A sophisticated algorithm is developed to analyze flow linear dichroism data on nucleic acids for individual base inclinations. Measured absorption and linear dichroism data for synthetic AT and GC polymers and natural DNAs are analyzed. The reliability of the algorithm is tested on data for the synthetic polymers, and the results are similar to earlier, more straightforward analyses. For the first time, specific base inclinations are derived for all four bases individually from the linear dichroism data for natural deoxyribonucleic acids. For B-form DNA in aqueous solution at moderate salt the inclinations from perpendicular are as follows: d(A) = 16.1 0.5; d(T) = 25.0 f 0.9; d(G) = 18.0 0.6; d(C) = 25.1 * 0.8 deg. Our results indicate that the bases in synthetic and natural DNAs are not perpendicular to the helix axis, not even in the B form. 1956, 78, 5235-5238. 2 109-2 124. 51 1-560. A. 1978, 75, 195-199. Biophys. Chem. U.S.

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CD spectra have been measured as a function of temperature for a number of ApA analogues with modified backbones. Oligonucleotides with these modified backbones are being used as antisense agents having potential as viral therapeutics. Results of these studies show that when a carbonyl is substituted for the phosphate to produce an uncharged backbone, the analogues that have either sugar or morpholino substitution do not stack. In contrast, when a morpholino group is substituted for the sugar and the phosphate is modified so as to be uncharged, there is strong base stacking. Stacking interactions in the phosphorus-linked morpholino analogues are at least as strong as those found in d(ApA). The stacking interactions in ApA are weak by comparison. Singular value decomposition demonstrates that the stacking is two state, and Taylor series decomposition yields a coefficient that measures base stacking interactions. The van't Hoff equation is applied to the base stacking coefficient from the Taylor series fitting to give thermodynamic parameters.

Flow linear dichroism measurements extended into the vacuum uv region yield inclinations for the base normal from the helix axis of 21 degrees for dA and 40 degrees for dT in the X-form of poly(dAdT).poly(dAdT). These inclination angles are similar to the B form of the synthetic polymer, but the axes around which the bases incline are different. Hydrogen-bonded base pairs are consistent with the geometry for the standard B, C, D, and Z forms of natural DNA, but will not fit into the A form. Fourier transform ir spectra indicate that the X form has sugar pucker and phosphate geometry similar to B-form DNA, and supports the dinucleotide repeat with two kinds of phosphates seen in earlier work, in analogy to Z-form DNA. Clearly, X-form DNA has a unique geometry.