AI Article Synopsis
- Different quantum mechanics methods were evaluated for studying how intercalators interact with DNA, finding that the WB97XD method with a specific basis set accurately reproduces results from the expensive MP2 method.
- Methylene blue trihydrate was found to intercalate into DNA base pairs, increasing the distance between them, with effects varying based on the DNA base type.
- The intercalation of methylene blue into the AA-TT base pair was most favorable with nitrogen orientation, resulting in a charge transfer from the intercalator to the DNA and notable changes in charge density primarily occurring at the heavy atom in the center of the system.
Article 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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| http://dx.doi.org/10.1007/978-94-017-9245-5_12 | DOI Listing |
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