[NMR paper] Applying Thymine Isostere 2,4-Difluoro-5-Methylbenzene as a NMR Assignment Tool and Probe of Homopyrimidine/Homopurine Tract Structural Dynamics.
Related ArticlesApplying Thymine Isostere 2,4-Difluoro-5-Methylbenzene as a NMR Assignment Tool and Probe of Homopyrimidine/Homopurine Tract Structural Dynamics.
Methods Enzymol. 2016;566:89-110
Authors: Brinson RG, Miller JT, Kahn JD, Le Grice SF, Marino JP
Abstract
Proton assignment of nuclear magnetic resonance (NMR) spectra of homopyrimidine/homopurine tract oligonucleotides becomes extremely challenging with increasing helical length due to severe cross-peak overlap. As an alternative to the more standard practice of (15)N and (13)C labeling of oligonucleotides, here, we describe a method for assignment of highly redundant DNA sequences that uses single-site substitution of the thymine isostere 2,4-difluoro-5-methylbenzene (dF). The impact of this approach in facilitating the assignment of intractable spectra and analyzing oligonucleotide structure and dynamics is demonstrated using A-tract and TATA box DNA and two polypurine tract-containing RNA:DNA hybrids derived from HIV-1 and the Saccharomyces cerevisiae long-terminal repeat-containing retrotransposon Ty3. Only resonances proximal to the site of dF substitution exhibit sizable chemical shift changes, providing spectral dispersion while still allowing chemical shift mapping of resonances from unaffected residues distal to the site of modification directly back to the unmodified sequence. It is further illustrated that dF incorporation can subtly alter the conformation and dynamics of homopyrimidine/homopurine tract oligonucleotides, and how these NMR observations can be correlated, in the cases of the TATA box DNA, with modulation in the TATA box-binding protein interaction using an orthogonal gel assay.
[NMR paper] Advantage of Applying OSC to (1)H NMR-Based Metabonomic Data of Celiac Disease.
Advantage of Applying OSC to (1)H NMR-Based Metabonomic Data of Celiac Disease.
Advantage of Applying OSC to (1)H NMR-Based Metabonomic Data of Celiac Disease.
Int J Endocrinol Metab. 2012;10(3):548-552
Authors: Rezaei-Tavirani M, Fathi F, Darvizeh F, Zali MR, Rostami Nejad M, Rostami K, Tafazzoli M, Arefi Oskouie A, Mortazavi-Tabatabaei SA
Abstract
BACKGROUND: Celiac disease (CD) is a disorder associated with body reaction to gluten. After the gluten intake, an immune reaction against the protein occurs and damages villi of small...
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07-12-2013 06:01 PM
iHADAMAC: a complementary tool for sequential resonance assignment of globular and highly disordered proteins
iHADAMAC: a complementary tool for sequential resonance assignment of globular and highly disordered proteins
Publication year: 2011
Source: Journal of Magnetic Resonance, Available online 9 November 2011</br>
Sophie*Feuerstein, Michael J.*Plevin, Dieter*Willbold, Bernhard*Brutscher</br>
An experiment, iHADAMAC, is presented that yields information on the amino-acid type of individual residues in a protein by editing theH-N correlations into 7 different 2D spectra, each corresponding to a different class of amino-acid types. Amino-acid type discrimination is realized via a Hadamard...
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11-10-2011 07:38 AM
[Question from NMRWiki Q&A forum] Tuning probe failed after a dual probe was replaced with a BBI probe
Tuning probe failed after a dual probe was replaced with a BBI probe
We generally use Dual to run 13C and BBI to run 2D. After changed the probe, the command "edhead" was used to set the probe. Put the sample tube, lock the solvent, and then type "atma" to tune the probe. We always do it like this, but now we can not tune the proton after installed the BBI probe (13C is OK). The dip can not be found by "atma", and "atmm" was also not work on forming a dip. What is the most possible reason for this error? How to solve it and avoid it in the future ? Thanks. (Instrument: Bruker 400 MHz,...
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08-23-2011 05:31 PM
[NMR paper] Proline-directed random-coil chemical shift values as a tool for the NMR assignment o
Proline-directed random-coil chemical shift values as a tool for the NMR assignment of the tau phosphorylation sites.
Related Articles Proline-directed random-coil chemical shift values as a tool for the NMR assignment of the tau phosphorylation sites.
Chembiochem. 2004 Jan 3;5(1):73-8
Authors: Lippens G, Wieruszeski JM, Leroy A, Smet C, Sillen A, Buée L, Landrieu I
NMR spectroscopy of the full-length neuronal Tau protein has proved to be difficult due to the length of the protein and the unfavorable amino acid composition. We show that the...
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11-24-2010 09:25 PM
[NMR paper] RESCUE: an artificial neural network tool for the NMR spectral assignment of proteins
RESCUE: an artificial neural network tool for the NMR spectral assignment of proteins.
Related Articles RESCUE: an artificial neural network tool for the NMR spectral assignment of proteins.
J Biomol NMR. 1999 Sep;15(1):15-26
Authors: Pons JL, Delsuc MA
The assignment of the 1H spectrum of a protein or a polypeptide is the prerequisite for advanced NMR studies. We present here an assignment tool based on the artificial neural network technology, which determines the type of the amino acid from the chemical shift values observed in the 1H...
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11-18-2010 08:31 PM
A new spin probe of protein dynamics
A new spin probe of protein dynamics: nitrogen relaxation in (15)n-(2)h amide groups.
Xu J, Millet O, Kay LE, Skrynnikov NR.
Contribution from the Department of Chemistry, Purdue University, West Lafayette, Indiana 47907, and Departments of Medical Genetics, Biochemistry, and Chemistry, University of Toronto, Toronto, Ontario M5S 1A8, Canada.
J Am Chem Soc. 2005 Mar 9;127(9):3220-9.
(15)N spin relaxation data have provided a wealth of information on protein dynamics in solution. Standard R(1), R(1)(rho), and NOE experiments aimed at (15)N amide moieties are complemented in this...
Applying Thymine Isostere 2,4-Difluoro-5-Methylbenzene as a NMR Assignment Tool and Probe of Homopyrimidine/Homopurine Tract Structural Dynamics.
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