Magnetic Alignment of Duplex and Quadruplex DNAs

Kung, Hsiang Chuan; Wang, Ke Yu; Goljer, Igor; Bolton, Philip H.

doi:10.1006/jmrb.1995.9987

Cited by 108 publications

(78 citation statements)

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“…RNA molecules can also be aligned spontaneously (magnetic field-induced alignment) owing to their large magnetic susceptibility (χ) tensor arising from constructive summation of the individual nucleobase χ-tensors [66][67][68] . The degree of alignment scales quadratically with the magnetic field strength for typical RNA samples (~40 nt)-at 900 MHz, the degree of alignment is ~3-to 6-fold smaller than the optimum level obtained by using ordering media.…”

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confidence: 99%

Characterizing the relative orientation and dynamics of RNA A-form helices using NMR residual dipolar couplings

et al. 2007

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We present a protocol for determining the relative orientation and dynamics of A-form helices in 13 C/ 15 N isotopically enriched RNA samples using NMR residual dipolar couplings (RDCs). Non-terminal Watson-Crick base pairs in helical stems are experimentally identified using NOE and trans-hydrogen bond connectivity and modeled using the idealized A-form helix geometry. RDCs measured in the partially aligned RNA are used to compute order tensors describing average alignment of each helix relative to the applied magnetic field. The order tensors are translated into Euler angles defining the average relative orientation of helices and order parameters describing the amplitude and asymmetry of interhelix motions. The protocol does not require complete resonance assignments and therefore can be implemented rapidly to RNAs much larger than those for which complete high-resolution NMR structure determination is feasible. The protocol is particularly valuable for exploring adaptive changes in RNA conformation that occur in response to biologically relevant signals. Following resonance assignments, the procedure is expected to take no more than 2 weeks of acquisition and data analysis time.

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confidence: 99%

Characterizing the relative orientation and dynamics of RNA A-form helices using NMR residual dipolar couplings

et al. 2007

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“…bax@nih.gov the introduction of isotopic enrichment procedures for RNA and DNA (Batey et al, 1992;Nikonowicz et al, 1992;Ono et al, 1994;Farmer et al, 1995;Zimmer and Crothers, 1995;Masse et al, 1998) and methods for weakly aligning nucleic acids relative to the magnetic field (Kung et al, 1995;Tjandra and Bax, 1997;Clore et al, 1998;Hansen et al, 1998;Ruckert and Otting, 2000;Sass et al, 2000;Tycko et al, 2000;Chou et al, 2001;Ishii et al, 2001;Meier et al, 2002;Ulmer et al, 2003), residual dipolar coupling (RDC) restraints are now also available. RDCs are particularly useful in nucleic acids, where the number of NOE restraints is typically relatively low, especially those involving long-range contacts.…”

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confidence: 99%

Resolution-optimized NMR measurement of 1DCH, 1DCC and 2DCH residual dipolar couplings in nucleic acid bases

et al. 2004

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New methods are described for accurate measurement of multiple residual dipolar couplings in nucleic acid bases. The methods use TROSY-type pulse sequences for optimizing resolution and sensitivity, and rely on the E.COSY principle to measure the relatively small two-bond 2 D CH couplings at high precision. Measurements are demonstrated for a 24-nt stem-loop RNA sequence, uniformly enriched in 13 C, and aligned in Pf1. The recently described pseudo-3D method is used to provide homonuclear 1 H-1 H decoupling, which minimizes cross-correlation effects and optimizes resolution. Up to seven 1 H-13 C and 13 C-13 C couplings are measured for pyrimidines (U and C), including 1 ). Only three dipolar couplings are linearly independent in planar structures such as nucleic acid bases, permitting cross validation of the data and evaluation of their accuracies. For the vast majority of dipolar couplings, the error is found to be less than ±3% of their possible range, indicating that the measurement accuracy is not limiting when using these couplings as restraints in structure calculations. Reported isotropic values of the one-and two-bond J couplings cluster very tightly for each type of nucleotide.

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“…Nucleic acids and paramagnetic proteins were primary biomolecular targets for these early investigations. [61][62][63][64][65] In nucleic acids, the diamagnetic susceptibility is dominated by the aromatic groups of base residues, wherein circulation of p-orbital electrons in response to the magnetic field results in an induced dipole moment that can reinteract with the magnetic field, and consequently cause an anisotropic preference in molecular orientation ( Figure 2B). The degree of alignment and hence magnitude of RDCs depends on the diamagnetic susceptibly anisotropy (Dv) and, importantly, on the square of the magnetic field strength (B 2 0 ).…”

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confidence: 99%

“…61 Nearly a decade later, Bolton and coworkers demonstrated measurements of heteronuclear CÀ ÀH field-induced RDCs in duplex and quadruplex DNAs. 62 Two years later, Bax, Tjandra, and coworkers 64 demonstrated the utility of measuring field RDCs…”

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Review NMR studies of RNA dynamics and structural plasticity using NMR residual dipolar couplings

et al. 2007

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An increasing number of RNAs are being discovered that perform their functions by undergoing large changes in conformation in response to a variety of cellular signals, including recognition of proteins and small molecular targets, changes in temperature, and RNA synthesis itself. The measurement of NMR residual dipolar couplings (RDCs) in partially aligned systems is providing new insights into the structural plasticity of RNA through combined characterization of large‐amplitude collective helix motions and local flexibility in noncanonical regions over a wide window of biologically relevant timescales (<milliseconds). Here, we review RDC methodology for studying RNA structural dynamics and survey what has been learnt thus far from application of these methods. Future methodological challenges are also identified. © 2007 Wiley Periodicals, Inc. Biopolymers 86: 384–402, 2007.This article was originally published online as an accepted preprint. The “Published Online” date corresponds to the preprint version. You can request a copy of the preprint by emailing the Biopolymers editorial office at biopolymers@wiley.com

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Magnetic Alignment of Duplex and Quadruplex DNAs

Cited by 108 publications

References 0 publications

Characterizing the relative orientation and dynamics of RNA A-form helices using NMR residual dipolar couplings

Characterizing the relative orientation and dynamics of RNA A-form helices using NMR residual dipolar couplings

Resolution-optimized NMR measurement of 1DCH, 1DCC and 2DCH residual dipolar couplings in nucleic acid bases

Review NMR studies of RNA dynamics and structural plasticity using NMR residual dipolar couplings

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