[NMR paper] 4'-C-[(4-trifluoromethyl-1H-1,2,3-triazol-1-yl)methyl]thymidine as a sensitive (19)F NMR sensor for the detection of oligonucleotide secondary structures.
4'-C-[(4-trifluoromethyl-1H-1,2,3-triazol-1-yl)methyl]thymidine as a sensitive (19)F NMR sensor for the detection of oligonucleotide secondary structures.
Related Articles4'-C-[(4-trifluoromethyl-1H-1,2,3-triazol-1-yl)methyl]thymidine as a sensitive (19)F NMR sensor for the detection of oligonucleotide secondary structures.
J Org Chem. 2014 Apr 18;79(8):3529-36
Authors: Granqvist L, Virta P
Abstract
4'-C-[(4-Trifluoromethyl-1H-1,2,3-triazol-1-yl)methyl]thymidine was synthesized and incorporated as a phosphoramidite into oligonucleotide sequences. Its applicability as a sensor for the (19)F NMR spectroscopic detection of DNA and RNA secondary structures was demonstrated. On DNA, the (19)F NMR measurements were focused on monitoring of duplex-triplex conversion, for which this fluorine-labeled 2'-deoxynucleoside proved to be a powerful sensor. This sensor seemingly favors DNA, but its behavior in the RNA environment also turned out to be informative. As a demonstration, invasion of a 2'-O-methyl oligoribonucleotide into an RNA hairpin model (HIV-1 TAR) was monitored by (19)F NMR spectroscopy. According to the thermal denaturation studies by UV spectroscopy, the effect of the 4'-C-(4-trifluoromethyl-1H-1,2,3-triazol-1-yl)methyl moiety on the stability of these DNA and RNA models was marginal.
[NMR paper] NMR Detection of Structures in the HIV-1 5'-Leader RNA That Regulate Genome Packaging
From Mendeley Biomolecular NMR group:
NMR Detection of Structures in the HIV-1 5'-Leader RNA That Regulate Genome Packaging
Science (2011). Volume: 334, Issue: 6053. Pages: 242-245. K. Lu, X. Heng, L. Garyu, S. Monti, E. L. Garcia, S. Kharytonchyk, B. Dorjsuren, G. Kulandaivel, S. Jones, a. Hiremath, S. S. Divakaruni, C. LaCotti, S. Barton, D. Tummillo, a. Hosic, K. Edme, S. Albrecht, a. Telesnitsky, M. F. Summers et al.
Published using Mendeley: The bibliography manager for researchers
nmrlearner
Journal club
0
08-24-2012 08:01 PM
[MWClarkson blog] Alternative side-chain structures from methyl CPMG
Alternative side-chain structures from methyl CPMG
http://www.researchblogging.org/public/citation_icons/rb2_large_gray.pngAs I have mentioned before on this blog, the use of tools like CS-ROSETTA holds the promise of determining protein structures using only the chemical shifts of its backbone atoms. In addition to potentially making NOEs and RDCs redundant, this technology allows biologists to determine the conformations of minor members of the structural ensemble, which are very difficult to obtain using conventional approaches in population-dominated techniques like NMR and X-ray...
nmrlearner
News from NMR blogs
0
06-21-2011 03:31 AM
Conformational Study of 9-Dehydro-9-Trifluoromethyl Cinchona Alkaloids via 19F NMR Spectroscopy: Emergence of Trifluoromethyl Moiety as a Conformational Stabilizer and a Probe
Conformational Study of 9-Dehydro-9-Trifluoromethyl Cinchona Alkaloids via 19F NMR Spectroscopy: Emergence of Trifluoromethyl Moiety as a Conformational Stabilizer and a Probe
G. K. Surya Prakash, Fang Wang, Chuanfa Ni, Jingguo Shen, Ralf Haiges, Andrei K. Yudin, Thomas Mathew and George A. Olah
http://pubs.acs.org/appl/literatum/publisher/achs/journals/content/jacsat/0/jacsat.ahead-of-print/ja202373d/aop/images/medium/ja-2011-02373d_0006.gif
Journal of the American Chemical Society
DOI: 10.1021/ja202373d
http://feeds.feedburner.com/~ff/acs/jacsat?d=yIl2AUoC8zA...
