ArticleNucleic acids research2017
Synthesis and incorporation of 13C-labeled DNA building blocks to probe structural dynamics of DNA by NMR.
Article in Nucleic acids research, 2017. 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.
- Folding and unfolding dynamics of a DNA aptamer studied by heteronuclearJournal of magnetic resonance (San Diego, Calif. : 1997) · 2026Article
- Advances in Isotope Labeling for Solution Nucleic Acid Nuclear Magnetic Resonance Spectroscopy.ChemPlusChem · 2025Review
- Structural Insights into Spare-Tire DNA G-Quadruplex from the HumanACS chemical biology · 2025Article
- Convenient syntheses of isotopically labeled pyrimidine 2'-deoxynucleosides and their 5-hydroxy oxidation products.Nucleosides, nucleotides & nucleic acids · 2025Article
- Syntheses of SpecificallyCurrent protocols · 2022Article
- Isotope Labels Combined with Solution NMR Spectroscopy Make Visible the Invisible Conformations of Small-to-Large RNAs.Chemical reviews · 2022Review
- A methyl-TROSY approach for NMR studies of high-molecular-weight DNA with application to the nucleosome core particle.Proceedings of the National Academy of Sciences of the United States of America · 2020Article
- Dynamics Studies of DNA with Non-canonical Structure Using NMR Spectroscopy.International journal of molecular sciences · 2020Review
- NMR probing of invisible excited states using selectively labeled RNAs.Journal of biomolecular NMR · 2018Article
- Characterizing micro-to-millisecond chemical exchange in nucleic acids using off-resonance RProgress in nuclear magnetic resonance spectroscopyReview
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7 authors.
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Abstract
We report the synthesis of atom-specifically 13C-modified building blocks that can be incorporated into DNA via solid phase synthesis to facilitate investigations on structural and dynamic features via NMR spectroscopy. In detail, 6-13C-modified pyrimidine and 8-13C purine DNA phosphoramidites were synthesized and incorporated into a polypurine tract DNA/RNA hybrid duplex to showcase the facile resonance assignment using site-specific labeling. We also addressed micro- to millisecond dynamics in the mini-cTAR DNA. This DNA is involved in the HIV replication cycle and our data points toward an exchange process in the lower stem of the hairpin that is up-regulated in the presence of the HIV-1 nucleocapsid protein 7. As another example, we picked a G-quadruplex that was earlier shown to exist in two folds. Using site-specific 8-13C-2'deoxyguanosine labeling we were able to verify the slow exchange between the two forms on the chemical shift time scale. In a real-time NMR experiment the re-equilibration of the fold distribution after a T-jump could be monitored yielding a rate of 0.012 min-1. Finally, we used 13C-ZZ-exchange spectroscopy to characterize the kinetics between two stacked X-conformers of a Holliday junction mimic. At 25°C, the refolding process was found to occur at a forward rate constant of 3.1 s-1 and with a backward rate constant of 10.6 s-1.
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