Analysis of NMR Distance Restraints - An Application To DNA and
RNA Hairpins

D 2005

Analysis of NMR Distance Restraints - An Application To DNA and RNA Hairpins

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

Basic information

Original name

Analysis of NMR Distance Restraints - An Application To DNA and RNA Hairpins

Name in Czech

Analýza experimentálních dat z NMR spekter - Aplikace metody pro DNA a RNA hairpiny

Authors

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

Edition

Brno, Konference mladých vědeckých pracovníků "Strukturní biofyzika makromolekul" p. 11-11, 1 pp. 2005

Publisher

Biofyzikální ústav AV CR a Masarykova univerzita-Přírodovědecká fakulta

Other information

Language

English

Type of outcome

Stať ve sborníku

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; NOESY; restraints

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

MSM0021622413, plan (intention)

Name: Proteiny v metabolismu a při interakci organismů s prostředím

Investor: Ministry of Education, Youth and Sports of the CR, Proteins in metabolism and interaction of organisms with the environment

Citovat

MATEJKOVÁ, Michaela, Petr NOVÁK, Radovan FIALA, Petr PADRTA and Vladimír SKLENÁŘ. Analysis of NMR Distance Restraints - An Application To DNA and RNA Hairpins. In Konference mladých vědeckých pracovníků "Strukturní biofyzika makromolekul". Brno: Biofyzikální ústav AV CR a Masarykova univerzita-Přírodovědecká fakulta, 2005, p. 11-11.

@inproceedings{702268,
   author = {Matejková, Michaela and Novák, Petr and Fiala, Radovan and Padrta, Petr and Sklenář, Vladimír},
   address = {Brno},
   booktitle = {Konference mladých vědeckých pracovníků "Strukturní biofyzika makromolekul"},
   keywords = {NMR; NOESY; restraints},
   language = {eng},
   location = {Brno},
   pages = {11-11},
   publisher = {Biofyzikální ústav AV CR a Masarykova univerzita-Přírodovědecká fakulta},
   title = {Analysis of NMR Distance Restraints - An Application To DNA and RNA Hairpins},
   year = {2005}
}

TY  - JOUR
ID  - 702268
AU  - Matejková, Michaela - Novák, Petr - Fiala, Radovan - Padrta, Petr - Sklenář, Vladimír
PY  - 2005
TI  - Analysis of NMR Distance Restraints - An Application To DNA and RNA Hairpins
PB  - Biofyzikální ústav AV CR a Masarykova univerzita-Přírodovědecká fakulta
CY  - Brno
KW  - NMR
KW  - NOESY
KW  - restraints
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. Analysis of NMR Distance Restraints - An Application To DNA and RNA Hairpins. In \textit{Konference mladých vědeckých pracovníků ''Strukturní biofyzika makromolekul''}. Brno: Biofyzikální ústav AV CR a Masarykova univerzita-Přírodovědecká fakulta, 2005, p.~11-11.

Detailed Information on Publication Record