ArticleNucleic acids research2015
Identification of a pKa-regulating motif stabilizing imidazole-modified double-stranded DNA.
Article in Nucleic acids research, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 10 papers.
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Who cites it
10 citing papers in PubMed.
- Article
- Recent advances in aptamer discovery, modification and improving performance.Biochemistry and biophysics reports · 2024Review
- Testing the Simplified Molecular Dynamics Approach to Improve the Reproduction of ECD Spectra and Monitor Aggregation.International journal of molecular sciences · 2024Article
- Chemically modified aptamers for improving binding affinity to the target proteinsFrontiers in cell and developmental biology · 2023Review
- A Novel Trimethylamine Oxide-Induced Model Implicates Gut Microbiota-Related Mechanisms in Frailty.Frontiers in cellular and infection microbiology · 2022Article
- Chemical Modification of Aptamers for Increased Binding Affinity in Diagnostic Applications: Current Status and Future Prospects.International journal of molecular sciences · 2020Review
- Tethered imidazole mediated duplex stabilization and its potential for aptamer stabilization.Nucleic acids research · 2018Article
- DNA Three Way Junction Core Decorated with Amino Acids-Like Residues-Synthesis and Characterization.Molecules (Basel, Switzerland) · 2016Article
- DNA Catalysis: The Chemical Repertoire of DNAzymes.Molecules (Basel, Switzerland) · 2015Review
- Versatile synthesis of amino acid functionalized nucleosides via a domino carboxamidation reaction.Beilstein journal of organic chemistry · 2014Article
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Authors and funding
7 authors.
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No grant is acknowledged in the PubMed record.
Abstract
The predictable 3D structure of double-stranded DNA renders it ideally suited as a template for the bottom-up design of functionalized nucleic acid-based active sites. We here explore the use of a 14mer DNA duplex as a scaffold for the precise and predictable positioning of catalytic functionalities. Given the ubiquitous participation of the histidine-based imidazole group in protein recognition and catalysis events, single histidine-like modified duplexes were investigated. Tethering histamine to the C5 of the thymine base via an amide bond, allows the flexible positioning of the imidazole function in the major groove. The mutual interactions between the imidazole and the duplex and its influence on the imidazolium pKaH are investigated by placing a single modified thymine at four different positions in the center of the 14mer double helix. Using NMR and unrestrained molecular dynamics, a structural motif involving the formation of a hydrogen bond between the imidazole and the Hoogsteen side of the guanine bases of two neighboring GC base pairs is established. The motif contributes to a stabilization against thermal melting of 6°C and is key in modulating the pKaH of the imidazolium group. The general features, prerequisites and generic character of the new pKaH-regulating motif are described.
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