Literature DB >> 19333476

A conformational transition in the structure of a 2'-thiomethyl-modified DNA visualized at high resolution.

Pradeep S Pallan1, Thazha P Prakash, Feng Li, Robert L Eoff, Muthiah Manoharan, Martin Egli.   

Abstract

Crystal structures of A-form and B-form DNA duplexes containing 2'-S-methyl-uridines reveal that the modified residues adopt a RNA-like C3'-endo pucker, illustrating that the replacement of electronegative oxygen at the 2'-carbon of RNA by sulfur does not appear to fundamentally alter the conformational preference of the sugar in the oligonucleotide context and sterics trump stereoelectronics.

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Year:  2009        PMID： 19333476      PMCID： PMC2909737          DOI： 10.1039/b822781k

Source DB:  PubMed          Journal:  Chem Commun (Camb)        ISSN： 1359-7345            Impact factor:   6.222


  32 in total

1.  Crystal structures of B-DNA with incorporated 2'-deoxy-2'-fluoro-arabino-furanosyl thymines: implications of conformational preorganization for duplex stability.

Authors:  I Berger; V Tereshko; H Ikeda; V E Marquez; M Egli
Journal:  Nucleic Acids Res       Date:  1998-05-15       Impact factor: 16.971

2.  SHELXL: high-resolution refinement.

Authors:  G M Sheldrick; T R Schneider
Journal:  Methods Enzymol       Date:  1997       Impact factor: 1.600

3.  Crystallography & NMR system: A new software suite for macromolecular structure determination.

Authors:  A T Brünger; P D Adams; G M Clore; W L DeLano; P Gros; R W Grosse-Kunstleve; J S Jiang; J Kuszewski; M Nilges; N S Pannu; R J Read; L M Rice; T Simonson; G L Warren
Journal:  Acta Crystallogr D Biol Crystallogr       Date:  1998-09-01

4.  RNA hydration: a detailed look.

Authors:  M Egli; S Portmann; N Usman
Journal:  Biochemistry       Date:  1996-07-02       Impact factor: 3.162

5.  Uniformly modified 2'-deoxy-2'-fluoro phosphorothioate oligonucleotides as nuclease-resistant antisense compounds with high affinity and specificity for RNA targets.

Authors:  A M Kawasaki; M D Casper; S M Freier; E A Lesnik; M C Zounes; L L Cummins; C Gonzalez; P D Cook
Journal:  J Med Chem       Date:  1993-04-02       Impact factor: 7.446

6.  Crystal structure analysis of a complete turn of B-DNA.

Authors:  R Wing; H Drew; T Takano; C Broka; S Tanaka; K Itakura; R E Dickerson
Journal:  Nature       Date:  1980-10-23       Impact factor: 49.962

7.  Covalent incorporation of selenium into oligonucleotides for X-ray crystal structure determination via MAD: proof of principle. Multiwavelength anomalous dispersion.

Authors:  Marianna Teplova; Christopher J Wilds; Zdzislaw Wawrzak; Valentina Tereshko; Quan Du; Nicolas Carrasco; Zhen Huang; Martin Egli
Journal:  Biochimie       Date:  2002-09       Impact factor: 4.079

8.  Conformational influence of the ribose 2'-hydroxyl group: crystal structures of DNA-RNA chimeric duplexes.

Authors:  M Egli; N Usman; A Rich
Journal:  Biochemistry       Date:  1993-04-06       Impact factor: 3.162

9.  Structural requirements at the catalytic site of the heteroduplex substrate for human RNase H1 catalysis.

Authors:  Walt F Lima; Josh G Nichols; Hongjiang Wu; Thazha P Prakash; Mike T Migawa; Tadensz K Wyrzykiewicz; Balkrishen Bhat; Stanley T Crooke
Journal:  J Biol Chem       Date:  2004-06-17       Impact factor: 5.157

10.  Insights into RNA/DNA hybrid recognition and processing by RNase H from the crystal structure of a non-specific enzyme-dsDNA complex.

Authors:  Pradeep S Pallan; Martin Egli
Journal:  Cell Cycle       Date:  2008-08-18       Impact factor: 4.534
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  8 in total

1.  The conformationally constrained N-methanocarba-dT analogue adopts an unexpected C4'-exo sugar pucker in the structure of a DNA hairpin.

Authors:  Pradeep S Pallan; Victor E Marquez; Martin Egli
Journal:  Biochemistry       Date:  2012-03-20       Impact factor: 3.162

Review 2.  The many twists and turns of DNA: template, telomere, tool, and target.

Authors:  Martin Egli; Pradeep S Pallan
Journal:  Curr Opin Struct Biol       Date:  2010-04-08       Impact factor: 6.809

Review 3.  Crystallographic studies of chemically modified nucleic acids: a backward glance.

Authors:  Martin Egli; Pradeep S Pallan
Journal:  Chem Biodivers       Date:  2010-01       Impact factor: 2.408

4.  Synthesis and characterization of oligodeoxyribonucleotides modified with 2'-thio-2'-deoxy-2'-S-(pyren-1-yl)methyluridine.

Authors:  Brooke A Anderson; Patrick J Hrdlicka
Journal:  Bioorg Med Chem Lett       Date:  2015-07-07       Impact factor: 2.823

5.  Structure, stability and function of 5-chlorouracil modified A:U and G:U base pairs.

Authors:  Amritraj Patra; Joel Harp; Pradeep S Pallan; Linlin Zhao; Mikhail Abramov; Piet Herdewijn; Martin Egli
Journal:  Nucleic Acids Res       Date:  2012-12-28       Impact factor: 16.971

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.  Surprising base pairing and structural properties of 2'-trifluoromethylthio-modified ribonucleic acids.

Authors:  Marija Košutić; Lukas Jud; Cyrielle Da Veiga; Marina Frener; Katja Fauster; Christoph Kreutz; Eric Ennifar; Ronald Micura
Journal:  J Am Chem Soc       Date:  2014-04-25       Impact factor: 15.419

8.  2'-Alkynyl spin-labelling is a minimally perturbing tool for DNA structural analysis.

Authors:  Jack S Hardwick; Marius M Haugland; Afaf H El-Sagheer; Denis Ptchelkine; Frank R Beierlein; Andrew N Lane; Tom Brown; Janet E Lovett; Edward A Anderson
Journal:  Nucleic Acids Res       Date:  2020-04-06       Impact factor: 16.971
  8 in total

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