Dependence of 13C NMR Chemical Shifts on Conformations of RNA Nucleosides and Nucleotides

Ebrahimi, Mohsen; Rossi, Paolo; Rogers, Christopher; Harbison, Gerard S.

doi:10.1006/jmre.2001.2314

Cited by 76 publications

(68 citation statements)

References 53 publications

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“…Base carbon chemical shifts (C2/C6/C8) are sensitive to changes in the glycosidic angle χ ( anti versus syn ) as well as stacking (Dejaegere et al, 1998; Xu et al, 2000; Ebrahimi et al, 2001; Fares et al, 2007; Ohlenschlager et al, 2008). The adenine C2 is sensitive to protonation of N1.…”

Section: General Protocol For Characterizing Rna Ess Using Low-to-mentioning

confidence: 99%

“…The adenine C2 is sensitive to protonation of N1. Sugar C1′ chemical shifts are sensitive to both sugar pucker and the glycosidic bond angle (Dejaegere & Case, 1998; Xu & Au-Yeung, 2000; Ebrahimi et al, 2001; Fares et al, 2007; Ohlenschlager et al, 2008). The 15 N chemical shifts are sensitive to the properties of H-bonding (see below) (Goswami et al, 1993) and also directly report on changes in 15 N protonation states (Büchner et al, 1978).…”

Section: General Protocol For Characterizing Rna Ess Using Low-to-mentioning

confidence: 99%

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Characterizing RNA Excited States Using NMR Relaxation Dispersion

Xue

Kellogg

Kimsey

et al. 2015

Methods in Enzymology

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Changes in RNA secondary structure play fundamental roles in the cellular functions of a growing number of non-coding RNAs. This chapter describes NMR-based approaches for characterizing microsecond-to-millisecond changes in RNA secondary structure that are directed toward short-lived and low-populated species often referred to as “excited states”. Compared to larger-scale changes in RNA secondary structure, transitions towards excited states do not require assistance from chaperones, are often orders of magnitude faster, and are localized to a small number of nearby base pairs in and around non-canonical motifs. Here we describe a procedure for characterizing RNA excited states using off-resonance R1ρ NMR relaxation dispersion utilizing low-to-high spin-lock fields (25–3000 Hz). R1ρ NMR relaxation dispersion experiments are used to measure carbon and nitrogen chemical shifts in base and sugar moieties of the excited state. The chemical shift data is then interpreted with the aid of secondary structure prediction to infer potential excited states that feature alternative secondary structures. Candidate structures are then tested by using mutations, single-atom substitutions, or by changing physiochemical conditions, such as pH and temperature, to either stabilize or destabilize the candidate excited state. The resulting chemical shifts of the mutants or under different physiochemical conditions are then compared to those of the ground and excited state. Application is illustrated with a focus on the transactivation response element (TAR) from the human immune deficiency virus type 1 (HIV-1), which exists in dynamic equilibrium with at least two distinct excited states.

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Section: General Protocol For Characterizing Rna Ess Using Low-to-mentioning

confidence: 99%

Section: General Protocol For Characterizing Rna Ess Using Low-to-mentioning

confidence: 99%

Characterizing RNA Excited States Using NMR Relaxation Dispersion

Xue

Kellogg

Kimsey

et al. 2015

Methods in Enzymology

View full text Add to dashboard Cite

show abstract

“…The goal of this analysis is to quantitatively assign the position of any set of chemical shifts with respect to the experimentally determined can1 and can2 clusters (10). Two basic techniques can be used: (1) midpoint of cluster means and (2) F-distribution test (28).…”

Section: Discussionmentioning

confidence: 99%

“…The methods that were just outlined here were used to test the accuracy of the calculated chemical shifts with respect to experiment (10). When appropriate, cross-testing was performed in order to rule out the possibility that a structure may belong to more than one group.…”

Section: Discussionmentioning

confidence: 99%

Calculation of 13C Chemical Shifts in RNA Nucleosides: Structure-13C Chemical Shift Relationships

Rossi

Harbison

2001

Journal of Magnetic Resonance

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Isotropic 13 C chemical shifts of the ribose sugar in model RNA nucleosides are calculated using SCF and DFT-GIAO ab initio methods for different combinations of ribose sugar pucker, exocyclic torsion angle, and glycosidic torsion angle. Idealized conformations were obtained using structures that were fully optimized by ab initio DFT methods starting with averaged parameters from a collection of crystallographic data. Solid-state coordinates of accurate crystal or neutron diffraction structures were also examined directly without optimization. The resulting 13 C chemical shifts for the two sets of calculations are then compared. The GIAO-DFT method overestimates the shifts by an average of 5 ppm while the GIAOSCF underestimates the shifts by the same amount. However, in the majority of cases the errors appear to be systematic, as the slope of a plot of calculated vs experimental shifts is very close to unity, with minimal scatter. The values of the 13 C NMR shifts of the ribose sugar are therefore sufficiently precise to allow for statistical separation of sugar puckering modes and exocyclic torsion angle conformers, based on the canonical equation model formulated in a previous paper.

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“…Nuclear magnetic resonance (NMR) spectroscopy has played an important role in understanding the structure of uracil and its derivatives [1][2][3][4][5][6]. In particular, the advent of high field magnets and good software have made it possible to probe the electronic structure by measuring the principal components of the chemical shift tensors and electric field gradient (EFG) tensors [7][8][9][10][11][12][13][14][15]. Similarly, nuclear quadrupolar resonance (NQR) spectroscopy has been used as a complementary method to study the EFG tensors [16,17].…”

Section: Introductionmentioning

confidence: 99%