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Journal Article

Optimal Destabilization of DNA Double Strands by Single-Nucleobase Caging

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Heinz,  Marcel       
Department of Theoretical Biophysics, Max Planck Institute of Biophysics, Max Planck Society;

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Stelzl,  Lukas S.       
Department of Theoretical Biophysics, Max Planck Institute of Biophysics, Max Planck Society;

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Hummer,  Gerhard       
Department of Theoretical Biophysics, Max Planck Institute of Biophysics, Max Planck Society;
Institute of Biophysics;

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Citation

Seyfried, P., Heinz, M., Pintér, G., Klötzner, D.-P., Becker, Y., Bolte, M., et al. (2018). Optimal Destabilization of DNA Double Strands by Single-Nucleobase Caging. Chemistry – A European Journal, 24(66), 17568-17576. doi:10.1002/chem.201804040.


Cite as: https://hdl.handle.net/21.11116/0000-0002-C20B-7
Abstract
Photolabile protecting groups are widely used to trigger oligonucleotide activity. The ON/OFF-amplitude is a critical parameter. An experimental setup has been developed to identify protecting group derivatives with superior caging properties. Bulky rests are attached to the cage moiety via Cu-catalyzed azide-alkyne cycloaddition post-synthetically on DNA. Interestingly, the decrease in melting temperature upon introducing o-nitrobenzyl-caged (NPBY-) and diethylaminocoumarin-cages (DEACM-) in DNA duplexes reaches a limiting value. NMR spectroscopy was used to characterize individual base-pair stabilities and determine experimental structures of a selected number of photocaged DNA molecules. The experimental structures agree well with structures predicted by MD simulations. Combined, the structural data indicate that once a sterically demanding group is added to generate a tri-substituted carbon, the sterically less demanding cage moiety points towards the neighboring nucleoside and the bulkier substituents remain in the major groove.