Literature DB >> 9580707

Oligoribonucleotide circularization by 'template-mediated' ligation with T4 RNA ligase: synthesis of circular hammerhead ribozymes.

L Wang1, D E Ruffner.   

Abstract

Circular hammerhead ribozymes were synthesized from linear oligoribonucleotides using T4 RNA ligase. Some of the precursors could not be efficiently circularized under standard conditions. For these molecules, the use of a DNA template allowed their efficient circularization. The template was designed to prevent the precursor from folding into an unsuitable structure. The template allowed circular ribozymes as small as 15 nucleotides in length to be efficiently synthesized at concentrations as high as 50 microM in the ligation reaction. The circular products retained their biological activity.

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Year:  1998        PMID: 9580707      PMCID: PMC147549          DOI: 10.1093/nar/26.10.2502

Source DB:  PubMed          Journal:  Nucleic Acids Res        ISSN: 0305-1048            Impact factor:   16.971


  12 in total

1.  Site-specific modification of pre-mRNA: the 2'-hydroxyl groups at the splice sites.

Authors:  M J Moore; P A Sharp
Journal:  Science       Date:  1992-05-15       Impact factor: 47.728

2.  Folding of circularly permuted transfer RNAs.

Authors:  T Pan; R R Gutell; O C Uhlenbeck
Journal:  Science       Date:  1991-11-29       Impact factor: 47.728

3.  Group I permuted intron-exon (PIE) sequences self-splice to produce circular exons.

Authors:  M Puttaraju; M D Been
Journal:  Nucleic Acids Res       Date:  1992-10-25       Impact factor: 16.971

4.  Initiation of protein synthesis by the eukaryotic translational apparatus on circular RNAs.

Authors:  C Y Chen; P Sarnow
Journal:  Science       Date:  1995-04-21       Impact factor: 47.728

5.  Synthesis of circular RNA in bacteria and yeast using RNA cyclase ribozymes derived from a group I intron of phage T4.

Authors:  E Ford; M Ares
Journal:  Proc Natl Acad Sci U S A       Date:  1994-04-12       Impact factor: 11.205

6.  Use of an engineered ribozyme to produce a circular human exon.

Authors:  S Mikheeva; M Hakim-Zargar; D Carlson; K Jarrell
Journal:  Nucleic Acids Res       Date:  1997-12-15       Impact factor: 16.971

7.  A new technique for the characterization of long-range tertiary contacts in large RNA molecules: insertion of a photolabel at a selected position in 16S rRNA within the Escherichia coli ribosome.

Authors:  P V Baranov; S S Dokudovskaya; T S Oretskaya; O A Dontsova; A A Bogdanov; R Brimacombe
Journal:  Nucleic Acids Res       Date:  1997-06-15       Impact factor: 16.971

8.  Fluorescence-, isotope- or biotin-labeling of the 5 '-end of single-stranded DNA/RNA using T4 RNA ligase.

Authors:  Y Kinoshita; K Nishigaki; Y Husimi
Journal:  Nucleic Acids Res       Date:  1997-09-15       Impact factor: 16.971

9.  5' exon requirement for self-splicing of the Tetrahymena thermophila pre-ribosomal RNA and identification of a cryptic 5' splice site in the 3' exon.

Authors:  J V Price; J Engberg; T R Cech
Journal:  J Mol Biol       Date:  1987-07-05       Impact factor: 5.469

10.  A circular trans-acting hepatitis delta virus ribozyme.

Authors:  M Puttaraju; A T Perrotta; M D Been
Journal:  Nucleic Acids Res       Date:  1993-09-11       Impact factor: 16.971

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  11 in total

1.  Y-ligation: an efficient method for ligating single-stranded DNAs and RNAs with T4 RNA ligase.

Authors:  K Nishigaki; K Taguchi; Y Kinoshita; T Aita; Y Husimi
Journal:  Mol Divers       Date:  1998       Impact factor: 2.943

2.  Discovery and characterization of a thermostable bacteriophage RNA ligase homologous to T4 RNA ligase 1.

Authors:  Thorarinn Blondal; Sigridur H Hjorleifsdottir; Olafur F Fridjonsson; Arnthor Aevarsson; Sigurlaug Skirnisdottir; Anna Gudny Hermannsdottir; Gudmundur O Hreggvidsson; Albert Vernon Smith; Jakob K Kristjansson
Journal:  Nucleic Acids Res       Date:  2003-12-15       Impact factor: 16.971

3.  miR-ID: a novel, circularization-based platform for detection of microRNAs.

Authors:  Pavan Kumar; Brian H Johnston; Sergei A Kazakov
Journal:  RNA       Date:  2010-12-17       Impact factor: 4.942

Review 4.  In vitro circularization of RNA.

Authors:  Sabine Müller; Bettina Appel
Journal:  RNA Biol       Date:  2016-09-26       Impact factor: 4.652

5.  Addition of non-genomically encoded nucleotides to the 3'-terminus of maize mitochondrial mRNAs: truncated rps12 mRNAs frequently terminate with CCA.

Authors:  M A Williams; Y Johzuka; R M Mulligan
Journal:  Nucleic Acids Res       Date:  2000-11-15       Impact factor: 16.971

6.  Phospho-RNA sequencing with circAID-p-seq.

Authors:  Alessia Del Piano; Tea Kecman; Michael Schmid; Ruggero Barbieri; Luciano Brocchieri; Silvia Tornaletti; Claudia Firrito; Luca Minati; Paola Bernabo; Ilaria Signoria; Fabio Lauria; Thomas H Gillingwater; Gabriella Viero; Massimiliano Clamer
Journal:  Nucleic Acids Res       Date:  2022-02-28       Impact factor: 16.971

7.  Preferential production of RNA rings by T4 RNA ligase 2 without any splint through rational design of precursor strand.

Authors:  Hui Chen; Kai Cheng; Xiaoli Liu; Ran An; Makoto Komiyama; Xingguo Liang
Journal:  Nucleic Acids Res       Date:  2020-05-21       Impact factor: 16.971

Review 8.  The design and synthesis of circular RNAs.

Authors:  Prisca Obi; Y Grace Chen
Journal:  Methods       Date:  2021-03-02       Impact factor: 3.608

9.  Identification and remediation of biases in the activity of RNA ligases in small-RNA deep sequencing.

Authors:  Anitha D Jayaprakash; Omar Jabado; Brian D Brown; Ravi Sachidanandam
Journal:  Nucleic Acids Res       Date:  2011-09-02       Impact factor: 16.971

Review 10.  RNA circularization strategies in vivo and in vitro.

Authors:  Sonja Petkovic; Sabine Müller
Journal:  Nucleic Acids Res       Date:  2015-02-06       Impact factor: 16.971

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