Refinement of d(GCGAAGC) hairpin structure using one- and
two-bond residual dipolar couplings

J 2002

Refinement of d(GCGAAGC) hairpin structure using one- and two-bond residual dipolar couplings

PADRTA, Petr, Richard ŠTEFL, Lukáš KRÁLÍK, Lukáš ŽÍDEK, Vladimír SKLENÁŘ et. al.

Basic information

Original name

Refinement of d(GCGAAGC) hairpin structure using one- and two-bond residual dipolar couplings

Authors

PADRTA, Petr (203 Czech Republic), Richard ŠTEFL (203 Czech Republic), Lukáš KRÁLÍK (203 Czech Republic), Lukáš ŽÍDEK (203 Czech Republic) and Vladimír SKLENÁŘ (203 Czech Republic, guarantor)

Edition

Journal of Biomolecular NMR, Dordrecht, Kluwer/Escom, 2002, 0925-2738

Other information

Language

English

Type of outcome

Článek v odborném periodiku

Field of Study

10600 1.6 Biological sciences

Country of publisher

Netherlands

Confidentiality degree

není předmětem státního či obchodního tajemství

Impact factor

Impact factor: 2.833

RIV identification code

RIV/00216224:14310/02:00006455

Organization unit

Faculty of Science

UT WoS

000178550700001

Keywords in English

DNA hairpin; NMR; refinement; residual dipolar couplings

Abstract

V originále

The structure of the 13C,15N-labeled d(GCGAAGC) hairpin, as determined by NMR spectroscopy and refined using molecular dynamics with NOE-derived distances, torsion angles, and residual dipolar couplings (RDCs), is presented. Although the studied molecule is of small size, it is demonstrated that the incorporation of diminutive RDCs can significantly improve local structure determination of regions undefined by the conventional restraints. Very good correlation between the experimental and back-calculated small one- and two-bond 1H-13C, 1H-15N, 13C-13C, and 13C-15N coupling constants has been attained. The final structures clearly show typical features of the miniloop architecture. The structure is discussed in context of the extraordinary stability of the d(GCGAAGC) hairpin, which originates from a complex interplay between the aromatic base stacking and hydrogen bonding interactions.

Links

LN00A016, research and development project

Name: BIOMOLEKULÁRNÍ CENTRUM

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

Citovat

PADRTA, Petr, Richard ŠTEFL, Lukáš KRÁLÍK, Lukáš ŽÍDEK and Vladimír SKLENÁŘ. Refinement of d(GCGAAGC) hairpin structure using one- and two-bond residual dipolar couplings. Journal of Biomolecular NMR. Dordrecht: Kluwer/Escom, 2002, vol. 24, No 1, p. 1-14. ISSN 0925-2738.

@article{405489,
   author = {Padrta, Petr and Štefl, Richard and Králík, Lukáš and Žídek, Lukáš and Sklenář, Vladimír},
   article_location = {Dordrecht},
   article_number = {1},
   keywords = {DNA hairpin; NMR; refinement; residual dipolar couplings},
   language = {eng},
   issn = {0925-2738},
   journal = {Journal of Biomolecular NMR},
   title = {Refinement of d(GCGAAGC) hairpin structure using one- and two-bond residual dipolar couplings},
   volume = {24},
   year = {2002}
}

TY  - JOUR
ID  - 405489
AU  - Padrta, Petr - Štefl, Richard - Králík, Lukáš - Žídek, Lukáš - Sklenář, Vladimír
PY  - 2002
TI  - Refinement of d(GCGAAGC) hairpin structure using one- and two-bond residual dipolar couplings
JF  - Journal of Biomolecular NMR
VL  - 24
IS  - 1
SP  - 1
EP  - 1
PB  - Kluwer/Escom
SN  - 09252738
KW  - DNA hairpin
KW  - NMR
KW  - refinement
KW  - residual dipolar couplings
N2  - The structure of the 13C,15N-labeled d(GCGAAGC) hairpin, as determined by NMR spectroscopy and refined using molecular dynamics with NOE-derived distances, torsion angles, and residual dipolar couplings (RDCs), is presented. Although the studied molecule is of small size, it is demonstrated that the incorporation of diminutive RDCs can significantly improve local structure determination of regions undefined by the conventional restraints. Very good correlation between the experimental and back-calculated small one- and two-bond 1H-13C, 1H-15N, 13C-13C, and 13C-15N coupling constants has been attained. The final structures clearly show typical features of the miniloop architecture. The structure is discussed in context of the extraordinary stability of the d(GCGAAGC) hairpin, which originates from a complex interplay between the aromatic base stacking and hydrogen bonding interactions.
ER  -

PADRTA, Petr, Richard ŠTEFL, Lukáš KRÁLÍK, Lukáš ŽÍDEK and Vladimír SKLENÁŘ. Refinement of d(GCGAAGC) hairpin structure using one- and two-bond residual dipolar couplings. \textit{Journal of Biomolecular NMR}. Dordrecht: Kluwer/Escom, 2002, vol.~24, No~1, p.~1-14. ISSN~0925-2738.

Detailed Information on Publication Record