We used Raman spectroscopy to study the conformational changes of DNA induced by Cd2+ ions in different Cd2+ concentrations solution. The experimental results show that when the Cd2+/PO2- ratio R increased from 0 to 3.0, the band 835.0 cm-1 shifted about 8 cm-1, and the overlapping spectra of 1446.0 and 1461.0 cm-1 separated and moved to 1441.0 and 1458.0 cm-1, respectively. This indicates that the conformation of DNA has changed from a “normal” B-form to a “modified” B'-form. At the same time, changes of other bands demonstrate that parts of base stacking collapse and some hydrogen bonds between AT are disrupted, AT base pairs are damaged more larger than GC base pairs.
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. N6H2（A）-N3 （G） and N7 （A）--N2H2（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.
A.C mismatches are studied by Raman spectral characterization of PolyA, PolyC, and their equimolar complex in solution of 0.14 mol/L Na^＋, pH7.0. Experimental results show that A.C mismatches occur to be A/B （mainly A） conformers, and unlike Watson-Crick base pairing, this kind of mismatches is stabilized by only one hydrogen bond involving cytosine N4H2 and adenine N7. The formation of A.C complex makes the base stacking interactions much stronger, and conformation of the backbone more ordered, which leads to obvious Raman hypochromic effect with some shifts in corresponding bands.
