Literature DB >> 18533676

A nonafluoro nucleoside as a sensitive 19f NMR probe of nucleic acid conformation.

Nivrutti B Barhate1, Rekha N Barhate, Pavol Cekan, Gary Drobny, Snorri Th Sigurdsson.   

Abstract

A nucleoside carrying a perfluorinated tert-butyl group ( 4) was prepared by a Sonogashira coupling of 5-iodo-2'-deoxyuridine with 4,4,4-trifluoro-3,3-bis(trifluoromethyl)-1-butyne in nearly quantitative yield and subsequently incorporated into DNA oligomers. Thermal denaturation studies showed that 4 had a negligible effect on duplex stability when compared to thymidine. Transition from single strand to duplex was monitored by (19)F NMR spectroscopy at micromolar concentrations of oligomers, demonstrating the sensitivity of 4 as an NMR reporter nucleoside.

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Year:  2008        PMID： 18533676      PMCID： PMC2735265          DOI： 10.1021/ol800872a

Source DB:  PubMed          Journal:  Org Lett        ISSN： 1523-7052            Impact factor:   6.005


  14 in total

1.  Determination of DNA minor groove width in distamycin-DNA complexes by solid-state NMR.

Authors:  Greg L Olsen; Elizabeth A Louie; Gary P Drobny; Snorri Th Sigurdsson
Journal:  Nucleic Acids Res       Date:  2003-09-01       Impact factor: 16.971

2.  Using solid-state 31P{19F} REDOR NMR to measure distances between a trifluoromethyl group and a phosphodiester in nucleic acids.

Authors:  Elizabeth A Louie; Panadda Chirakul; Vinodhkumar Raghunathan; Snorri Th Sigurdsson; Gary P Drobny
Journal:  J Magn Reson       Date:  2005-10-04       Impact factor: 2.229

3.  Ribose 2'-F labeling: a simple tool for the characterization of RNA secondary structure equilibria by 19F NMR spectroscopy.

Authors:  Christoph Kreutz; Hanspeter Kählig; Robert Konrat; Ronald Micura
Journal:  J Am Chem Soc       Date:  2005-08-24       Impact factor: 15.419

Review 4.  Use of 19F NMR to probe protein structure and conformational changes.

Authors:  M A Danielson; J J Falke
Journal:  Annu Rev Biophys Biomol Struct       Date:  1996

5.  Incorporation of 2'-deoxy-5-(trifluoromethyl)uridine and 5-cyano-2'-deoxyuridine into DNA.

Authors:  J C Markley; P Chirakul; D Sologub; S T Sigurdsson
Journal:  Bioorg Med Chem Lett       Date:  2001-09-17       Impact factor: 2.823

6.  Synthesis of 5-fluoropyrimidine nucleotides as sensitive NMR probes of RNA structure.

Authors:  Mirko Hennig; Lincoln G Scott; Edit Sperling; Wolfgang Bermel; James R Williamson
Journal:  J Am Chem Soc       Date:  2007-11-09       Impact factor: 15.419

7.  A comparative study of the thermal stability of oligodeoxyribonucleotides containing 5-substituted 2'-deoxyuridines.

Authors:  M Ahmadian; P Zhang; D E Bergstrom
Journal:  Nucleic Acids Res       Date:  1998-07-01       Impact factor: 16.971

8.  The bulge region of HIV-1 TAR RNA binds metal ions in solution.

Authors:  Mikołaj Olejniczak; Zofia Gdaniec; Artur Fischer; Tomasz Grabarkiewicz; Lukasz Bielecki; Ryszard W Adamiak
Journal:  Nucleic Acids Res       Date:  2002-10-01       Impact factor: 16.971

9.  Dissection of the ion-induced folding of the hammerhead ribozyme using 19F NMR.

Authors:  C Hammann; D G Norman; D M Lilley
Journal:  Proc Natl Acad Sci U S A       Date:  2001-05-01       Impact factor: 11.205

10.  Monitoring tat peptide binding to TAR RNA by solid-state 31P-19F REDOR NMR.

Authors:  Greg L Olsen; Thomas E Edwards; Pritilekha Deka; Gabriele Varani; Snorri Th Sigurdsson; Gary P Drobny
Journal:  Nucleic Acids Res       Date:  2005-06-16       Impact factor: 16.971
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  11 in total

Review 1.  New frontiers and developing applications in 19F NMR.

Authors:  Jian-Xin Yu; Rami R Hallac; Srinivas Chiguru; Ralph P Mason
Journal:  Prog Nucl Magn Reson Spectrosc       Date:  2012-11-02       Impact factor: 9.795

2.  Investigation of higher-order RNA G-quadruplex structures in vitro and in living cells by 19F NMR spectroscopy.

Authors:  Hong-Liang Bao; Yan Xu
Journal:  Nat Protoc       Date:  2018-03-08       Impact factor: 13.491

3.  Natural-like replication of an unnatural base pair for the expansion of the genetic alphabet and biotechnology applications.

Authors:  Lingjun Li; Mélissa Degardin; Thomas Lavergne; Denis A Malyshev; Kirandeep Dhami; Phillip Ordoukhanian; Floyd E Romesberg
Journal:  J Am Chem Soc       Date:  2013-10-23       Impact factor: 15.419

4.  5-Fluoro pyrimidines: labels to probe DNA and RNA secondary structures by 1D 19F NMR spectroscopy.

Authors:  Barbara Puffer; Christoph Kreutz; Ulrike Rieder; Marc-Olivier Ebert; Robert Konrat; Ronald Micura
Journal:  Nucleic Acids Res       Date:  2009-12       Impact factor: 16.971

5.  In situ monitoring of backbone thioester exchange by 19F NMR.

Authors:  William C Pomerantz; Erik B Hadley; Charles G Fry; Samuel H Gellman
Journal:  Chembiochem       Date:  2009-09-04       Impact factor: 3.164

6.  2'-SCF3 uridine-a powerful label for probing structure and function of RNA by 19F NMR spectroscopy.

Authors:  Katja Fauster; Christoph Kreutz; Ronald Micura
Journal:  Angew Chem Int Ed Engl       Date:  2012-11-19       Impact factor: 15.336

7.  Expanding the Scope of 2'-SCF3 Modified RNA.

Authors:  Lukas Jud; Marija Košutić; Veronika Schwarz; Markus Hartl; Christoph Kreutz; Klaus Bister; Ronald Micura
Journal:  Chemistry       Date:  2015-06-12       Impact factor: 5.236

8.  Characterization of human telomere RNA G-quadruplex structures in vitro and in living cells using 19F NMR spectroscopy.

Authors:  Hong-Liang Bao; Takumi Ishizuka; Takashi Sakamoto; Kenzo Fujimoto; Tamayo Uechi; Naoya Kenmochi; Yan Xu
Journal:  Nucleic Acids Res       Date:  2017-05-19       Impact factor: 16.971

9.  Studying DNA G-Quadruplex Aptamer by 19F NMR.

Authors:  Takumi Ishizuka; Atsushi Yamashita; Yujiro Asada; Yan Xu
Journal:  ACS Omega       Date:  2017-12-12

Review 10.  Synthesis and applications of theranostic oligonucleotides carrying multiple fluorine atoms.

Authors:  Valeriy G Metelev; Alexei A Bogdanov
Journal:  Theranostics       Date:  2020-01-01       Impact factor: 11.556
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