Free Energy Calculations Predict Sequence Specificity in DNA-Drug Complexes
- 1 January 1992
- journal article
- research article
- Published by Taylor & Francis in Nucleosides and Nucleotides
- Vol. 11 (1), 167-173
- https://doi.org/10.1080/07328319208021159
Abstract
Molecular dynamics simulations of DNA-netropsin complexes in water were performed using the thermodynamic cycle-perturbation method to calculate the free energy difference between complexes with an adenine-containing binding site and corresponding complexes where adenines are replaced by 2,6-diaminopurines (dap). The calculations predict a free energy difference of 3.7±0.9 kcal/mol (at 300K) in favour of netropsin binding to an (AATT)2 DNA sequence compared to a (dapdapTT)2 sequence.Keywords
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