Indicator of the Stacking Interaction in the DNA Double-Helical Structure: ChiraSac Study

The double-helical structures of DNA are experimentally distinguished by the circular dichroism (CD) spectra. The CD spectra are quite different between the left- and right-handed double-helical structures of DNA. The lowest peak is negative for the left-handed Z-DNA but positive for the right-handed B-DNA. Using the Z-DNA model with a strong stacking interaction, we examined whether the CD spectra depend on the distance between the two base pairs, deoxy-guanosine (dG) and deoxy-cytidine (dC). The result showed that the feature of the SAC-CI CD spectra changes from Z-DNA to B-DNA when increasing the distance between the two base pairs. Therefore, we concluded that the stacking interaction is the origin of the lowest negative peak, being the feature of the CD spectra of Z-DNA, and at the same time that the lack of the negative peak at about 290-300 nm of the CD spectra of B-DNA is due to the weak stacking interaction in B-DNA.