Structure of A-DNA in solution.

Abstract

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 4X174DNA [5386 base pairs (bp) long] and a 172-bp fragment of sea urchin SS 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 4X174 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 ofonly 2.6 A 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 4X174 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 ofB-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. Values of the optical dichroism associated with known absorption bands in these substances are intrinsically related to their structural parameters. Using the technique of electric linear dichroism, two studies (9-11) of DNA in aqueous alcoholic solution have, however, resulted in entirely divergent observations with respect to the values of the Oichroism of the A-structure. Wu et al. (9), using small fragments [180 base pairs (bp)] of enzymatically cleaved pBR322, observed that the linear dichroism became more negative in alcoholic solutions under conditions where the A-structure is expected to predominate, while Lee and Charney (10, 11), using sonicated calf-thymus DNA with mean lengths of about 250 and 1300 bp, observed that the dichroism becomes less negative (than in aqueous nonalcoholic solutions) under similar conditions. In the latter study, unsonicated "native" calf thymus DNA appeared to aggregate under the same conditions, and no significance could be attributed to the measured dichroism of this high molecular weight sample in alcoholic solution. I...

Linear dichroism spectroscopy of nucleic acids

“…The origin behind these structural variations is still unclear however. The flow LD results on E. coli DNA in 80 % trifluorethanol obtained by Edmondson & Johnson (19856), which indicate a smaller optical factor, are in reasonable agreement with the observations of Matsuoka & Norden (1983 a) and Charney & Chen (1987). As a result of the shorter base-pair axial translation (0-25-0-28 nm instead of C34 nm) in conjunction with the inclination of bases, exciton interactions should affect more the wavelength dependence of the optical factor for the A than for the B form (Matsuoka & Norden, 1982 c).…”

“…7 and 9): the predicted variation of LD r with wavelength was observed and a limiting value of about -1-25 for the optical factor was obtained in accordance with an effective angle a = 77 0 at 260 nm as theoretically expected for a base tilt of about 19 0 (Matsuoka & Norden, 1982. Also electric dichroism measurements (Charney & Chen, 1987;Simpson & Stafford, 1983) show a lower amplitude of the optical factor for DNA fragments in 75-80 % alcoholic solution; a value of -1-03 for the optical factor may suggest, however, an even larger effective tilt than in the fibre A form. As mentioned earlier, the flow LD r profile of DNA in alcohol (Fig.…”

Boundary conditions for free A-DNA in solution and the relation of local to global DNA structures at reduced water activity

“…The dichroism parameters for the other DNA fragments are similar. The present results on the limit linear dichroism of A-DNA are consistent with those of Charney and Chen ( 1987 ), but are different from those reported by Wu et al ( 1981 ). The ξ ∞ values indicate that the bases are inclined at an average angle of ~70° with respect to the helix axis both for the A- and the B-form under the given experimental conditions.…”

“…Electro-optical techniques are most attractive for the analysis of DNA because the high optical anisotropy of DNA together with the high electrical anisotropy at low-salt concentrations used for A-DNA provides an optimal basis for accurate results (Fredericq and Houssier 1973 ; Porschke and Antosiewicz 2007 ). Some reports on electro-optical measurements of A-DNA have been published (Charney and Chen 1987 ; Wu et al 1981 ), partly with contradictory results. In the present investigation, the BA transition is analyzed in more detail over a range of different chain lengths and with special emphasis on the aggregation/condensation controversy.…”

Mechanochemical study of NaDNA and NaDNA-netropsin fibers in ethanol-water and trifluoroethanol-water solutions

“…The TFE-induced B-A transition of dissolved DNA was studied early (Ivanov and Krylov, 1992;Ivanov et al, 1983Ivanov et al, , 1985Charney and Chen, 1987;Minchenkova et al, 1986). For native DNA, the transition was found to occur in the region 65-70% TFE.…”