Impact of nucleic acid self-alignment in a strong magnetic
field on the interpretation of indirect spin–spin interactions

J 2016

Impact of nucleic acid self-alignment in a strong magnetic field on the interpretation of indirect spin–spin interactions

VAVRINSKÁ, Andrea, Jiří ZELINKA, Jakub ŠEBERA, Vladimír SYCHROVSKÝ, Radovan FIALA et. al.

Základní údaje

Originální název

Impact of nucleic acid self-alignment in a strong magnetic field on the interpretation of indirect spin–spin interactions

Autoři

VAVRINSKÁ, Andrea (703 Slovensko), Jiří ZELINKA (203 Česká republika, domácí), Jakub ŠEBERA (203 Česká republika), Vladimír SYCHROVSKÝ (203 Česká republika), Radovan FIALA (203 Česká republika, domácí), Rolf BOELENS (528 Nizozemské království), Vladimír SKLENÁŘ (203 Česká republika, domácí) a Lukáš TRANTÍREK (203 Česká republika, garant, domácí)

Vydání

Journal of biomolecular NMR, Dordrecht, Springer, 2016, 0925-2738

Další údaje

Jazyk

angličtina

Typ výsledku

Článek v odborném periodiku

Obor

10610 Biophysics

Stát vydavatele

Nizozemské království

Utajení

není předmětem státního či obchodního tajemství

Odkazy

URL

Impakt faktor

Impact factor: 2.410

Kód RIV

RIV/00216224:14740/16:00087769

Organizační jednotka

Středoevropský technologický institut

DOI

http://dx.doi.org/10.1007/s10858-015-0005-x

UT WoS

000372168000006

Klíčová slova anglicky

Nucleic acid; Self-alignment; Magnetic susceptibility; Scalar coupling; Dipolar coupling; Karplus equation

Štítky

AKR, rivok

Změněno: 16. 3. 2017 12:17, Mgr. Eva Špillingová

Anotace

V originále

Heteronuclear and homonuclear direct (D) and indirect (J) spin-spin interactions are important sources of structural information about nucleic acids (NAs). The Hamiltonians for the D and J interactions have the same functional form; thus, the experimentally measured apparent spin-spin coupling constant corresponds to a sum of J and D. In biomolecular NMR studies, it is commonly presumed that the dipolar contributions to Js are effectively canceled due to random molecular tumbling. However, in strong magnetic fields, such as those employed for NMR analysis, the tumbling of NA fragments is anisotropic because the inherent magnetic susceptibility of NAs causes an interaction with the external magnetic field. This motional anisotropy is responsible for non-zero D contributions to Js. Here, we calculated the field-induced D contributions to 33 structurally relevant scalar coupling constants as a function of magnetic field strength, temperature and NA fragment size. We identified two classes of Js, namely 1JCH and 3JHH couplings, whose quantitative interpretation is notably biased by NA motional anisotropy. For these couplings, the magnetic field-induced dipolar contributions were found to exceed the typical experimental error in J-coupling determinations by a factor of two or more and to produce considerable over- or under-estimations of the J coupling-related torsion angles, especially at magnetic field strengths >12 T and for NA fragments longer than 12 bp. We show that if the non-zero D contributions to J are not properly accounted for, they might cause structural artifacts/bias in NA studies that use solution NMR spectroscopy.

Návaznosti

ED1.1.00/02.0068, projekt VaV

Název: CEITEC - central european institute of technology

GA13-28310S, projekt VaV

Název: Evolučně konzervované strukturní vlastnosti centromerické a telomerické DNA

Investor: Grantová agentura ČR, Evolucne konzervované strukturní vlastnosti centromerické a telomerické DNA

GA16-10504S, projekt VaV

Název: Charakterizace struktury nukleových kyselin v komplexním prostředí živých buněk pomocí vysoce rozlišené NMR spektroskopie

Investor: Grantová agentura ČR, Charakterizace struktury nukleových kyselin v komplexním prostředí živých buněk pomocí vysoce rozlišené NMR spektroskopie

Citovat

VAVRINSKÁ, Andrea, Jiří ZELINKA, Jakub ŠEBERA, Vladimír SYCHROVSKÝ, Radovan FIALA, Rolf BOELENS, Vladimír SKLENÁŘ a Lukáš TRANTÍREK. Impact of nucleic acid self-alignment in a strong magnetic field on the interpretation of indirect spin–spin interactions. Journal of biomolecular NMR. Dordrecht: Springer, 2016, roč. 64, č. 1, s. 53-62. ISSN 0925-2738. Dostupné z: https://dx.doi.org/10.1007/s10858-015-0005-x.

