Three-Dimensional Diffusion-Ordered NMR Spectroscopy: The Homonuclear COSY–DOSY Experiment

Wu, Donghui; Chen, Aidi; Johnson, Charles S.

doi:10.1006/jmra.1996.0142

Cited by 111 publications

(68 citation statements)

References 4 publications

(5 reference statements)

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Since then several 1-3D versions of diffusion NMR experiments have been developed even in combination with regular magnetization transfer experiments (COSY, NOESY, TOCSY, HMQC, etc.) to provide MW information for samples being analyzed [32,[34][35][36][37][38][39]. Different forms of diffusion NMR experiments have been applied for diverse varieties of systems including inorganic materials [37,[40][41][42], organic molecules [17,23,24,28,[43][44][45][46][47][48][49] and polymers of different kinds (inorganic and organic polymers, polysaccharides, proteins) [21,37,[50][51][52][53][54][55][56][57][58][59][60][61][62].…”

mentioning

confidence: 99%

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

Ambrus¹,

Yang²

2007

Analytical Biochemistry

View full text Add to dashboard Cite

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 ...

show abstract

mentioning

confidence: 99%

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

Ambrus¹,

Yang²

2007

Analytical Biochemistry

View full text Add to dashboard Cite

show abstract

“…However, it may now become necessary to distinguish individual ligands from each other as well as the protein background. A number of diffusion-edited 2D NMR experiments have been reported that can enhance the selectivity of the diffusion measurements by capitalizing on evolution due to spin-spin coupling in the second dimension (75)(76)(77). However, the additional time required for the acquisition, analysis, and interpretation of diffusion-edited 2D NMR experiments is contrary to the aim of rapid throughput analysis.…”

Section: Discrimination Of Ligand Resonances Against the Protein Backmentioning

confidence: 96%

Measuring ligand‐protein binding using NMR diffusion experiments

Lucas

Larive

2004

Concepts Magnetic Resonance

105

View full text Add to dashboard Cite

ABSTRACT:Characterization of ligand-protein interactions is important because many biologically important processes are mediated by the binding of a small molecule to an enzyme or cell-surface receptor. Pulsed-field gradient nuclear magnetic resonance (PFG-NMR) spectroscopy measurements of diffusion coefficients permit noninvasive, quantitative analysis of binding over a broad range of dissociation constants and ligand:protein concentration ratios. An arsenal of specific and selective PFG-NMR methods has been developed by exploiting differential behaviors of small molecule ligands and macromolecular proteins. A discussion of several PFG-NMR methods and their relevant applications reveals the analytical value of using PFG-NMR diffusion measurements for studying ligandprotein binding.

show abstract

“…For 3D DOSY the basic experimental setup includes a BPPLED sequence followed by a standard 2D sequence. Examples of DOSY-HMQC (Heteronuclear multiple quantum coherence spectroscopy), DOSY-COSY (COrrelation SpectroscopY), DOSY-NOESY (Nuclear Overhauser Effect SpectroscopY) and DOSY-TOCSY (Total Correlation SpectroscopY) have been described [29][30][31][32][33][34][35][36][37][38][39][40]. With 3D techniques, an experimenter further resolves species that are somewhat overlapped in the diffusion dimension by following the different spin systems.…”

Section: Uses In Counterfeit Medicationmentioning

confidence: 99%

NMR Chromatography: Molecular Diffusion in the Presence of Pulsed Field Gradients in Analytical Chemistry Applications

Heisel¹,

Goto²,

Krishnan³

2012

AJAC

View full text Add to dashboard Cite

Nuclear magnetic resonance (NMR) spectroscopy is an excellent analytical tool for precise structural characterization of organic and bio-molecules. Though NMR is often used to characterize a single compound in solution, emerging experimental methods using pulsed-field-gradients (PFGs) allow structural dynamic characterization of several compounds, simultaneously in the same solution. NMR as a chromatography tool is often an overlooked application by analytical chemists. Therefore, in this article we introduce the concept of NMR based diffusion measurements, basic operational methods and novel applications. We expect this article to increase the overall use and appreciation of NMR-based diffusion measurements in general and in particular, in analytical chemistry applications.

show abstract

Three-Dimensional Diffusion-Ordered NMR Spectroscopy: The Homonuclear COSY–DOSY Experiment

Cited by 111 publications

References 4 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

Measuring ligand‐protein binding using NMR diffusion experiments

NMR Chromatography: Molecular Diffusion in the Presence of Pulsed Field Gradients in Analytical Chemistry Applications

Contact Info

Product

Resources

About