nmrlearner
Journal club
0
06-14-2011 02:30 AM
Selective Detection of 13CHD2 Signals from a Mixture of 13CH3/13CH2D/13CHD2 Methyl Isotopomers in Proteins
Selective Detection of 13CHD2 Signals from a Mixture of 13CH3/13CH2D/13CHD2 Methyl Isotopomers in Proteins
Publication year: 2011
Source: Journal of Magnetic Resonance, In Press, Accepted Manuscript, Available online 4 January 2011</br>
Xinli, Liao , Vitali, Tugarinov</br>
In NMR spectra of partially deuterated proteins methyl correlations are commonly observed as a combination of signals from 13CH3, 13CH2D and 13CHD2 isotopomers. In a number of NMR applications, methyl groups of the 13CHD2 variety are targeted because of their AX-like character and concomitant simplification of the...
nmrlearner
Journal club
0
01-05-2011 11:03 AM
[NMR paper] Sensitive high resolution inverse detection NMR spectroscopy of proteins in the solid
Sensitive high resolution inverse detection NMR spectroscopy of proteins in the solid state.
Related Articles Sensitive high resolution inverse detection NMR spectroscopy of proteins in the solid state.
J Am Chem Soc. 2003 Dec 24;125(51):15831-6
Authors: Paulson EK, Morcombe CR, Gaponenko V, Dancheck B, Byrd RA, Zilm KW
A new indirect detection scheme for obtaining (15)N/(1)H shift correlation spectra in crystalline proteins is described. Excellent water suppression is achieved without the need for pulsed field gradients, and using only a...
nmrlearner
Journal club
0
11-24-2010 09:16 PM
[NMR paper] Cytosine deaminase and thymidine kinase gene therapy in a Dunning rat prostate tumour
Cytosine deaminase and thymidine kinase gene therapy in a Dunning rat prostate tumour model: absence of bystander effects and characterisation of 5-fluorocytosine metabolism with 19F-NMR spectroscopy.
Related Articles Cytosine deaminase and thymidine kinase gene therapy in a Dunning rat prostate tumour model: absence of bystander effects and characterisation of 5-fluorocytosine metabolism with 19F-NMR spectroscopy.
Gene Ther. 2002 Dec;9(23):1564-75
Authors: Corban-Wilhelm H, Hull WE, Becker G, Bauder-Wüst U, Greulich D, Debus J
The rat...
nmrlearner
Journal club
0
11-24-2010 08:58 PM
Investigation of the utility of selective methyl protonation for determination of membrane protein structures
Investigation of the utility of selective methyl protonation for determination of membrane protein structures
Steve C. C. Shih, Ileana Stoica and Natalie K. Goto
Journal of Biomolecular NMR; 2008; 42(1); pp 49-58
Abstract
Polytopic α-helical membrane proteins present one of the final frontiers for protein structural biology, with significant challenges causing severe under-representation in the protein structure databank. However, with the advent of hardware and methodology geared to the study of large molecular weight complexes, solution NMR is being increasingly considered as a tool...
Kirby
Journal club
0
09-22-2008 12:00 AM
Simultaneous detection of amide and methyl correlations using a time shared NMR experiment: application to binding epitope mapping
Simultaneous detection of amide and methyl correlations using a time shared NMR experiment: application to binding epitope mapping
Peter Würtz, Olli Aitio, Maarit Hellman and Perttu Permi
Journal of Biomolecular NMR; 2007; 39(2) pp 97 - 105
Abstract:
Simultaneous recording of different NMR parameters is an efficient way to reduce the overall experimental time and speed up structural studies of biological macromolecules. This can especially be beneficial in the case of fast NMR-based drug screening applications or for collecting NOE restraints, where prohibitively long data collection...
![4'-C-[(4-trifluoromethyl-1H-1,2,3-triazol-1-yl)methyl]thymidine as a sensitive (19)F NMR sensor for the detection of oligonucleotide secondary structures.](http://www.bionmr.com/forum/iconimages/journal-club-9/4-c-%5B-4-trifluoromethyl-1h-1-2-3-triazol-1-yl-methyl%5Dthymidine-sensitive-19-f-nmr-sensor-detection-oligonucleotide-secondary-structures_ltr.gif)
4'-C-[(4-trifluoromethyl-1H-1,2,3-triazol-1-yl)methyl]thymidine as a sensitive (19)F NMR sensor for the detection of oligonucleotide secondary structures.
Linear Mode
