Caution concerning the use of sodium 2,2‐dimethyl‐2‐silapentane‐5‐sulfonate (DSS) as a reference for proton NMR chemical shift studies

Lam, Yiu‐Fai; Kotowycz, George

doi:10.1016/0014-5793(77)80301-3

Cited by 21 publications

(15 citation statements)

References 11 publications

(2 reference statements)

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“…We have calculated stability constants from their published results [27], and find that the value obtained, K = 0.8 k 0.4 M-' (27 "C), agrees well with our value.…”

Section: Resultssupporting

confidence: 83%

“…Their results [27] also indicate that at [ATP] > 0.3 M significant hydrophobic interaction occurs between ATP (either monomer or self-stacked) and tert-butyl alcohol, the resonance of the latter also being shifted upfield by z 0.06 ppm at [ATP] = 0.56 M. The stability constant for this hydrophobic interaction must be very small, K < 0.3 M-I. In the light of our recent results on hydrophobic interactions between the trimethylsilyl moiety and 2,2'-bipyridyl or 1 ,lo-phenanthroline [7], and our studies on stacking interactions between the bases of nucleotides and aromatic coinpounds [17-191, this observation [27] seems very interesting as it suggests that hydrophobic interactions between purine moieties of nucleotides and aliphatic groups, e.g.…”

Section: Resultsmentioning

confidence: 99%

“…Two independent reports which mention the concentration dependence of the NMR of ATP have appeared since this paper was written [29,30]. One assumes that only dimers are formed 1291 and thus deduces KD = 0.45 M-' ; the other, the definitive paper of the preliminary communication [27] mentioned above, assumes without evidence that the upfield shift is the same in dimers, trimers, tetramers, etc., and deduces that K = 0.9 M -' for the monomer/dimer and dimer/trimer equilibria [30]. Both reports agree in general with ours, although, because of the different models used, rather lower stability constants are obtained.…”

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confidence: 99%

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A Proton Nuclear-Magnetic-Resonance Study of Self-Stacking in Purine and Pyrimidine Nucleosides and Nucleotides

Mitchell

Sigel

1978

Eur J Biochem

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The concentration dependence of the chemical shifts of the protons H-2, H-8 and H-I' of A T P and of Mg(ATP)'-, of all non-labile protons of adenosine, of H-5, H-6 and H-I' of UTP, and of H-5, H-6, H-l', and H-2' of uridine have been measured. The results for the purine derivatives are consistent with the isodesmic model of indefinite non-cooperative stacking; for adenosine K = 15For the pyrimidines, uridine and UTP, stacking is much weaker and the stability constant could only be estimated; for uridine K 2 0.5 M-l, and for UTP K z 0.3 M-'.Self-association of adenine [l] and purine [l], and of several purine nucleosides [2], including adenosine and inosine, has been observed by vapour pressure osmometry. It was concluded that indefinite noncooperative stacking occurred, and stability constants were calculated [2]; for adenosine K = 4.5 M-'. For pyrimidines, e.g. uridine, the interaction is very much weaker, and the calculated [l] stability constant is only 0.6 M-l. The NMR spectra of purine nucleosides are shifted in concentrated (0.1 M) solution, and this was attributed to the effect of the ring current in the stacked complexes ; however no significant shift was observed with the pyrimidine nucleosides uridine and thymidine [3] owing to the much smaller ring current in the pyrimidines [4]. In this early work external references were used; Bovey [5] repeated the experiment on purine using internal sodium trimethylsilylpropane sulphonate as reference, and concluded that, as no significant upfield shift of H-2 or H-6 is observed and as H-8 actually moves downfield, no stacking occurs. However sodium trimethylsilylpropane sulphonate is an unreliable reference in the presence of aromatic compounds [6,7], and thus, despite the use of an external reference, the earlier work is probably more reliable.An upfield shift due to stacking has also been observed [8-101 in NMR studies of adenosine 2: 3' and 5'monophosphates : the relaxation times of the protons H-2 and H-8, and the variation of the upfield chemical shift of the resonances H-1 ', H-2, and H-8 were said [9] to indicate 'head to tail' stacking, with the five-memAbbreviation. NMR, nuclear magnetic resonance. bered and six-membered rings alternating in the stack. These 'H NMR studies [8-101, a 'H NMR study [ll], ultracentrifuge studies 112,131 and a kinetic study [14] show that adenosine 5'-monophosphate [8 -121 and other adenine derivatives [13,14] do not merely dimerize, but form 'indefinite' stacks. Although difference ultraviolet spectroscopy [15] and difference circular dichroism [15,16] have been used to study the self-association of ATP, and the effect of pH, temperature, and of magnesium ions on this association, shifts in the 'H NMR spectrum of ATP, which would confirm that this association is due to stacking, have not been reported.In the course of a series of studies[l7-191 on the stacking in binary systems such as bipyridyl/ATP4-, phenanthroline/ATP4-, and bipyridyl/UTP4-, and in the ternary systems such as Zn2 /bipyridyl/ATP4-, Mg2 ' /phenanthrol...

