PARALLEL DOUBLE HELICES OF DNA - CONFORMATIONAL-ANALYSIS OF REGULAR HELICES WITH THE 2ND-ORDER SYMMETRY AXIS

We have performed a conformational analysis of DNA double helices with parallel directed back-bone strands connected with the second order symmetry axis being at the same time the helix axis. The calculations were made for homopolymers poly(dA) ·poly(dA), poly(dC) ·poly(dC), poly(dG) ·poly(dG), and poly(dT) ·poly(dT). All possible variants of hydrogen bonding of base pairs of the same name were studied for each polymer. The maps of backbone chain geometrical existence were constructed. Conformational and helical parameters corresponding to local minima of conformational energy of “parallel” DNA helices, calculated at atom-atom approximation, were determined. The dependence of conformational energy on the base pair and on the hydrogen bond type was analysed. Two major conformational advantageous for “parallel” DNA’s do not depend much on the hydrogen-bonded base pair type were indicated. One of them coincided with the conformational region typical for “antiparallel” DNA in particular for the B-form DNA Conformational energy of “parallel” DNA depends on the base pair type and for the most part is similar to the conformational energy of “antiparallel” B-DNA. © 1990 Adenine Press.