Sensitivity improvement in proton-detected two-dimensional heteronuclear correlation NMR spectroscopy

Palmer, Arthur G.; Cavanagh, John; Wright, Peter E.; Rance, Mark

doi:10.1016/0022-2364(91)90036-s

Cited by 710 publications

(754 citation statements)

References 19 publications

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“…Remarkably, all resonances change their chemical shift either in the 15 is a well-known effect, 30,33 which has for example been observed in 31 P-NMR studies of ATP derivatives. 11 This effect can be attributed to the fast on-and off-rates of first-shell ligandexchange of Mg 2+ , which is in the order of the NMR time scale.…”

mentioning

confidence: 81%

“…at A20 and the flanking GU wobble pairs, the 5'-terminus, the tetraloop and the two helical regions. 30 In order to identify direct N7 coordination of Mg 2+ at these sites, we performed a series of 2 J-[ 1 H, 15 N]-HSQC experiments 31,32 that were optimized for the 11.4 Hz coupling between H8 and N7 of purine bases. Thereby we used two D6-27 constructs in which either all adenosine or all guanosine nucleotides were 13 C, 15 N isotope labelled.…”

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confidence: 99%

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Metal ion-N7 coordination in a ribozyme branch domain by NMR

Erat¹,

Kovacs²,

Sigel³

2010

Journal of Inorganic Biochemistry

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The N7 of purine nucleotides presents one of the most dominant metal ion binding sites in nucleic acids. However, the interactions between kinetically labile metal ions like Mg2+ and these nitrogen atoms are inherently difficult to observe in large RNAs. Rather than using the insensitive direct N-15 detection, here we have used (2)J-H-1,N-15]-HSQC (Heteronuclear Single Quantum Coherence) NMR experiments as a fast and efficient method to specifically observe and characterize such interactions within larger RNA constructs. Using the 27 nucleotides long branch domain of the yeast-mitochondrial group II intron ribozyme Sc.ai5 gamma as an example, we show that direct N7 coordination of a Mg2+ ion takes place in a tetraloop nucleotide. A second Mg2+ ion, located in the major groove at the catalytic branch site, coordinates mainly in an outer-sphere fashion to the highly conserved flanking GU wobble pairs but not to N7 of the sandwiched branch adenosine. (C)

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confidence: 81%

mentioning

confidence: 99%

Metal ion-N7 coordination in a ribozyme branch domain by NMR

Erat¹,

Kovacs²,

Sigel³

2010

Journal of Inorganic Biochemistry

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“…Sensitivity-enhanced heteronuclear single quantum coherence spectroscopy (HSQC) spectra were obtained (Kay et al, 1992;Palmer et al, 1991). Transients were acquired with a 1-sec relaxation delay, 8 scans per increment, a 1 H spectral width of 7,200 Hz (acquisition time of 142 ms) and a 13 C spectral width of 15,000 Hz with a maximum evolution time of 133 ms.…”

Section: Indirect Detection Of 13 C Metabolites With Two-dimensional mentioning

confidence: 99%

Pyruvate Improves Recovery after PARP-1-Associated Energy Failure Induced by Oxidative Stress in Neonatal Rat Cerebrocortical Slices

Zhang

Yang

Ying

et al. 2006

J Cereb Blood Flow Metab

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Previous neuron and glial cell culture studies of excessive poly (ADP-ribose) polymerase (PARP-1) activation found NAD + depletion, glycolytic arrest, and cell death that could be avoided by exogenous tricarboxylic acid cycle (TCA) metabolites, especially pyruvate (pyr). Pyruvate neuroprotection has been attributed to cytosolic NAD + replenishment, TCA metabolism, and antioxidant activity. We investigated the first two mechanisms in respiring cerebrocortical slices after a 1-h H 2 O 2 exposure to activate PARP-1. H 2 O 2 was followed by a 4-h recovery with oxy-artificial cerebrospinal fluid superfusion having either: (1) no glucose (glc) or pyruvate; (2) 10 mmol/L glc only; (3) 10 mmol/L pyruvate only; (4) both 10 mmol/L glc and 10 mmol/L pyruvate. Poly-ADPribosylation was quantified from Western blots and immunohistochemistry. Perchloric acid extracts were quantified with 14.1 T 31 P nuclear magnetic resonance spectroscopy. Just after H 2 O 2 exposure, ATP and NAD + decreased by E50%, PCr decreased by 75%, and the ADP/ATP ratio approximately doubled. ATP and NAD + changes, but not PCr changes, were nearly eliminated if PARP inhibitors accompanied the H 2 O 2 . Recovery with both pyruvate and glc was better than with glc alone, having higher ATP (0.161 versus 0.075, P < 0.01) and PCr levels (0.144 versus 0.078, P < 0.01), and higher viable cell counts in TUNEL and Fluoro-Jade B staining. Two-dimensional [ 1 H-13 C] HSQC spectra showed metabolism during recovery of 13 C glc or pyr. Pyruvate metabolism was primarily via pyruvate dehydrogenase, with some via pyruvate carboxylation. Pyruvate superfusion of PARPinjured brain slices helps replenish NAD + while providing metabolic fuel. Although this augments recovery, a strong antioxidant role for pyruvate has not been ruled out.

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“…Since the inception of NMR spectroscopy, spectroscopists have sought to improve the sensitivity of this intrinsically insensitive technique, for example through pulse sequence design [1,2,3,4,5], the development of cryogenic probes [6], and the application of dynamic nuclear polarisation [7,8,9]. Of course, as technology has developed, so has the desire to study increasingly large, complex or dilute samples -as has the desire to make efficient use of valuable spectrometer time.…”

Section: Introductionmentioning

confidence: 99%

An analysis of NMR sensitivity enhancements obtained using non-uniform weighted sampling, and the application to protein NMR

Waudby

Christodoulou

2012

Journal of Magnetic Resonance

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Non-uniform weighted sampling (NUWS) is a sampling strategy, related to nonuniform sampling (NUS) in the limit of long acquisition times, in which each indirect increment of a multidimensional spectrum is sampled multiple times according to some weighting function. As the spectrum is fully sampled it can be processed in a conventional manner by the discrete Fourier transform, making the analysis of sensitivity much more straightforward than for NUS data. Previously, 2-3 fold increases in signal-to-noise ratio (SNR) have been reported using NUWS. However, as the sampling schedule acts as a window function, the observed SNR must be compared with uniformly sampled data apodized using the same weighting function. On doing this, we calculate more modest improvements of 10-20% in SNR, and these are verified experimentally for spectra of α-synuclein and YFP. Nevertheless, we prove that NUWS always improves the sensitivity compared with identically processed uniformly sampled data, and when combined with rapid recycling experiments such as the SOFAST-HMQC, NUWS methods have the potential to make a useful and practical contribution to sensitivity-limited measurements.

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Sensitivity improvement in proton-detected two-dimensional heteronuclear correlation NMR spectroscopy

Cited by 710 publications

References 19 publications

Metal ion-N7 coordination in a ribozyme branch domain by NMR

Metal ion-N7 coordination in a ribozyme branch domain by NMR

Pyruvate Improves Recovery after PARP-1-Associated Energy Failure Induced by Oxidative Stress in Neonatal Rat Cerebrocortical Slices

An analysis of NMR sensitivity enhancements obtained using non-uniform weighted sampling, and the application to protein NMR

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