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Literature DB >> 6159633

Chemical probes for higher-order structure in RNA.

Abstract

Three chemical reactions can probe the secondary and tertiary interactions of RNA molecules in solution. Dimethyl sulfate monitors the N-7 of guanosines and senses tertiary interactions there, diethyl pyrocarbonate detects stacking of adenosines, and an alternate dimethyl sulfate reaction examines the N-3 of cytidines and thus probes base pairing. The reactions work between 0 degrees C and 90 degrees C and at pH 4.5--8.5 in a variety of buffers. As an example we follow the progressive denaturation of yeast tRNAPhe terminally labeled with 32P as the tertiary and secondary structures sequentially melt out. A single autoradiograph of a terminally labeled molecule locates regions of higher-order structure and identifies the bases involved.

Entities: Chemical Species

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Year: 1980 PMID： 6159633 PMCID： PMC349909 DOI： 10.1073/pnas.77.8.4679

Source DB: PubMed Journal: Proc Natl Acad Sci U S A ISSN： 0027-8424 Impact factor: 11.205

25 in total

1. STRUCTURE OF A RIBONUCLEIC ACID.

Authors: R W HOLLEY; J APGAR; G A EVERETT; J T MADISON; M MARQUISEE; S H MERRILL; J R PENSWICK; A ZAMIR
Journal: Science Date: 1965-03-19 Impact factor: 47.728

2. The use of nuclease P1 in sequence analysis of end group labeled RNA.

Authors: M Silberklang; A M Gillum; U L RajBhandary
Journal: Nucleic Acids Res Date: 1977-12 Impact factor: 16.971

3. UV shadowing--a new and convenient method for the location of ultraviolet-absorbing species in polyacrylamide gels.

Authors: S M Hassur; H W Whitlock
Journal: Anal Biochem Date: 1974-05 Impact factor: 3.365

4. Studies on polynucleotides. LXXXII. Yeast phenylalanine transfer ribonucleic acid: partial digestion with ribonuclease T-1 and derivation of the total primary structure.

Authors: U L RajBhandary; S H Chang
Journal: J Biol Chem Date: 1968-02-10 Impact factor: 5.157

5. Molecular conformations and structure transitions of RNA complementary helices and their possible biological significance.

Authors: S Arnott; W Fuller; A Hodgson; I Prutton
Journal: Nature Date: 1968-11-09 Impact factor: 49.962

6. Crystallographic refinement of yeast phenylalanine transfer RNA at 2-5A resolution.

Authors: A Jack; J E Ladner; A Klug
Journal: J Mol Biol Date: 1976-12-25 Impact factor: 5.469

7. Structural domains of transfer RNA molecules.

Authors: G J Quigley; A Rich
Journal: Science Date: 1976-11-19 Impact factor: 47.728

Review 8. E. coli RNA polymerase interacts homologously with two different promoters.

Authors: U Siebenlist; R B Simpson; W Gilbert
Journal: Cell Date: 1980-06 Impact factor: 41.582

9. RNA-ligant interactions. (I) Magnesium binding sites in yeast tRNAPhe.

Authors: S R Holbrook; J L Sussman; R W Warrant; G M Church; S H Kim
Journal: Nucleic Acids Res Date: 1977-08 Impact factor: 16.971

10. Site specific enzymatic cleavage of RNA.

Authors: H Donis-Keller
Journal: Nucleic Acids Res Date: 1979-09-11 Impact factor: 16.971

161 in total

1. An unusual structure formed by antisense-target RNA binding involves an extended kissing complex with a four-way junction and a side-by-side helical alignment.

Authors: F A Kolb; C Malmgren; E Westhof; C Ehresmann; B Ehresmann; E G Wagner; P Romby
Journal: RNA Date: 2000-03 Impact factor: 4.942

2. Probing the structure of RNAIII, the Staphylococcus aureus agr regulatory RNA, and identification of the RNA domain involved in repression of protein A expression.

Authors: Y Benito; F A Kolb; P Romby; G Lina; J Etienne; F Vandenesch
Journal: RNA Date: 2000-05 Impact factor: 4.942

Chemical probes for higher-order structure in RNA.

1. STRUCTURE OF A RIBONUCLEIC ACID.

2. The use of nuclease P1 in sequence analysis of end group labeled RNA.

3. UV shadowing--a new and convenient method for the location of ultraviolet-absorbing species in polyacrylamide gels.

4. Studies on polynucleotides. LXXXII. Yeast phenylalanine transfer ribonucleic acid: partial digestion with ribonuclease T-1 and derivation of the total primary structure.

5. Molecular conformations and structure transitions of RNA complementary helices and their possible biological significance.

6. Crystallographic refinement of yeast phenylalanine transfer RNA at 2-5A resolution.

7. Structural domains of transfer RNA molecules.

Review 8. E. coli RNA polymerase interacts homologously with two different promoters.

9. RNA-ligant interactions. (I) Magnesium binding sites in yeast tRNAPhe.

10. Site specific enzymatic cleavage of RNA.

1. An unusual structure formed by antisense-target RNA binding involves an extended kissing complex with a four-way junction and a side-by-side helical alignment.

2. Probing the structure of RNAIII, the Staphylococcus aureus agr regulatory RNA, and identification of the RNA domain involved in repression of protein A expression.

3. The peculiar architectural framework of tRNASec is fully recognized by yeast AspRS.

4. Intramolecular secondary structure rearrangement by the kissing interaction of the Neurospora VS ribozyme.

5. High affinity nucleic acid aptamers for streptavidin incorporated into bi-specific capture ligands.

6. Roles of the influenza virus polymerase and nucleoprotein in forming a functional RNP structure.

7. Structural organization of a viral IRES depends on the integrity of the GNRA motif.

8. Oligonucleotide directed misfolding of RNA inhibits Candida albicans group I intron splicing.

9. Mapping of psoralen cross-linked nucleotides in RNA.

10. Domain V of 23S rRNA contains all the structural elements necessary for recognition by the ErmE methyltransferase.