Folding of circularly permuted transfer RNAs.

All of the ribose-phosphate linkages in yeast tRNA(Phe) that could be cleaved without affecting the folding of the molecule have been determined in a single experiment. Circular permutation analysis subjects circular tRNA molecules to limited alkaline hydrolysis in order to generate one random break per molecule. Correctly folded tRNAs were identified by lead cleavage at neutral pH, a well-characterized reaction that requires proper folding of tRNA(Phe). Surprisingly, most of the circularly permuted tRNA molecules folded correctly. This result suggests that the tRNA folding motif could occur internally within other RNA sequences, and a computer search of Genbank entries has identified many examples of such motifs.

[1]  L. Minchenkova,et al.  Different conformations of double‐stranded nucleic acid in solution as revealed by circular dichroism , 1973, Biopolymers.

[2]  A. Rich,et al.  Structural domains of transfer RNA molecules. , 1976, Science.

[3]  G. Keith,et al.  Specific cleavages of pure tRNAs by plumbous ions. , 1976, Biochimica et biophysica acta.

[4]  O. Uhlenbeck,et al.  Reactions at the termini of tRNA with T4 RNA ligase. , 1978, Nucleic acids research.

[5]  Aaron Klug,et al.  Crystallographic and biochemical investigation of the lead(II)-catalyzed hydrolysis of yeast phenylalanine tRNA. , 1985 .

[6]  E Westhof,et al.  Crystallographic refinement of yeast aspartic acid transfer RNA. , 1985, Journal of molecular biology.

[7]  T. Cech,et al.  The intervening sequence RNA of Tetrahymena is an enzyme. , 1986, Science.

[8]  O. Uhlenbeck,et al.  Characterization of two RNA-catalyzed RNA cleavage reactions. , 1987, Cold Spring Harbor symposia on quantitative biology.

[9]  O. Uhlenbeck.  A small catalytic oligoribonucleotide , 1987, Nature.

[10]  O. Uhlenbeck,et al.  Biochemical and physical characterization of an unmodified yeast phenylalanine transfer RNA transcribed in vitro. , 1988, Proceedings of the National Academy of Sciences of the United States of America.

[11]  J. Ebel,et al.  Characterization of the lead(II)-induced cleavages in tRNAs in solution and effect of the Y-base removal in yeast tRNAPhe. , 1988, Biochemistry.

[12]  T. Dreher,et al.  Mutational analysis of the sequence and structural requirements in brome mosaic virus RNA for minus strand promoter activity. , 1988, Journal of molecular biology.

[13]  K. Luger,et al.  Correct folding of circularly permuted variants of a beta alpha barrel enzyme in vivo. , 1989, Science.

[14]  O. Uhlenbeck,et al.  Synthesis of small RNAs using T7 RNA polymerase. , 1989, Methods in enzymology.

[15]  T. Dreher,et al.  Replication in vivo of mutant brome mosaic virus RNAs defective in aminoacylation. , 1989, Journal of molecular biology.

[16]  O. Uhlenbeck,et al.  Lead-catalyzed cleavage of yeast tRNAPhe mutants. , 1990, Biochemistry.

[17]  Daniel Gautheret,et al.  Pattern searching/alignment with RNA primary and secondary structures: an effective descriptor for tRNA , 1990, Comput. Appl. Biosci..