NMR diffusion measurements to characterise membrane transport and solute binding

Waldeck, A. Reginald; Kuchel, Philip W.; Lennon, Alison; Chapman, Bogdan E.

doi:10.1016/s0079-6565(96)01034-5

Cited by 251 publications

(240 citation statements)

References 75 publications

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“…The method uses a special pulse-sequence to obtain a series of NMR spectra using field-gradients and is capable of determining diffusion coefficients of molecules without any concentrationgradient [19,20]. The intensity of the detected proton signal belonging to a particular molecular entity at a certain gradient level is dependent mostly on the rate of diffusion of that molecule as the gradient eliminates more signal intensity of molecules in faster motion.…”

Section: Nih Public Accessmentioning

confidence: 99%

“…For automatic 2D-processing, the standard 2D DOSY processing protocol was applied in XWINNMR software with logarithmic scaling in the F1 (diffusion coefficient) dimension. For manual curve-fitting, the intensities of selected peaks in the 1D proton spectra measured at different gradient strengths were fitted using the equation I=I 0 exp(−Dγ 2 g 2 δ 2 (Δ−δ/3)) [→sqrt(−ln(I/Io))=sqrt(D*)g] [19] to obtain the apparent diffusion coefficient D*. In this theoretical equation the following physical quantities are symbolized: I, the actual (measured) peak intensity; I 0 , peak intensity at zero gradient strength; D, diffusion coefficient; γ, gyromagnetic ratio (of proton); g, gradient strength; δ, length of gradient; and Δ, diffusion time.…”

Section: Nmr Experimentsmentioning

confidence: 99%

“…Diffusion ordered NMR spectroscopy is a method for the identification of different molecular weight (macro)molecules present in solution at millimolar concentrations, while the successful acquisition of the signal requires a sufficient concentration of each component [16][17][18][19][20][21][22][23][24][25][26][27][28][29][30][31][32][33]. The method uses a special pulse-sequence to obtain a series of NMR spectra using field-gradients and is capable of determining diffusion coefficients of molecules without any concentrationgradient [19,20].…”

mentioning

confidence: 99%

“…The number of identifiable components in solution is only limited by resolution (if species exchange slowly on NMR time scale) [25,26]. Comparing the diffusion coefficients of target molecules to that of reference(s), the molecular weight can be calculated [19]. The MWs of the applied references should be extended to both sides of the MW range of the molecule being analyzed, taking the most probable oligomerization orders expected into consideration.…”

mentioning

confidence: 99%

“…The MWs of the applied references should be extended to both sides of the MW range of the molecule being analyzed, taking the most probable oligomerization orders expected into consideration. It is preferable, but not a requirement, that the chemical nature of the references and the molecule in question is similar; what is more important is the shape, which determines how molecules behave during diffusion [19].…”

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Diffusion-ordered nuclear magnetic resonance spectroscopy for analysis of DNA secondary structural elements

Ambrus¹,

Yang²

2007

Analytical Biochemistry

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Structure determination of secondary DNA structural elements, such as G-quadruplexes, gains an increasing importance as fundamental physiological roles are being associated with the formation of such structures in vivo. A truncated native DNA sequence generally requires further optimization to obtain a candidate with desired NMR properties for structural analysis in solution. The optimum sequence is expected to form one dominant, stable molecular entity in solution with well-resolved NMR peaks. However, DNA sequences are prone to form structures composed of one, two, three or four strands depending on sequence and solution conditions. The thorough characterization of the molecularity (stoichiometry and molecular weight) and appropriate solution conditions for sequences with different modifications traditionally applies analytical techniques that generally do not represent the solution conditions for NMR structure determination. Here we present the application of diffusion ordered NMR spectroscopy as a useful analytical tool for the optimization and analysis of DNA secondary structural elements, specifically, the DNA G-quadruplex structures, including those formed in the human telomeric sequence and in the promoter regions of bcl-2 and c-myc genes. KeywordsDNA; NMR; DOSY; quadruplex; bcl-2; human telomere; c-myc Structural analysis of unusual DNA motifs with particular emphasis on G-quadruplexes and imotifs has a central role in the identification and characterization of molecular targets related to these structures [1][2][3][4][5][6][7]. Such structures are implicated in several physiologically important regulatory processes, with special emphasis on carcinogenesis [4][5][6][7][8][9][10][11][12]. Most of the structural studies on these elements have been performed by NMR spectroscopy. In most cases the related nucleotide sequence bearing the actual physiological function in vivo needs to be truncated/ elongated and/or mutated in order to obtain a successful candidate for NMR structure determination [3][4][5][6][7]13]. This NMR candidate should be a well-defined molecular entity in physiologically relevant solution conditions (ionic strength, pH, temperature) representing the same conformation as the original sequence. Appropriate modification of the sequence by mutation/truncation/elongation will force the molecule to form a single stable structure without altering crucial connectivities (conformation) of the structure.* To whom correspondence should be addressed at the Department of Pharmacology and Toxicology, College of Pharmacy, University of Arizona, 1703 E. Mabel St., P.O. Box 210207, room 101/406, Tucson, Arizona 85721, USA; Tel: +1 520 626 6749/626 5969, Fax: +1 520 626 2466, E-mail: ambrus@pharmacy.arizona.edu, yangd@pharmacy.arizona.edu.Publisher's Disclaimer: This is a PDF file of an unedited manuscript that has been accepted for publication. As a service to our customers we are providing this early version of the manuscript. The manuscript will undergo copyediting, typesetting, and review of ...

