Structure of poly 8-bromoadenylic acid: conformational studies by CPF energy calculations

Abstract

Poly 8-bromoadenylic acid [poly(8BrA)] is the only known all-syn polynucleotide. It shows a helix-coil transition with a melting curve centred around 55° 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, θ' = 216°, ω'= 280°, ω = 294°, θ = 179°, χ = 243°. and ψ = 57°. Such a conformation leads to approximately 8 nucleotide units per turn of the helix and an axial rise of 3.9A°. 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.