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Characterizing slow chemical exchange in nucleic acids by carbon CEST and low spin-lock field R(1?) NMR spectroscopy.

ABSTRACT: Quantitative characterization of dynamic exchange between various conformational states provides essential insights into the molecular basis of many regulatory RNA functions. Here, we present an application of nucleic-acid-optimized carbon chemical exchange saturation transfer (CEST) and low spin-lock field R(1?) relaxation dispersion (RD) NMR experiments in characterizing slow chemical exchange in nucleic acids that is otherwise difficult if not impossible to be quantified by the ZZ-exchange NMR experiment. We demonstrated the application on a 47-nucleotide fluoride riboswitch in the ligand-free state, for which CEST and R(1?) RD profiles of base and sugar carbons revealed slow exchange dynamics involving a sparsely populated (p ~ 10%) and shortly lived (? ~ 10 ms) NMR "invisible" state. The utility of CEST and low spin-lock field R(1?) RD experiments in studying slow exchange was further validated in characterizing an exchange as slow as ~60 s(-1).

SUBMITTER: Zhao B

PROVIDER: S-EPMC4755283 | biostudies-literature | 2014 Jan

REPOSITORIES: biostudies-literature

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Characterizing slow chemical exchange in nucleic acids by carbon CEST and low spin-lock field R(1ρ) NMR spectroscopy.

Zhao Bo B Hansen Alexandar L AL Zhang Qi Q

Journal of the American Chemical Society 20131218 1

Quantitative characterization of dynamic exchange between various conformational states provides essential insights into the molecular basis of many regulatory RNA functions. Here, we present an application of nucleic-acid-optimized carbon chemical exchange saturation transfer (CEST) and low spin-lock field R(1ρ) relaxation dispersion (RD) NMR experiments in characterizing slow chemical exchange in nucleic acids that is otherwise difficult if not impossible to be quantified by the ZZ-exchange NM ...[more]

PMID: 24299272

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Project description:BackgroundR1ρ (or spin-lock) imaging is prone to artifacts arising from field inhomogeneities that may impact the R1ρ quantification. Previous research has proposed two types of method to manage the artifacts in continuous-wave constant amplitude spin-lock, one is based on the composite block pulses to compensate for the field imperfections, another category uses adiabatic pulses in the R1ρ pre-pulse to excite and reverse the magnetization (named adiabatic prepared approach). Although both methods have proved their efficiency in alleviating artifacts, we observed that the adiabatic pulse approach could produce much lower R1ρ dispersion in human knee cartilage than the block pulse method (characterized by the R1ρ difference ∆R1ρ =11.4 Hz (from spin-lock field 50 to 500 Hz) for the block pulse method vs. ∆R1ρ =4.5 Hz for the adiabatic pulse approach). Prompted by this observation, the purpose of this study was to investigate the underlying factors that may affect the R1ρ dispersion through numerical simulations based on the two-pool exchanging Bloch-McConnell equations.MethodsThe effects of free water pool size Pa (from 0.80 to 0.95), chemical exchange rate kb (from the bound to free water pool, ranged from 500 to 3,000 Hz), adiabatic pulse duration Tp (from 5.0 to 25 ms), and the chemical shift of the bound pool ppmb (from 1.0 to 5.0 ppm) were examined on the degree of the R1ρ dispersion for the two R1ρ imaging methods.ResultsIn general, the greater the ppmb, kb, Tp, and the smaller Pa, the more significant difference in R1ρ dispersion between the block and adiabatic approaches, with the dispersion curve of the adiabatic method becoming flatter.ConclusionsThe adiabatic prepared approach may compromise the R1ρ dispersion, the effect is determined by the combination of the tissue and radiofrequency (RF) pulse properties. It is suggested that care should be taken when using the adiabatically prepared approach to study R1ρ dispersion.

Dataset Information

Characterizing slow chemical exchange in nucleic acids by carbon CEST and low spin-lock field R(1?) NMR spectroscopy.

Publications

Characterizing slow chemical exchange in nucleic acids by carbon CEST and low spin-lock field R(1ρ) NMR spectroscopy.

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