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Hyperpolarized NMR Reveals Low-Populated Folding Intermediates in DNA
Milan Zachrdla1, Ertan Turhan1, Michala Bučková2,3
1Institute of Biological Chemistry, Faculty of Chemistry, University of Vienna, Währinger Str. 38, 1090 Vienna, Austria.
Journal of the American Chemical Society
|December 8, 2025
Summary
Hyperpolarized Nuclear Magnetic Resonance (NMR) significantly boosts signal detection for DNA structures. This advanced technique enables the study of low-abundance DNA folding intermediates, crucial for applications like liquid biopsies.
Area of Science:
- Biophysics
- Structural Biology
- Spectroscopy
Background:
- Nuclear Magnetic Resonance (NMR) spectroscopy is vital for atomic-level characterization of nucleic acid structures in solution.
- However, NMR suffers from low sensitivity, limiting analysis of complex DNA targets like high-molecular-weight, low-abundance, or polymorphic DNAs.
- Dissolution dynamic nuclear polarization (dDNP) offers a potential solution to overcome NMR's sensitivity limitations.
Purpose of the Study:
- To investigate the efficacy of hyperpolarized aqueous buffers, generated via dDNP, in enhancing 1H NMR signals for various DNA motifs.
- To demonstrate the utility of these enhanced signals for structural fingerprinting and detecting low-populated DNA folding intermediates.
- To establish hyperpolarized NMR as a sensitive tool for DNA structure and folding analysis.
Main Methods:
- Generation of hyperpolarized aqueous buffers using dissolution dynamic nuclear polarization (dDNP).
- Application of these hyperpolarized buffers to dissolve and analyze various DNA motifs using 1H NMR spectroscopy.
- Quantification of signal enhancement for labile imino and amino proton resonances.
Main Results:
- Significant enhancement of 1H NMR signals for multiple DNA motifs dissolved in hyperpolarized buffers, up to ~200-fold for imino protons and ~370-fold for amino protons.
- Demonstrated utility of enhanced signals as structural fingerprints for DNA folding topologies.
- Enabled direct observation of previously undetectable low-populated folding intermediates in DNA polymorphs like G-quadruplexes (G4) and i-motifs (iM).
Conclusions:
- Hyperpolarized NMR spectroscopy dramatically enhances sensitivity for probing DNA structures.
- This technique allows for the direct observation of transient DNA folding intermediates, expanding structural analysis capabilities.
- Hyperpolarized NMR opens new possibilities for studying DNA in contexts such as liquid biopsies and cell-free DNA analysis.
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