@article{1324105,
   author = {Vavrinská, Andrea and Zelinka, Jiří and Šebera, Jakub and Sychrovský, Vladimír and Fiala, Radovan and Boelens, Rolf and Sklenář, Vladimír and Trantírek, Lukáš},
   article_location = {Dordrecht},
   article_number = {1},
   doi = {http://dx.doi.org/10.1007/s10858-015-0005-x},
   keywords = {Nucleic acid; Self-alignment; Magnetic susceptibility; Scalar coupling; Dipolar coupling; Karplus equation},
   language = {eng},
   issn = {0925-2738},
   journal = {Journal of biomolecular NMR},
   title = {Impact of nucleic acid self-alignment in a strong magnetic field on the interpretation of indirect spin–spin interactions},
   url = {http://link.springer.com/article/10.1007/s10858-015-0005-x},
   volume = {64},
   year = {2016}
}

TY  - JOUR
ID  - 1324105
AU  - Vavrinská, Andrea - Zelinka, Jiří - Šebera, Jakub - Sychrovský, Vladimír - Fiala, Radovan - Boelens, Rolf - Sklenář, Vladimír - Trantírek, Lukáš
PY  - 2016
TI  - Impact of nucleic acid self-alignment in a strong magnetic field on the interpretation of indirect spin–spin interactions
JF  - Journal of biomolecular NMR
VL  - 64
IS  - 1
SP  - 53-62
EP  - 53-62
PB  - Springer
SN  - 09252738
KW  - Nucleic acid
KW  - Self-alignment
KW  - Magnetic susceptibility
KW  - Scalar coupling
KW  - Dipolar coupling
KW  - Karplus equation
UR  - http://link.springer.com/article/10.1007/s10858-015-0005-x
L2  - http://link.springer.com/article/10.1007/s10858-015-0005-x
N2  - Heteronuclear and homonuclear direct (D) and indirect (J) spin-spin interactions are important sources of structural information about nucleic acids (NAs). The Hamiltonians for the D and J interactions have the same functional form; thus, the experimentally measured apparent spin-spin coupling constant corresponds to a sum of J and D. In biomolecular NMR studies, it is commonly presumed that the dipolar contributions to Js are effectively canceled due to random molecular tumbling. However, in strong magnetic fields, such as those employed for NMR analysis, the tumbling of NA fragments is anisotropic because the inherent magnetic susceptibility of NAs causes an interaction with the external magnetic field. This motional anisotropy is responsible for non-zero D contributions to Js. Here, we calculated the field-induced D contributions to 33 structurally relevant scalar coupling constants as a function of magnetic field strength, temperature and NA fragment size. We identified two classes of Js, namely 1JCH and 3JHH couplings, whose quantitative interpretation is notably biased by NA motional anisotropy. For these couplings, the magnetic field-induced dipolar contributions were found to exceed the typical experimental error in J-coupling determinations by a factor of two or more and to produce considerable over- or under-estimations of the J coupling-related torsion angles, especially at magnetic field strengths >12 T and for NA fragments longer than 12 bp. We show that if the non-zero D contributions to J are not properly accounted for, they might cause structural artifacts/bias in NA studies that use solution NMR spectroscopy.
ER  -

VAVRINSKÁ, Andrea, Jiří ZELINKA, Jakub ŠEBERA, Vladimír SYCHROVSKÝ, Radovan FIALA, Rolf BOELENS, Vladimír SKLENÁŘ a Lukáš TRANTÍREK. Impact of nucleic acid self-alignment in a strong magnetic field on the interpretation of indirect spin–spin interactions. \textit{Journal of biomolecular NMR}. Dordrecht: Springer, 2016, roč.~64, č.~1, s.~53-62. ISSN~0925-2738. Dostupné z: https://dx.doi.org/10.1007/s10858-015-0005-x.

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