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“…We have calculated stability constants from their published results [27], and find that the value obtained, K = 0.8 k 0.4 M-' (27 "C), agrees well with our value.…”

Section: Resultssupporting

confidence: 83%

Section: Resultsmentioning

confidence: 99%

mentioning

confidence: 99%

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A Proton Nuclear-Magnetic-Resonance Study of Self-Stacking in Purine and Pyrimidine Nucleosides and Nucleotides

Mitchell

Sigel

1978

Eur J Biochem

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“…Water-soluble 1 H NMR internal standards, DSS and TSP have been reported to interact with proteins and other macromolecules causing their resonances to broaden and shift (Bell et al 1989;Kriat et al 1992;Lam and Kotowycz 1977;Live and Chan 1973;Nowick et al 2003;Shimizu et al 1994). In addition, the chemical shift of TSP has been shown to vary with pH (De Marco 1977), temperature (Farrant et al 1994;Wishart et al 1995) and protein concentration (Shimizu et al 1994).…”

Section: Resultsmentioning

confidence: 99%

4,4-Dimethyl-4-silapentane-1-ammonium trifluoroacetate (DSA), a promising universal internal standard for NMR-based metabolic profiling studies of biofluids, including blood plasma and serum

et al. 2008

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Nuclear magnetic resonance (NMR)-based metabolic profiling of biofluids and tissues are of key interest to enhance biomarker discovery for disease, drug efficacy and toxicity studies. Urine and blood plasma/ serum are the biofluids of most interest as they are the most accessible in both clinical and preclinical studies. However, proteinaceous fluids, such as blood serum or plasma, represent the greatest technical challenge since the chemical shift (d) and line-width (m 1/2 ) of internal standards currently used for aqueous NMR samples are greatly affected by protein binding. We have therefore investigated the suitability of 4,4-dimethyl-4-silapentane-1-ammonium trifluoroacetate (DSA) as a universal internal standard for biofluids. Proton ( 1 H) NMR spectroscopy was used to determine the effect of serum pH (3, 7.4 and 10) and DSA concentration on the overall lineshape and position of the trimethylsilyl resonance of DSA. The results were compared to that of 3-(trimethylsilyl)propionic acid sodium salt (TSP). Both the chemical shift and line-width of the DSA peak were not significantly affected by pH or DSA concentration, whereas these parameters for TSP showed large variations due to protein binding. Furthermore, the peak area of DSA correlated linearly with its concentration under all pH conditions, whilst no linear correlation was observed with TSP. Overall, in contrast to TSP, these results support the use of DSA as an accurate universal internal chemical shift reference and concentration/normalisation standard for biofluids. In the case of proteinaceous biofluids such as serum, where no current standard is available, this offers a considerable saving in both operator and spectrometer time.

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“…When the common internal reference con~pound DSS was used (sodium-2,2-dimethyl-2-silopentane-5-sulphonate), it was found that this reference signal shifted with the ATP concentration. DSS is therefore not a satisfactory reference compound for these studies (24).…”

Section: Proton Magnetic Resonance Experimentsmentioning

confidence: 99%

Nuclear magnetic resonance studies on the self-association of adenosine 5′-triphosphate in aqueous solutions

Lam¹,

Kotowycz²

1977

Can. J. Chem.

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YIU-FAI LAM and GEORGE KOTOWYCZ. Can. J. Chem. 55,3620 (1977). The self-association of adenosine 5'-triphosphate (ATP) in aqueous, basic solutions has been studied. The results indicate that the monomer-dimer-trimer equilibrium model for base association fits the data well, but so does a model which includes higher order species. This indicates that the ATP n~olecules in solution can undergo indefinite linear self-association. The average value of the association constant based on the 'H and 31P chemical shift measurements with indefinite linear self-association and each step has the same equilibrium constant. Heyn and Bretz (2) could not assign a unique geometry for the ATP molecules in the stack but feel that head-to-tail association of the adenine bases is most likely. Further circular dichroism measurements (3) were interpreted in terms of a monomer-dimer model. At a p H of 2.8 and 20°C, a dimerization constant of 88 M-' was obtained. In the complex, the charged phosphate of one ATP molecule interacts electrostatically with the charged adenine ring of the second ATP molecule. In this model, the two adenine rings are stacked head-to-tail and the ATP molecule is in the anti conforn~ation (3). At basic pH's, the model of Heyn and Bretz (2) was applied (3) and an association constant of 51 M-I was obtained (2O0C, p H 8.7) with no MgCI, present. Stacking interactions have also been studied in the presence of 0.154 M NaCl (1) and a monomer-dimer-trimer association model at acidic pH's describes the data best of all.Nuclear magnetic resonance (nmr) experiments also offer valuable information concerning the self-association of ATP. Based on the ring proton chemical shift studies carried out at a Can. J. Chem. Downloaded from www.nrcresearchpress.com by 54.213.204.173 on 05/09/18For personal use only.

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Caution concerning the use of sodium 2,2‐dimethyl‐2‐silapentane‐5‐sulfonate (DSS) as a reference for proton NMR chemical shift studies

Cited by 21 publications

References 11 publications

A Proton Nuclear-Magnetic-Resonance Study of Self-Stacking in Purine and Pyrimidine Nucleosides and Nucleotides

A Proton Nuclear-Magnetic-Resonance Study of Self-Stacking in Purine and Pyrimidine Nucleosides and Nucleotides

4,4-Dimethyl-4-silapentane-1-ammonium trifluoroacetate (DSA), a promising universal internal standard for NMR-based metabolic profiling studies of biofluids, including blood plasma and serum

Nuclear magnetic resonance studies on the self-association of adenosine 5′-triphosphate in aqueous solutions

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