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SynopsisThe helix-coil transition and conformational structure of poly(8-bromoadenylic acid) (poly(8BrA)J have been investigated using 'H-and 13C-nmr, CD, and ir spectroscopy. The results have been compared with the structure of the related 5'-mono-and polynucleotides. The chemical shifts of H(2'), H(3'), C(2'), and C(3') nmr signals show an interesting correlation with both the puckering of ribose ring and glycosidic bond torsion angle. Poly(8BrA) shows an upfield shift of the C(3') signal and a downfield shift of the H(3') signal compared to the chemical shifts in poly(A). These shifts are consistent with a C(3') endo-syn conformation for poly(8BrA). A similar effect has been reported previously and is also observed here on the C(2') and H(2') signals when the preferred conformation is C(2')endo-syn (e.g., in 5'-8BrAMP). The chemical-shift parameters thus act as a probe for studying s y n -t anti and N -t S equilibria in solutions. The three-bond lH-I3C coupling constants between H(1') and C(8) and C(4) have been measured in poly(8BrA) and 5'-8BrAMP and their structural implications have been discussed. The observed preference of a C(3')endo-syn conformation for poly(8BrA), coupled with other evidence, throws doubt on the validity of a correlation previously reported whereby a syn conformation is associated with a C(2')endo ribose pucker. The backbone conformation of randomly coiled poly(8BrA) is very similar to the structures found in polyribonucleotides: poly(A) and poly(U). All three polymers show strong preferences for the backbone angles found in RNA helices. The CD spectrum of poly(8BrA) has a striking relationship to that of poly(A). The signs of all extrema are inverted, and the magnitudes are related by a constant factor. We suggest that these differences result from a change in the angle between coupled transition moment vectors in the two polymers. Infrared spectra of poly(8BrA) in HzO and DzO solution are reported for the frequency range below 1400 cm-l. The antisymmetric >PO; stretching vibration is observed at an unusually low frequency in the helix (1214 cm-l). The symmetric >PO; stretch occurs at -1095 cm-I but is not resolved from a ring vibration near this frequency. A conformationally sensitive band, characteristic of helical RNA structures, is observed at 817 cm-' and disappears when the helix is melted. This observation confirms the conclusion that ordered poly(8BrA) has a regular helical structure with an RNA backbone conformation. A stereochemical explanation is provided for the failure of poly(8BrA) (or other syn polymers) to form double helices with anti-polyribonucleotides.

Poly 8-bromoadenylic acid [poly(BBrA)] is the only known all-syn polynucleotide. It shows a helix-coil transition with a melting curve centred around 55 degrees C. Energy calculations based on classical potential functions have been used to explore the three-dimensional structure of this polymer in helix and random coil. It is concluded that the ordered state is a helix of two parallel strands with a two-fold rotation axis, and the duplex is stabilised by hydrogen bonds involving N1 and H6. Each strand has a conformation with C3' endo geometry, phi' = 216 degrees, omega' = 280 degrees, omega = 294 degrees, phi = 179 degrees, chi = 243 degrees and psi = 57 degrees. Such a conformation leads to approximately 8 nucleotide units per turn of the helix and an axial rise of 3.9A degrees. The structure of poly(8BrA) has been compared with that of the related polymer poly(A) which forms a double helical structure in acidic conditions with bases in the anti conformation and with interstrand hydrogen-bonds between N7 and H6. This is the first time that a specific geometrical model of a novel polynucleotide structure has been produced initially by potential energy calculations, though such calculations on a number of known structures have been reported previously.