NMR Distance Restraints At Low temperatures : An Application To
DNA Hairpin

J 2005

NMR Distance Restraints At Low temperatures : An Application To DNA Hairpin

MATEJKOVÁ, Michaela, Petr NOVÁK, Radovan FIALA, Petr PADRTA, Vladimír SKLENÁŘ et. al.

Basic information

Original name

NMR Distance Restraints At Low temperatures : An Application To DNA Hairpin

Name in Czech

Měření a extrakce experimentálních dat z NMR spekter za nízkých teplot : Aplikace metody pro DNA hairpin.

Authors

MATEJKOVÁ, Michaela, Petr NOVÁK, Radovan FIALA, Petr PADRTA and Vladimír SKLENÁŘ

Edition

Materials Structure, Praha, The Czech and Slovak Cryst. Assoc. 2005, 1211-5894

Other information

Language

English

Type of outcome

Článek v odborném periodiku

Field of Study

10600 1.6 Biological sciences

Country of publisher

Czech Republic

Confidentiality degree

není předmětem státního či obchodního tajemství

Organization unit

Faculty of Science

Keywords in English

NMR;structure;DNA

Abstract

ORIG CZ

V originále

Number of the experimental NMR distance restraints extracted at the ambient temperature is remarkably decreased by an internal mobility in a molecule, mostly chemical exchange. This problem can be avoided by NMR measurements at lower temperatures. To achieve the lowest temperature while keeping the liquid state and minimize the chemical exchange, the NMR experiments can be performed using the slowly cooled capillaries. The aim of the present study is to investigate possibilities of NMR measurements in liquid state at the temperatures below 273 K and applicability of this approach to a nucleic acid fragment. For this purpose, the d(GCGAAGC) hairpin has been chosen because its structure has been previously solved precisely by NMR spectroscopy. We have performed a new structure calculation of this molecule using the low temperature NMR measurements and compared the precision of the newly calculated and known structures. A series of the 2D-NOESY spectra with the mixing times in a range of 50 to 400 ms has been measured at 268K. The NOESY cross-peaks for the different mixing times were integrated using the SPARKY program and the results were employed to derive the inter-proton distance restraints. Then, the numbers of distance restraints extracted at 268 K and 303 K were compared. In case of nonexchangeable protons, these numbers were comparable due to the significant spectral overlaps in the NOESY spectra measured at 268 K. While, there was almost twice higher number of exchangeable proton distances extracted at 268 K compared to 303 K and these restraints helped increase the precision of the calculated structure of the d(GCGAAGC).

In Czech

Cílem této studie bylo porovnat množství experimentálních dat získaných z NMR spekter hairpinu d(GCGAAGC), změřených při teplotách 303K a 268K. Při teplotách pod 273K dochází k spomalení chemické výměny a intramolekulárních pohybů, čímž se zvýší množství experimentálních NMR dat oproti situaci při běžné teplotě. To to se potrvdilo i v případě našeho vzorku.

Links

LN00A016, research and development project

Name: BIOMOLEKULÁRNÍ CENTRUM

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

Citovat

MATEJKOVÁ, Michaela, Petr NOVÁK, Radovan FIALA, Petr PADRTA and Vladimír SKLENÁŘ. NMR Distance Restraints At Low temperatures : An Application To DNA Hairpin. Materials Structure. Praha: The Czech and Slovak Cryst. Assoc., 2005, vol. 12, No 1, p. 33-33. ISSN 1211-5894.

@article{571120,
   author = {Matejková, Michaela and Novák, Petr and Fiala, Radovan and Padrta, Petr and Sklenář, Vladimír},
   article_location = {Praha},
   article_number = {1},
   keywords = {NMR;structure;DNA},
   language = {eng},
   issn = {1211-5894},
   journal = {Materials Structure},
   title = {NMR Distance Restraints At Low temperatures : An Application To DNA Hairpin},
   volume = {12},
   year = {2005}
}

TY  - JOUR
ID  - 571120
AU  - Matejková, Michaela - Novák, Petr - Fiala, Radovan - Padrta, Petr - Sklenář, Vladimír
PY  - 2005
TI  - NMR Distance Restraints At Low temperatures : An Application To DNA Hairpin
JF  - Materials Structure
VL  - 12
IS  - 1
SP  - 33-33
EP  - 33-33
PB  - The Czech and Slovak Cryst. Assoc.
SN  - 12115894
KW  - NMR;structure;DNA
N2  - Number of the experimental NMR distance restraints extracted at the ambient temperature is remarkably decreased by an internal mobility in a molecule, mostly chemical exchange. This problem can be avoided by NMR measurements at lower temperatures. To achieve the lowest temperature while keeping the liquid state and minimize the chemical exchange, the NMR experiments can be performed using the slowly cooled capillaries. The aim of the present study is to investigate possibilities of NMR measurements in liquid state at the temperatures below 273 K and applicability of this approach to a nucleic acid fragment. For this purpose, the d(GCGAAGC) hairpin has been chosen because its structure has been previously solved precisely by NMR spectroscopy. We have performed a new structure calculation of this molecule using the low temperature NMR measurements and compared the precision of the newly calculated and known structures. A series of the 2D-NOESY spectra with the mixing times in a range of 50 to 400 ms has been measured at 268K. The NOESY cross-peaks for the different mixing times were integrated using the SPARKY program and the results were employed to derive the inter-proton distance restraints. Then, the numbers of distance restraints extracted at 268 K and 303 K were compared. In case of nonexchangeable protons, these numbers were comparable due to the significant spectral overlaps in the NOESY spectra measured at 268 K. While, there was almost twice higher number of exchangeable proton distances extracted at 268 K compared to 303 K and these restraints helped increase the precision of the calculated structure of the d(GCGAAGC).
ER  -

MATEJKOVÁ, Michaela, Petr NOVÁK, Radovan FIALA, Petr PADRTA and Vladimír SKLENÁŘ. NMR Distance Restraints At Low temperatures : An Application To DNA Hairpin. \textit{Materials Structure}. Praha: The Czech and Slovak Cryst. Assoc., 2005, vol.~12, No~1, p.~33-33. ISSN~1211-5894.

Detailed Information on Publication Record