A DFT Analysis of NMR Scalar Interactions Across the Glycosidic
Bond in DNA

J 2003

A DFT Analysis of NMR Scalar Interactions Across the Glycosidic Bond in DNA

MUNZAROVÁ, Markéta and Vladimír SKLENÁŘ

Basic information

Original name

A DFT Analysis of NMR Scalar Interactions Across the Glycosidic Bond in DNA

Authors

MUNZAROVÁ, Markéta (203 Czech Republic) and Vladimír SKLENÁŘ (203 Czech Republic, guarantor)

Edition

Journal of the American Chemical Society, Washington, D.C. American Chemical Society, 2003, 0002-7863

Other information

Language

English

Type of outcome

Článek v odborném periodiku

Field of Study

10403 Physical chemistry

Country of publisher

Czech Republic

Confidentiality degree

není předmětem státního či obchodního tajemství

Impact factor

Impact factor: 6.516

RIV identification code

RIV/00216224:14310/03:00008630

Organization unit

Faculty of Science

Keywords in English

NUCLEIC-ACIDS; CONSTANTS; OLIGONUCLEOTIDES; NMR

Abstract

V originále

Abstract. The relationship between the glycosidic torsion angle c, the three-bond couplings 3JC2/4-H1' and 3JC6/8-H1', and the one-bond coupling 1JC1'-H1' in deoxyribonucleosides and a number of uracil cyclo-nucleosides has been analyzed using density functional theory. The influence of the sugar pucker and the hydroxymethyl conformation has also been considered. The parameters of the Karplus relationships between the three-bond couplings and c depend strongly on the aromatic base. 3JC2/4-H1' reveals different behavior for deoxyadenosine, deoxyguanosine, and deoxycytidine as compared to deoxythymidine and deoxyuridine. In the case of 3JC6/8-H1', an opposite trans to cis ratio of couplings is obtained for pyrimidine nucleosides in contrast to purine nucleosides. The extremes of the Karplus curves are shifted by ca. 10o with respect to syn and anti-periplanar orientations of the coupled nuclei. The change in the sugar pucker from S to N decreases 3JC2/4-H1' and 3JC6/8-H1' while increasing 1JC1'-H1' for the syn rotamers, whereas all of the trends are reversed for the anti rotamers. The influence of the sugar pucker on 1JC1'-H1' is interpreted in terms of interactions between the nO4', sigma C1'-H1' orbitals. The 1JC1'-H1' are related to chi through a generalized Karplus relationship, which combines cos(chi) and cos2(chi) functions with mutually different phase shifts that implicitly accounts for a significant portion of the related sugar pucker effects. Most of theoretical 3JC2/4-H1' and 3JC6/8-H1' for uracil cyclo-nucleosides compare well with available experimental data. 3JC6/8-H1' couplings for all C2-bridged nucleosides are up to 3 Hz smaller than in the genuine nucleosides with the corresponding chi, revealing a non-local aspect of the spin-spin interactions across the glycosidic bond. Theoretical 1JC1'-H1' are underestimated with respect to the experiment by ca. 10% but reproduce the trends in 1JC1'-H1' vs. chi.

Links

LN00A016, research and development project

Name: BIOMOLEKULÁRNÍ CENTRUM

Investor: Ministry of Education, Youth and Sports of the CR, Biomolecular Center

Citovat

MUNZAROVÁ, Markéta and Vladimír SKLENÁŘ. A DFT Analysis of NMR Scalar Interactions Across the Glycosidic Bond in DNA. Journal of the American Chemical Society. Washington, D.C.: American Chemical Society, 2003, vol. 125, No 12, p. 3649-3658. ISSN 0002-7863.

@article{485416,
   author = {Munzarová, Markéta and Sklenář, Vladimír},
   article_location = {Washington, D.C.},
   article_number = {12},
   keywords = {NUCLEIC-ACIDS; CONSTANTS; OLIGONUCLEOTIDES; NMR},
   language = {eng},
   issn = {0002-7863},
   journal = {Journal of the American Chemical Society},
   title = {A DFT Analysis of NMR Scalar Interactions Across the Glycosidic Bond in DNA},
   volume = {125},
   year = {2003}
}

TY  - JOUR
ID  - 485416
AU  - Munzarová, Markéta - Sklenář, Vladimír
PY  - 2003
TI  - A DFT Analysis of NMR Scalar Interactions Across the Glycosidic Bond in DNA
JF  - Journal of the American Chemical Society
VL  - 125
IS  - 12
SP  - 3649
EP  - 3649
PB  - American Chemical Society
SN  - 00027863
KW  - NUCLEIC-ACIDS
KW  - CONSTANTS
KW  - OLIGONUCLEOTIDES
KW  - NMR
N2  - Abstract. The relationship between the glycosidic torsion angle c, the three-bond couplings 3JC2/4-H1' and 3JC6/8-H1', and the one-bond coupling 1JC1'-H1' in deoxyribonucleosides and a number of uracil cyclo-nucleosides has been analyzed using density functional theory. The influence of the sugar pucker and the hydroxymethyl conformation has also been considered. The parameters of the Karplus relationships between the three-bond couplings and c depend strongly on the aromatic base. 3JC2/4-H1' reveals different behavior for deoxyadenosine, deoxyguanosine, and deoxycytidine as compared to deoxythymidine and deoxyuridine. In the case of 3JC6/8-H1', an opposite trans to cis ratio of couplings is obtained for pyrimidine nucleosides in contrast to purine nucleosides. The extremes of the Karplus curves are shifted by ca. 10o with respect to syn and anti-periplanar orientations of the coupled nuclei. The change in the sugar pucker from S to N decreases 3JC2/4-H1' and 3JC6/8-H1' while increasing 1JC1'-H1' for the syn rotamers, whereas all of the trends are reversed for the anti rotamers. The influence of the sugar pucker on 1JC1'-H1' is interpreted in terms of interactions between the nO4', sigma C1'-H1' orbitals. The 1JC1'-H1' are related to chi through a generalized Karplus relationship, which combines cos(chi) and cos2(chi) functions with mutually different phase shifts that implicitly accounts for a significant portion of the related sugar pucker effects. Most of theoretical 3JC2/4-H1' and 3JC6/8-H1' for uracil cyclo-nucleosides compare well with available experimental data. 3JC6/8-H1' couplings for all C2-bridged nucleosides are up to 3 Hz smaller than in the genuine nucleosides with the corresponding chi, revealing a non-local aspect of the spin-spin interactions across the glycosidic bond. Theoretical 1JC1'-H1' are underestimated with respect to the experiment by ca. 10% but reproduce the trends in 1JC1'-H1' vs. chi.
ER  -

MUNZAROVÁ, Markéta and Vladimír SKLENÁŘ. A DFT Analysis of NMR Scalar Interactions Across the Glycosidic Bond in DNA. \textit{Journal of the American Chemical Society}. Washington, D.C.: American Chemical Society, 2003, vol.~125, No~12, p.~3649-3658. ISSN~0002-7863.

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