Computer-aided molecular modeling and design of DNA-inserting molecules

Klein-de Gunst, F.J.M., Boom, J.H. and Liskamp, R.M.J. (1992) Computer-aided molecular modeling and design of DNA-inserting molecules. Journal of Computer-Aided Molecular Design, 6(1), pp. 33-46. (doi: 10.1007/BF00124385)

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Intercalators are molecules capable of sliding between base pairs without disturbing the overall stacking pattern. In addition, there may exist molecules capable of inserting into a base pair thereby disrupting the hydrogen bonds and replacing them with new hydrogen bonds. A molecule probably capable of inserting, i.e., an insertor, is the diketopiperazine cyclo-[Gly-Gly] (1). A barbiturate (2), alloxan (3), a pyrimidine derivative (4) and a hydantoin (5) were also studied as possible insertors. Furthermore, molecules such as ethyleneurea (6), succinimide (7), as well as a malonamide derivative (8) and oxamide derivatives (9–11) were studied in order to investigate the arrangement and the number of hydrogen bonds necessary for insertion. Molecules 12–14 were designed and studied for their capacity to act as bisinsertors and/or bisintercalators. These molecules feature two diketopiperazine moieties which are connected via a diphenyl(thio)ether, i.e., 12 and 13, or a bisphenol A spacer, i.e., 14. The latter molecule (14) seems a promising candidate as a bisinsertor.

Item Type:Articles
Glasgow Author(s) Enlighten ID:Liskamp, Professor Robert
Authors: Klein-de Gunst, F.J.M., Boom, J.H., and Liskamp, R.M.J.
College/School:College of Science and Engineering > School of Chemistry
Journal Name:Journal of Computer-Aided Molecular Design
ISSN (Online):1573-4951

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