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Key insights for the improvement of caging groups

December 2013. Photolabile protecting groups are a versatile tool to trigger reactions by light irradiation. In a study just published in the journal Angewandte Chemie International Edition, a team of scientists at the Goethe University Frankfurt has investigated the influence of the absolute configuration of the 1-(2-nitrophenyl)ethyl (NPE) cage group on a 15-base-pair duplex DNA.

Using UV melting, the scientists determined the global stability of the unmodified and the selectively (S)- and (R)-NPE-modified DNA sequences, respectively. They observed a differently destabilizing effect for the two NPE stereoisomers on the global stability. Analysis of the temperature dependence of imino proton exchange rates measured by NMR spectroscopy revealed that this effect can be attributed to decreased base pair stabilities of the caged and the 3′-neighbouring base pair, respectively. NMR-based structural models of the modified duplexes provide a structural basis for the distinct effect of the (S)- and the (R)-NPE group.

These findings offer the possibility to optimize the caging strategy to obtain the maximum desired effect with a single cage group. Such rational optimization will improve wide spread application of nucleobase cages in chemical biology.

 

Contacts:

Harald Schwalbe
Institute of Organic Chemistry and Chemical Biology
schwalbe@em.uni-frankfurt.de

Alexander Heckel
Institute of Organic Chemistry and Chemical Biology
heckel@em.uni-frankfurt.de

 

Full reference:
Steinert HS, Schäfer F, Jonker HRA, Heckel A, Schwalbe H (2013) Influence of the absolute configuration of NPE-caged cytosine on DNA single base pair stability. Angew Chem Int Edit:DOI: 10.1002/anie.201307852. More...