Literature DB >> 9649634

Chemical mapping of co-existing RNA structures.

A R Schröder1, T Baumstark, D Riesner.   

Abstract

In many cases RNA can assume co-existing or meta-stable structures preventing structure determination by chemical mapping. A novel method is described, by which RNA is modified with dimethyl sulphate without shifting the distribution of different structures. The different structures are then separated in native gel electrophoresis, and structure determination by primer extension can be carried out separately for each structure.

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Year:  1998        PMID： 9649634      PMCID： PMC147709          DOI： 10.1093/nar/26.14.3449

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


  10 in total

1.  The computer simulation of RNA folding pathways using a genetic algorithm.

Authors:  A P Gultyaev; F H van Batenburg; C W Pleij
Journal:  J Mol Biol       Date:  1995-06-30       Impact factor: 5.469

2.  Viroid processing: switch from cleavage to ligation is driven by a change from a tetraloop to a loop E conformation.

Authors:  T Baumstark; A R Schröder; D Riesner
Journal:  EMBO J       Date:  1997-02-03       Impact factor: 11.598

3.  Effects of RNA secondary structure on alternative splicing of pre-mRNA: is folding limited to a region behind the transcribing RNA polymerase?

Authors:  L P Eperon; I R Graham; A D Griffiths; I C Eperon
Journal:  Cell       Date:  1988-07-29       Impact factor: 41.582

4.  RNA synthesis: strategies for the use of bacteriophage RNA polymerases.

Authors:  G Krupp
Journal:  Gene       Date:  1988-12-10       Impact factor: 3.688

5.  Temperature-gradient gel electrophoresis. Thermodynamic analysis of nucleic acids and proteins in purified form and in cellular extracts.

Authors:  V Rosenbaum; D Riesner
Journal:  Biophys Chem       Date:  1987-05-09       Impact factor: 2.352

Review 6.  Probing the structure of RNAs in solution.

Authors:  C Ehresmann; F Baudin; M Mougel; P Romby; J P Ebel; B Ehresmann
Journal:  Nucleic Acids Res       Date:  1987-11-25       Impact factor: 16.971

7.  Only one of four possible secondary structures of the central conserved region of potato spindle tuber viroid is a substrate for processing in a potato nuclear extract.

Authors:  T Baumstark; D Riesner
Journal:  Nucleic Acids Res       Date:  1995-11-11       Impact factor: 16.971

8.  Mutations affecting primer RNA interaction with the replication repressor RNA I in plasmid CoIE1: potential RNA folding pathway mutants.

Authors:  B Polisky; X Y Zhang; T Fitzwater
Journal:  EMBO J       Date:  1990-01       Impact factor: 11.598

9.  Multiple pathways of reversion in viroids for conservation of structural elements.

Authors:  F Qu; C Heinrich; P Loss; G Steger; P Tien; D Riesner
Journal:  EMBO J       Date:  1993-05       Impact factor: 11.598

Review 10.  Chemical and computer probing of RNA structure.

Authors:  N A Kolchanov; I I Titov; I E Vlassova; V V Vlassov
Journal:  Prog Nucleic Acid Res Mol Biol       Date:  1996
  10 in total
  8 in total

1.  Conformational changes involved in initiation of minus-strand synthesis of a virus-associated RNA.

Authors:  Guohua Zhang; Jiuchun Zhang; Anna T George; Tilman Baumstark; Anne E Simon
Journal:  RNA       Date:  2005-11-21       Impact factor: 4.942

2.  Detection and analysis of hairpin II, an essential metastable structural element in viroid replication intermediates.

Authors:  Astrid R W Schröder; Detlev Riesner
Journal:  Nucleic Acids Res       Date:  2002-08-01       Impact factor: 16.971

3.  A mini-RNA containing the tetraloop, wobble-pair and loop E motifs of the central conserved region of potato spindle tuber viroid is processed into a minicircle.

Authors:  O Schrader; T Baumstark; D Riesner
Journal:  Nucleic Acids Res       Date:  2003-02-01       Impact factor: 16.971

Review 4.  Probing RNA structure in vivo.

Authors:  David Mitchell; Sarah M Assmann; Philip C Bevilacqua
Journal:  Curr Opin Struct Biol       Date:  2019-09-13       Impact factor: 6.809

Review 5.  RNA architecture influences plant biology.

Authors:  Jiaying Zhu; Changhao Li; Xu Peng; Xiuren Zhang
Journal:  J Exp Bot       Date:  2021-05-18       Impact factor: 6.992

6.  Glyoxals as in vivo RNA structural probes of guanine base-pairing.

Authors:  David Mitchell; Laura E Ritchey; Hongmarn Park; Paul Babitzke; Sarah M Assmann; Philip C Bevilacqua
Journal:  RNA       Date:  2017-10-13       Impact factor: 4.942

Review 7.  RNA conformational changes in the life cycles of RNA viruses, viroids, and virus-associated RNAs.

Authors:  Anne E Simon; Lee Gehrke
Journal:  Biochim Biophys Acta       Date:  2009-06-06

8.  RNA structure probing to characterize RNA-protein interactions on a low abundance pre-mRNA in living cells.

Authors:  Jodi L Bubenik; Melissa Hale; Ona McConnell; Eric Wang; Maurice S Swanson; Robert Spitale; J Andrew Berglund
Journal:  RNA       Date:  2020-12-11       Impact factor: 5.636
  8 in total

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