Abstract
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.Electronic supplementary materialThe online version of this article (doi:10.1007/s10858-015-0005-x) contains supplementary material, which is available to authorized users.
Highlights
The major sources of structural information from NMR measurements of biomolecules in isotropic solution are nuclear Overhauser enhancements (NOEs), which provide information about short (\5 A ) inter-proton distances, and indirect spin–spin interactions that are characterized by scalar coupling constants (J), which provide information about torsion angles (Roberts 1993; Wijmenga and van Buuren 1998)
The usefulness of the field-induced RDCs (fiRDCs) for the structural characterization of nucleic acids and their complexes was demonstrated by number of studies (Al-Hashimi 2013; Al-Hashimi et al 2001b; Zhang and Al-Hashimi 2008), the contributions from fiRDCs to apparent J couplings are among the current most overlooked sources of artifacts in the structure determination of nucleic acids
With recent advances in NMR instrumentation as well as in the automation of the nucleic acid structure determination process, NMR spectroscopy is becoming accessible to a growing community of non-expert users employing pre-programmed ‘‘black-box’’ routines for the interpretation of acquired primary NMR data
Summary
The major sources of structural information from NMR measurements of biomolecules in isotropic solution are nuclear Overhauser enhancements (NOEs), which provide information about short (\5 A ) inter-proton distances, and indirect spin–spin interactions that are characterized by scalar coupling constants (J), which provide information about torsion angles (Roberts 1993; Wijmenga and van Buuren 1998). In addition to these two sources, direct spin– spin interactions (D), known as (residual) dipolar couplings (RDCs), reveal the relative orientations of inter-nuclear vectors with respect to the direction of the external magnetic field. The structure determination of nucleic acids, axially symmetric and elongated NA constructs, strongly depends on the use of direct and indirect spin–spin interactions due to the inherently low proton density and the absence of longrange contacts (Zhou et al 1999)
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