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13C-detected NMR experiments for measuring chemical shifts and coupling constants in nucleic acid bases

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Abstract

The paper presents a set of two-dimensional experiments that utilize direct 13C detection to provide proton–carbon, carbon–carbon and carbon–nitrogen correlations in the bases of nucleic acids. The set includes a 13C-detected proton–carbon correlation experiment for the measurement of 13C–13C couplings, the CaCb experiment for correlating two quaternary carbons, the HCaCb experiment for the 13C–13C correlations in cases where one of the carbons has a proton attached, the HCC-TOCSY experiment for correlating a proton with a network of coupled carbons, and a 13C-detected 13C–15N correlation experiment for detecting the nitrogen nuclei that cannot be detected via protons. The IPAP procedure is used for extracting the carbon–carbon couplings and/or carbon decoupling in the direct dimension, while the S3E procedure is preferred in the indirect dimension of the carbon–nitrogen experiment to obtain the value of the coupling constant. The experiments supply accurate values of 13C and 15N chemical shifts and carbon–carbon and carbon–nitrogen coupling constants. These values can help to reveal structural features of nucleic acids either directly or via induced changes when the sample is dissolved in oriented media.

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Abbreviations

AP:

anti-phase

DIPAP:

Double IPAP

DSS:

4,4-dimethyl 4-silapentane sodium sulfonate

HSQC:

Heteronuclear single-quantum correlation

INEPT:

Insensitive nuclei enhancement by polarization transfer

IP:

In-phase

PCM:

Polarizable continuum model

RDC:

Residual dipolar coupling

S3E:

Spin-state selective excitation

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Acknowledgments

The work was supported by the grants MSM0021622413 to RF and LC06030 to VS provided by the Ministry of Education of the Czech Republic and by the FSG-V-RNA project of the 6th Framework Program of the European Union, Contract No. 503455. We are indebted to David Staple and Sam Butcher for the U6 ISL sample, to Wolfgang Bermel and Helena Kovacs for stimulating discussions and help in the implementation of the pulse sequences, and to Petr Novák for an assistance in the evaluation of scalar couplings.

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  1. National Centre for Biomolecular Research, Masaryk University, Kotlářská 2, Brno, 611 37, Czech Republic

    Radovan Fiala & Vladimír Sklenář

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  1. Radovan Fiala
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  2. Vladimír Sklenář
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Correspondence to Vladimír Sklenář.

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Fiala, R., Sklenář, V. 13C-detected NMR experiments for measuring chemical shifts and coupling constants in nucleic acid bases. J Biomol NMR 39, 153–163 (2007). https://doi.org/10.1007/s10858-007-9184-4

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  • DOI: https://doi.org/10.1007/s10858-007-9184-4

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