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Section: Nih Public Accessmentioning

confidence: 99%

Section: Nmr Experimentsmentioning

confidence: 99%

mentioning

confidence: 99%

mentioning

confidence: 99%

mentioning

confidence: 99%

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Diffusion-ordered nuclear magnetic resonance spectroscopy for analysis of DNA secondary structural elements

Ambrus¹,

Yang²

2007

Analytical Biochemistry

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Self-diffusion measurements of organic molecules in PDMS and water in sodium alginate membranes

Muzzalupo

Ranieri

Golemme

et al. 1999

J. Appl. Polym. Sci.

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ABSTRACT:The self-diffusion of some organic molecules in silicone rubber and of water and water-ethanol mixtures in sodium alginate membranes was investigated to obtain information on the transport behavior in these systems. The temperature dependence of self-diffusion was examined by the pulsed field gradient NMR technique. The experimental data confirm the homogeneous amorphous nature of PDMS and the affinity of silicone rubber to apolar solvents. The interrelations between solvent and polymer structures of the sodium alginate membrane varying the temperature have been obtained using differential scanning calorimetric. The results have been compared with the trend of self-diffusion coefficients, and structure modifications of the membranes have been evidenced. The overall results confirm the potentialities of the technique used in measuring transport parameter in polymeric membranes.

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Dependence of Enantioselectivity on the Distribution of a Chiral Hydrogenation Catalyst between an Aqueous and a Micellar Phase: Investigations Using Pulsed Field Gradient Spin Echo NMR Spectroscopy

et al. 2001

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The enantioselectivity obtained from rhodium complex catalyzed hydrogenations conducted in water can often be increased considerably by the addition of amphiphiles. At present the reasons for this increase in selectivity are not fully understood. The application of pulsed field gradient spin echo NMR (PGSE-NMR) spectroscopy to determine the average diffusion coefficients of the catalysts in both known and novel examples of asymmetric hydrogenation shows definitively that the increase in enantioselectivity is coupled with an aggregation of the catalyst to the micelles. This aggregation or solubilization of the catalyst in the micelles leads to the formation of a new colloidal phase in the aqueous solution. This phase has stronger hydrophobic properties, and thus the hydrogenation is more comparable to those conducted in a hydrophobic or less polar organic solvent. In the case of anionic amphiphiles, which form amphiphilic salts with the cationic catalyst, the embedment of the catalyst complex into the micelle is generally complete. The whole hydrogenation then takes place exclusively inside the micelles, leading to high enantioselectivity. If the catalyst is not completely embedded into the micelle, for example in the cases of nonionic or cationic surfactant solutions, the solubility of the substrate plays an important role. For soluble substrates the hydrogenation of the substrate occurs predominately in the aqueous phase itself, leading to very poor enantioselectivities. In these cases, only the use of a large excess of amphiphile, far above the critical micelle concentration (cmc), will lead to higher enantioselectivities due to a shift of the equilibrium towards the micellar bonded forms of catalyst and substrate. In contrast, poorly soluble substrates exhibit a high tendency to be incorporated into micelles, which leads to much higher enantioselectivities if the cmc of the surfactant is small enough. Changes in the cmc of amphiphiles caused by their aggregation with catalysts could also be estimated. The variation in selectivity observed for the catalysts containing seven-membered, flexible chelate rings is apparently due to changes in their conformation in the less polar micellar medium, and this effect is also seen in organic solvents. As expected, catalysts containing smaller chelate rings show this effect to a considerably lower extent since they are conformationally more rigid.

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NMR diffusion measurements to characterise membrane transport and solute binding

Cited by 251 publications

References 75 publications

Diffusion-ordered nuclear magnetic resonance spectroscopy for analysis of DNA secondary structural elements

Diffusion-ordered nuclear magnetic resonance spectroscopy for analysis of DNA secondary structural elements

Self-diffusion measurements of organic molecules in PDMS and water in sodium alginate membranes

Dependence of Enantioselectivity on the Distribution of a Chiral Hydrogenation Catalyst between an Aqueous and a Micellar Phase: Investigations Using Pulsed Field Gradient Spin Echo NMR Spectroscopy

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