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.

Základní údaje

Originální název

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

Autoři

PADRTA, Petr (203 Česká republika), Richard ŠTEFL (203 Česká republika), Lukáš KRÁLÍK (203 Česká republika), Lukáš ŽÍDEK (203 Česká republika) a Vladimír SKLENÁŘ (203 Česká republika, garant)

Vydání

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

Další údaje

Jazyk

angličtina

Typ výsledku

Článek v odborném periodiku

Obor

10600 1.6 Biological sciences

Stát vydavatele

Nizozemské království

Utajení

není předmětem státního či obchodního tajemství

Impakt faktor

Impact factor: 2.833

Kód RIV

RIV/00216224:14310/02:00006455

Organizační jednotka

Přírodovědecká fakulta

UT WoS

000178550700001

Klíčová slova anglicky

DNA hairpin; NMR; refinement; residual dipolar couplings

Štítky

DNA hairpin, NMR, REFINEMENT, residual dipolar couplings

Změněno: 20. 6. 2008 12:55, prof. RNDr. Vladimír Sklenář, DrSc.

Anotace

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.

Návaznosti

LN00A016, projekt VaV

Název: BIOMOLEKULÁRNÍ CENTRUM

Investor: Ministerstvo školství, mládeže a tělovýchovy ČR, Biomolekulární centrum

Citovat

PADRTA, Petr, Richard ŠTEFL, Lukáš KRÁLÍK, Lukáš ŽÍDEK a Vladimír SKLENÁŘ. Refinement of d(GCGAAGC) hairpin structure using one- and two-bond residual dipolar couplings. Journal of Biomolecular NMR. Dordrecht: Kluwer/Escom, 2002, roč. 24, č. 1, s. 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 a 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, roč.~24, č.~1, s.~1-14. ISSN~0925-2738.

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