Optimal destabilization of DNA double strands by single-nucleobase caging

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 supe
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.
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Author:Patrick Seyfried, Marcel Heinz, György Pintér, Dean-Paulos Klötzner, Yvonne Becker, Michael Bolte, Hendrik R. A. Jonker, Lukas S. Stelzl, Gerhard Hummer, Harald Schwalbe, Alexander Heckel
URN:urn:nbn:de:hebis:30:3-516147
DOI:http://dx.doi.org/10.1002/chem.201804040
Parent Title (English):Chemistry
Document Type:Article
Language:English
Year of Completion:2019
Year of first Publication:2018
Publishing Institution:Universitätsbibliothek Johann Christian Senckenberg
Release Date:2019/11/06
Tag:DNA; NMR spectroscopy; click chemistry; computational chemistry; nucleobases; oligonucleotides; photochemistry
Volume:24
Pagenumber:9
First Page:17568
Last Page:17576
Note:
Gefördert durch: European Union: Horizon 2020. Infrastructure for NMR, EM and X-rays for Translational Research, iNEXT, H2020 Grant # 653706
HeBIS PPN:455917981
Institutes:Biochemie, Chemie und Pharmazie
Dewey Decimal Classification:540 Chemie und zugeordnete Wissenschaften
570 Biowissenschaften; Biologie
Sammlungen:Universitätspublikationen
Licence (German):License Logo Veröffentlichungsvertrag für Publikationen

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