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Updated: Apr 21, 2026

Author Spotlight: Characterizing DNA G-Quadruplex by Bis-3-Chloropiperidine Based Chemical Mapping
Published on: May 12, 2023
Binding modes and interaction mechanism between different base pairs and methylene blue trihydrate: a quantum
Peijun Xu1, Jinguang Wang, Yong Xu
1School of Physics and Electronic Technology, Liaoning Normal University, Dalian, Liaoning, China.
Abstract:
Different quantum mechanic methods have been evaluated for the calculation of binding modes and interactions between intercalators with different DNA base pairs by comparing with the results of MP2, which is very expensive, indicating that WB97XD method under 6-311+G* basis set is able to efficiently reproduce MP2 results. We discovered that the methylene blue trihydrate intercalated into the DNA base pairs, and DNA intercalation increased the distance between DNA base pairs, depending on the types of DNA bases. According to the binding energy results, it was found that the intercalation of methylene blue trihydrate into AA-TT base pair was more favorable in the orientation of nitrogen than other directions and intercalation, and the electric charge was transferred from methylene blue trihydrate to the AA-TT base pair. The analysis of change in the charge density shows that changes often take place in the heavy atom in the middle of the system which the charge density changes most remarkable.
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