Liao Yu-Bo(廖昱博)a)b), Meng Yao-Yong(孟耀勇)a)†, Lei Hao-Dong(雷浩东)a), and Wang Ying(王英)b)
a Photonic Chinese Medicine Laboratory, South China Normal University, Guangzhou 510631, China; b Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou 510640, China
Abstract G--A mismatches are non-canonical base pairs that widely occur in native nucleic acids. They have been found to be functionally important in adopting unusual structures. In this paper, G--A mispairing was studied by Raman spectral characterization of Polyadenylic acid (PolyA), Polyguanylic acid (PolyG) and their equimolar mixture in solution of 0.08 mol/L Na$^{+}$, pH7.0. The experiment showed the following three results. (1) At the experimental conditions used in the present work, PolyA and G--A complexes existed as single-stranded and double-stranded helix of A form, respectively. And PolyG mainly occurred to be anti-parallel quadruplex conformers. (2) The formation of G--A complexes, on one hand strengthened parts of base stacking interactions especially for PolyG, leading to Raman hypochromism effect with some corresponding bands shifting, and on the other hand weakened other base stacking interactions especially for PolyA to a certain degree. During this process, the backbone of PolyG underwent a significant change, but PolyA still conserved its main chain conformation. (3) The formation of G--A complexes was stabilized by two interbase hydrogen-bond interactions (i.e. N6H$_{2 }$(A)---N3 (G) and N7 (A)---N2H$_{2 }$(G)) and a third hydrogen bond between O2' (G) and N6 (A). The third hydrogen bond was responsible for the remarkable changes of PolyG backbone conformation.
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