is near the theoretical limit (-1.50) for DNA with base planes perpendicular to the helical axis. Transformation of this DNA and also of the 172-bp fragment to the A-structure in alcohol solutions reduces the experimental value of the dichroism to about -1.04, which agrees almost exactly with the value of -1.03 calculated for the A-form crystal. The base-pair translation along the helical axis was determined from relaxation of the DNA dichroism when the electric field is turned off. The 172-bp fragment is found to have a base-pair translation of only 2.6 angstrom in the A-structure and is thus the same as in A-DNA fibers and in the A-form oligomers crystals. We conclude from the coincidence of the base-pair translation and the apparent values of the base tilt that the A structures are identical or nearly so in the solution and solid states. Comparison of the φ X174 data with data on smaller DNA fragments and with the data on the 172-bp sea urchin gene fragment unambiguously confirms that, in aqueous solution, the experimental reduced electric dichroism of B-DNA is highly dependent on molecular length, while the dichroism of the A-DNA form in alcoholic solutions is independent of molecular length at least in the range from 172 to 5386 bp.