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Sugar Pucker Modulates the Cross-Correlated Relaxation Rates across the Glycosidic Bond in DNA

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Contribution from the Institute of Organic Chemistry and Biochemistry AS CR, Prague, Czech Republic, Institute of Organic Chemistry, Johannes Kepler University, Linz, Austria, Rudjer Boskovic Institute, Zagreb, Croatia, Institute of Biophysis AS CR, Brno, Czech Republic, and Faculty of Biological Sciences, University of South Bohemia and Institute of Parasitology AS CR, Branišovská 31, CZ-37005 České Budějovice, Czech Republic
Cite this: J. Am. Chem. Soc. 2005, 127, 42, 14663–14667
Publication Date (Web):September 28, 2005
https://doi.org/10.1021/ja050894t
Copyright © 2005 American Chemical Society
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Abstract

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The dependence of N1/9 and C1‘ chemical shielding (CS) tensors on the glycosidic bond orientation (χ) and sugar pucker (P) in the DNA nucleosides 2‘-deoxyadenosine, 2‘-deoxyguanosine, 2‘-deoxycytidine, and 2‘-deoxythymidine was studied using the calculation methods of quantum chemistry. The results indicate that these CS-tensors exhibit a significant degree of conformational dependence on χ and P structural parameters. The presented data test underlying assumptions of currently established methods for interpretation of cross-correlated relaxation rates between the N1/9 chemical shielding tensor and C1‘−H1‘ dipole−dipole (Ravindranathan et al. J. Biomol. NMR2003, 27, 365−75. Duchardt et al. J. Am. Chem. Soc. 2004, 126, 1962−70) and highlight possible limitations of these methods when applied to DNA.

 Institute of Organic Chemistry and Biochemistry AS CR.

 Johannes Kepler University.

§

 Rudjer Boskovic Institute.

 Institute of Biophysis AS CR.

*

In papers with more than one author, the asterisk indicates the name of the author to whom inquiries about the paper should be addressed.

 University of South Bohemia and Institute of Parasitology AS CR.

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Calculated N1/9 and C1‘ CS-tensors for dGua, dAde, dCyt, and dThy as a function of χ and sugar pucker. This material is available free of charge via Internet at http://pubs.acs.org.

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  23. Jörg Rinnenthal, Christian Richter, Jan Ferner, Elke Duchardt, Harald Schwalbe. Quantitative Γ-HCNCH: determination of the glycosidic torsion angle χ in RNA oligonucleotides from the analysis of CH dipolar cross-correlated relaxation by solution NMR spectroscopy. Journal of Biomolecular NMR 2007, 39 (1) , 17-29. https://doi.org/10.1007/s10858-007-9167-5

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