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.

Basic information

Original name

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

Authors

VAVRINSKÁ, Andrea (703 Slovakia), Jiří ZELINKA (203 Czech Republic, belonging to the institution), Jakub ŠEBERA (203 Czech Republic), Vladimír SYCHROVSKÝ (203 Czech Republic), Radovan FIALA (203 Czech Republic, belonging to the institution), Rolf BOELENS (528 Netherlands), Vladimír SKLENÁŘ (203 Czech Republic, belonging to the institution) and Lukáš TRANTÍREK (203 Czech Republic, guarantor, belonging to the institution)

Edition

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

Other information

Language

English

Type of outcome

Článek v odborném periodiku

Field of Study

10610 Biophysics

Country of publisher

Netherlands

Confidentiality degree

není předmětem státního či obchodního tajemství

References:

URL

Impact factor

Impact factor: 2.410

RIV identification code

RIV/00216224:14740/16:00087769

Organization unit

Central European Institute of Technology

DOI

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

UT WoS

000372168000006

Keywords in English

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

Abstract

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.

Links

ED1.1.00/02.0068, research and development project

Name: CEITEC - central european institute of technology

GA13-28310S, research and development project

Name: Evolučně konzervované strukturní vlastnosti centromerické a telomerické DNA

Investor: Czech Science Foundation

GA16-10504S, research and development project

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

Investor: Czech Science Foundation

Citovat

VAVRINSKÁ, Andrea, Jiří ZELINKA, Jakub ŠEBERA, Vladimír SYCHROVSKÝ, Radovan FIALA, Rolf BOELENS, Vladimír SKLENÁŘ and 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, vol. 64, No 1, p. 53-62. ISSN 0925-2738. Available from: 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 and 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, vol.~64, No~1, p.~53-62. ISSN~0925-2738. Available from: https://dx.doi.org/10.1007/s10858-015-0005-x.

Detailed Information on Publication Record