Influence of the sugar configuration on the structure of DNA by conformational analysis of the deoxyribose‐phosphate unit

Abstract

SynopsisThe conformational analysis by the Extended Huckel Theory of the deoxyribose-phosphate unit in the principal configurations of the sugar is discussed. The work is divided into three parts in order t o determine the role of the different elements constituting such a unit. 1) The simultaneous study, for the four principal configurations of the sugar, of the possible ranges of the rotational parameters $ and 6' with P 3 and P 5 without their oxygen atoms.2) The study of the influence of the oxygen atoms, situated on P 3 and P5, on the rotations $ and 6' for the C3'endo and C2'endo sugar configurations.3) The study of the influence of a nucleohase on the rotation $, and whether the oxygen atoms of the phosphate groups should be taken into account or not.The results show the equivalences C3'endo N C2'ero and CS'endo N C3'eno; that the allowed angular ranges of our rotational parameters depend, in some degree on the chosen sugar configuration; and that the rotations $ and 6' appear as "quasi" independent. In addition, an energetic classification which, according to the Extended Huckel Theory, seems to show that the C2'endo sugar configuration is the most favored for our unit was established; it was shown that the introduction of the oxygen atoms has no influence on the rotation $, but on the contrary leads to a restriction of the possible range for the 6' parameter; and it was determined that the influence of the adenine base fixed in its position of minimal energy (i.e., anti-conformation) on the rotation $, as a function of the presence or absence of the oxygen atoms, is relatively limited.

Principles of Nucleic Acid Structure

“…In addition, the readers' attention is drawn to a few recent publications selected out of a vast literature concerning theoretical investigations on polynucleotide conformation (794)(795)(796)(797)(798)(799)(800)(801)(802)(803)(804)(805)(806)(807)(808), the flexibility ofthe double helix (809)(810)(811)(812)(813)(814)(815)(816)(817), and spectroscopic investigations of polynucleotide structures (818)(819)(820)(821)(822)(823)(824). The biochemical structure-function correlations are treated in reviews for DNA (792) and for RNA (793).…”

Examen par la méthode des orbitales moléculaires des préférences conformationnelles intrinsèques du squelette des acides nucléiques

“…pour tous les angles de la chahe sucre-phosphate, sauf pour w' et w ; (2) ceci conduit A penser que les formes A bases en "stacking" ou "destaking" de ces triplets DNA proviennent de la flexibilith en (w', w ) elle-m6me gouverv6e par des transconformations du type 2E + 3E en fonction de la temperature.…”

“…Cette schematisation n'exclut pas, cependant, la necessite de connakre toutes les cartes isohergetiques afin de pouvoir s'y reporter pour tout probl&me de type particulier. pour tous les angles de la chahe sucre-phosphate, sauf pour w' et w ; (2) ceci conduit A penser que les formes A bases en "stacking" ou "destaking" de ces triplets DNA proviennent de la flexibilith en (w', w ) elle-m6me gouverv6e par des transconformations du type 2E + 3E en fonction de la temperature.…”