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.

Infrared linear dichroism has been employed to investigate the inclination of the bases in films of poly[d(AC)].poly[d(GT)], poly[d(AG)].poly[d(CT)], and natural DNAs (from Escherichia coli and calf thymus). All DNAs investigated assume the B-form at high (> 94%) relative humidity. Poly[d(AC)].poly[d(GT)], E. coli DNA, and calf thymus DNA assume the A-form at low (75%) relative humidity, whereas poly[d(AG)].poly[d(CT)] assumes the C-form at low (66%) relative humidity. Infrared linear dichroism demonstrates that the bases for DNA in films are highly inclined from perpendicular to the helix axis, even for B-DNA. C-DNA has almost same inclinations as in B-DNA, and the inclinations are slightly increased in A-DNA. These inclination angles confirm our earlier UV linear dichroism results for the orientation of the bases for DNA in solution. Infrared linear dichroism has also been used to obtain conformational angles for the phosphodiester backbone geometry of the A-, B-, and C-forms of DNA.

Flow linear dichroism is used to measure specific inclinations for each of the four bases in poly[d(AC)].poly[d(GT)] and poly[d(AG)].poly[d(CT)] in both the B and A forms. For the B form in solution the bases are found to have a sizable inclination. Inclination is increased in the A form, as expected. In all cases the pyrimidines are more inclined than the purines.

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.

SYNOPSISThe Z-form of poly(dG-m5dC)~poly(dG-m5dC) in 85% ethanol/MOPS and the Z-form poly ( rG-rC ) . poly ( rG-rC) in 4.8 M NaClO,, 20% ethanol are studied by flow linear dichroism. Simultaneous analysis of the isotropic absorption and linear dichroism data yields the angle of inclination of the base normal relative to the helix axis, and the orientation of the axis around which the bases incline. For the Z-form of poly(dGm5dC) .poly(dG-m5dC) the inclination angles are 31.3" for guanine, and 27.9" for cytosine; for the Z-form of poly(rG-rC).poly(rG-rC) they are 25.0" for guanine, and 23.3" for cytosine. The inclination angles for the Z-form DNA are similar to those for the Zform, and the angles for Z-form RNA are somewhat smaller. The axes of inclination for guanine and cytosine are similar in all three left-handed forms. 0 1995 John Wiley & Sons, Inc.