Literature DB >> 15556400

Nucleic acid crystallography: current progress.

Martin Egli1.   

Abstract

Fifty years after the publication of the DNA double helix model by Watson and Crick, new nucleic acid structures keep emerging at an ever-increasing rate. The past three years have brought a flurry of new oligonucleotide structures, including those of a Hoogsteen-paired DNA duplex, Holliday junctions, DNA-drug complexes, quadruplexes, a host of RNA motifs and various nucleic acid analogues. Major advances were also made in terms of the structure and function of catalytic RNAs. These range from improved models of the phosphodiester cleavage reactions catalyzed by the hairpin and hepatitis delta virus ribozymes to the visualization of a complete active site of a group I self-splicing intron with bound 5'- and 3'-exons. These triumphs are complemented by a refined understanding of cation-nucleic-acid interactions and new routes to the generation of derivatives for phasing of DNA and RNA structures.

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Year:  2004        PMID: 15556400     DOI: 10.1016/j.cbpa.2004.09.004

Source DB:  PubMed          Journal:  Curr Opin Chem Biol        ISSN: 1367-5931            Impact factor:   8.822


  16 in total

1.  Comparison of mode analyses at different resolutions applied to nucleic acid systems.

Authors:  Adam W Van Wynsberghe; Qiang Cui
Journal:  Biophys J       Date:  2005-08-12       Impact factor: 4.033

2.  Efficient substrate cleavage catalyzed by hammerhead ribozymes derivatized with selenium for X-ray crystallography.

Authors:  Gary Brandt; Nicolas Carrasco; Zhen Huang
Journal:  Biochemistry       Date:  2006-07-25       Impact factor: 3.162

3.  Conformational transitions in RNA single uridine and adenosine bulge structures: a molecular dynamics free energy simulation study.

Authors:  André Barthel; Martin Zacharias
Journal:  Biophys J       Date:  2006-01-06       Impact factor: 4.033

4.  Synthesis of a 2'-Se-thymidine phosphoramidite and its incorporation into oligonucleotides for crystal structure study.

Authors:  Jia Sheng; Jiansheng Jiang; Jozef Salon; Zhen Huang
Journal:  Org Lett       Date:  2007-01-31       Impact factor: 6.005

5.  Metal binding motif in the active site of the HDV ribozyme binds divalent and monovalent ions.

Authors:  Narayanan Veeraraghavan; Abir Ganguly; Jui-Hui Chen; Philip C Bevilacqua; Sharon Hammes-Schiffer; Barbara L Golden
Journal:  Biochemistry       Date:  2011-03-09       Impact factor: 3.162

Review 6.  Chemistry and structural biology of DNA damage and biological consequences.

Authors:  Michael P Stone; Hai Huang; Kyle L Brown; Ganesh Shanmugam
Journal:  Chem Biodivers       Date:  2011-09       Impact factor: 2.408

7.  Investigation of the Reactivity of Oligodeoxynucleotides with Glyoxal and KMnO(4) Chemical Probes by Electrospray Ionization Mass Spectrometry.

Authors:  Carol Parr; Sarah E Pierce; Suncerae I Smith; Jennifer S Brodbelt
Journal:  Int J Mass Spectrom       Date:  2011-07-01       Impact factor: 1.986

8.  A coarse-grained model for assisting the investigation of structure and dynamics of large nucleic acids by ion mobility spectrometry-mass spectrometry.

Authors:  S Vangaveti; R J D'Esposito; J L Lippens; D Fabris; S V Ranganathan
Journal:  Phys Chem Chem Phys       Date:  2017-06-14       Impact factor: 3.676

9.  Structure determination of DNA methylation lesions N1-meA and N3-meC in duplex DNA using a cross-linked protein-DNA system.

Authors:  Lianghua Lu; Chengqi Yi; Xing Jian; Guanqun Zheng; Chuan He
Journal:  Nucleic Acids Res       Date:  2010-03-11       Impact factor: 16.971

10.  DNA A-tracts are not curved in solutions containing high concentrations of monovalent cations.

Authors:  Earle Stellwagen; Justin P Peters; L James Maher; Nancy C Stellwagen
Journal:  Biochemistry       Date:  2013-06-06       Impact factor: 3.162

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