Literature DB >> 10333742

New developments in structure determination of pseudoknots.

C W Hilbers1, P J Michiels, H A Heus.   

Abstract

Recently, several high-resolution structures of-RNA pseudoknots have become available. Here we review the progress in this area. The majority of the structures obtained belong to the classical or H-type pseudoknot family. The most complicated pseudoknot structure elucidated so far is the Hepatitis Delta Virus ribozyme, which forms a nested double pseudoknot. In particular, the structure-function relationships of the H-type pseudoknots involved in translational frameshifting have received much attention. All molecules considered show interesting new structural motifs.

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Year:  1998        PMID: 10333742     DOI: 10.1002/(SICI)1097-0282(1998)48:2<137::AID-BIP4>3.0.CO;2-H

Source DB:  PubMed          Journal:  Biopolymers        ISSN: 0006-3525            Impact factor:   2.505


  22 in total

1.  PseudoBase: a database with RNA pseudoknots.

Authors:  F H van Batenburg; A P Gultyaev; C W Pleij; J Ng; J Oliehoek
Journal:  Nucleic Acids Res       Date:  2000-01-01       Impact factor: 16.971

2.  PseudoBase: structural information on RNA pseudoknots.

Authors:  F H van Batenburg; A P Gultyaev; C W Pleij
Journal:  Nucleic Acids Res       Date:  2001-01-01       Impact factor: 16.971

3.  Cross-talk between orientation-dependent recognition determinants of a complex control RNA element, the enterovirus oriR.

Authors:  W J Melchers; J M Bakkers; H J Bruins Slot; J M Galama; V I Agol; E V Pilipenko
Journal:  RNA       Date:  2000-07       Impact factor: 4.942

4.  A novel method for finding tRNA genes.

Authors:  Vickie Tsui; Tom Macke; David A Case
Journal:  RNA       Date:  2003-05       Impact factor: 4.942

5.  PSEUDOVIEWER2: Visualization of RNA pseudoknots of any type.

Authors:  Kyungsook Han; Yanga Byun
Journal:  Nucleic Acids Res       Date:  2003-07-01       Impact factor: 16.971

6.  Structural elements in the 5'-untranslated region of giardiavirus transcript essential for internal ribosome entry site-mediated translation initiation.

Authors:  Srinivas Garlapati; Ching C Wang
Journal:  Eukaryot Cell       Date:  2005-04

7.  Structural basis for ribosome recruitment and manipulation by a viral IRES RNA.

Authors:  Jennifer S Pfingsten; David A Costantino; Jeffrey S Kieft
Journal:  Science       Date:  2006-11-23       Impact factor: 47.728

8.  From knotted to nested RNA structures: a variety of computational methods for pseudoknot removal.

Authors:  Sandra Smit; Kristian Rother; Jaap Heringa; Rob Knight
Journal:  RNA       Date:  2008-01-29       Impact factor: 4.942

9.  tRNA-mRNA mimicry drives translation initiation from a viral IRES.

Authors:  David A Costantino; Jennifer S Pfingsten; Robert P Rambo; Jeffrey S Kieft
Journal:  Nat Struct Mol Biol       Date:  2007-12-23       Impact factor: 15.369

Review 10.  The structural and functional diversity of metabolite-binding riboswitches.

Authors:  Adam Roth; Ronald R Breaker
Journal:  Annu Rev Biochem       Date:  2009       Impact factor: 23.643

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