Femtogenix has published a research article on the use of molecular dynamics simulations to evaluate DNA sequence-selectivity of G-A cross-linking PBD-duocarmycin dimers.
The pyrrolobenzodiazepine (PBD) and duocarmycin families (CPI and CBI units) are DNA-interactive agents that covalently bond to guanine (G) and adenine (A) bases in the minor groove. These moieties have been joined together to create synthetic dimers capable of cross-linking G–G, A–A, and G–A bases. In this study, the team used molecular dynamics simulations to predict the preferred DNA recognition sequences for previously published molecular types and then compared these predictions with the cross-linking sites published in the literature.
The molecular dynamics simulation methodologies were shown to accurately predict and interpret how DNA cross-linking agents of the PBD and/or CPI/CBI variety interact in the minor groove of DNA. These methodologies may be used to assist the design of future libraries.
The full article is accessible via the following link: http://www.sciencedirect.com/science/article/pii/S0960894X16310502