scholarly journals Base and Sugar Requirements for RNA Cleavage of Essential Nucleoside Residues in Internal Loop B of the Hairpin Ribozyme: Implications for Secondary Structure

1996 ◽  
Vol 24 (4) ◽  
pp. 573-581 ◽  
Author(s):  
S. Schmidt ◽  
L. Beigelman ◽  
A. Karpeisky ◽  
N. Usman ◽  
U. S. Sorensen ◽  
...  
Keyword(s):  
Secondary Structure ◽  
Rna Cleavage ◽  
Hairpin Ribozyme ◽  
Internal Loop

Architecture of the U5 small nuclear RNA

1994 ◽  
Vol 14 (3) ◽  
pp. 2180-2190
Author(s):  
D N Frank ◽  
H Roiha ◽  
C Guthrie
Keyword(s):  
Secondary Structure ◽  
Comparative Sequence Analysis ◽  
Fungal Species ◽  
Deletion Analysis ◽  
Small Nuclear Rna ◽  
Stem Loop ◽  
Internal Loop ◽  
Nuclear Rna ◽  
Sequence Elements ◽  
U5 Snrna

We have used comparative sequence analysis and deletion analysis to examine the secondary structure of the U5 small nuclear RNA (snRNA), an essential component of the pre-mRNA splicing apparatus. The secondary structure of Saccharomyces cerevisiae U5 snRNA was studied in detail, while sequences from six other fungal species were included in the phylogenetic analysis. Our results indicate that fungal U5 snRNAs, like their counterparts from other taxa, can be folded into a secondary structure characterized by a highly conserved stem-loop (stem-loop 1) that is flanked by a moderately conserved internal loop (internal loop 1). In addition, several of the fungal U5 snRNAs include a novel stem-loop structure (ca. 30 nucleotides) that is adjacent to stem-loop 1. By deletion analysis of the S. cerevisiae snRNA, we have demonstrated that the minimal U5 snRNA that can complement the lethal phenotype of a U5 gene disruption consists of (i) stem-loop 1, (ii) internal loop 1, (iii) a stem-closing internal loop 1, and (iv) the conserved Sm protein binding site. Remarkably, all essential, U5-specific primary sequence elements are encoded by a 39-nucleotide domain consisting of stem-loop 1 and internal loop 1. This domain must, therefore, contain all U5-specific sequences that are essential for splicing activity, including binding sites for U5-specific proteins.

Chemical synthesis of an artificially branched hairpin ribozyme variant with RNA cleavage activity

Tetrahedron ◽  
2004 ◽  
Vol 60 (41) ◽  
pp. 9273-9281 ◽  
Author(s):  
Sergei A. Ivanov ◽  
Eugene M. Volkov ◽  
Tatiana S. Oretskaya ◽  
Sabine Müller
Keyword(s):  
Chemical Synthesis ◽  
Rna Cleavage ◽  
Hairpin Ribozyme ◽  
Cleavage Activity

scholarly journals Architecture of the U5 small nuclear RNA.

1994 ◽  
Vol 14 (3) ◽  
pp. 2180-2190 ◽  
Author(s):  
D N Frank ◽  
H Roiha ◽  
C Guthrie
Keyword(s):  
Secondary Structure ◽  
Comparative Sequence Analysis ◽  
Fungal Species ◽  
Deletion Analysis ◽  
Small Nuclear Rna ◽  
Stem Loop ◽  
Internal Loop ◽  
Nuclear Rna ◽  
Sequence Elements ◽  
U5 Snrna

We have used comparative sequence analysis and deletion analysis to examine the secondary structure of the U5 small nuclear RNA (snRNA), an essential component of the pre-mRNA splicing apparatus. The secondary structure of Saccharomyces cerevisiae U5 snRNA was studied in detail, while sequences from six other fungal species were included in the phylogenetic analysis. Our results indicate that fungal U5 snRNAs, like their counterparts from other taxa, can be folded into a secondary structure characterized by a highly conserved stem-loop (stem-loop 1) that is flanked by a moderately conserved internal loop (internal loop 1). In addition, several of the fungal U5 snRNAs include a novel stem-loop structure (ca. 30 nucleotides) that is adjacent to stem-loop 1. By deletion analysis of the S. cerevisiae snRNA, we have demonstrated that the minimal U5 snRNA that can complement the lethal phenotype of a U5 gene disruption consists of (i) stem-loop 1, (ii) internal loop 1, (iii) a stem-closing internal loop 1, and (iv) the conserved Sm protein binding site. Remarkably, all essential, U5-specific primary sequence elements are encoded by a 39-nucleotide domain consisting of stem-loop 1 and internal loop 1. This domain must, therefore, contain all U5-specific sequences that are essential for splicing activity, including binding sites for U5-specific proteins.

Essential nucleotide sequences and secondary structure elements of the hairpin ribozyme.

1993 ◽  
Vol 12 (6) ◽  
pp. 2567-2573 ◽  
Author(s):  
A. Berzal-Herranz ◽  
S. Joseph ◽  
B.M. Chowrira ◽  
S.E. Butcher ◽  
J.M. Burke
Keyword(s):  
Secondary Structure ◽  
Nucleotide Sequences ◽  
Hairpin Ribozyme

The Secondary Structure of a Fourteen-Nucleotide Fragment of the Hairpin Ribozyme

1997 ◽  
Vol 232 (2) ◽  
pp. 444-448
Author(s):  
James D. Brinegar ◽  
Arnold Hampel ◽  
Gerald M. Alter ◽  
Phillip Cruz
Keyword(s):  
Secondary Structure ◽  
Hairpin Ribozyme

Effects of Secondary Structure on DNA and RNA Cleavage by Diplatinum(II)†

Biochemistry ◽  
1998 ◽  
Vol 37 (39) ◽  
pp. 13736-13743 ◽  
Author(s):  
Pamela J. Carter ◽  
Klaus M. Breiner ◽  
H. Holden Thorp
Keyword(s):  
Secondary Structure ◽  
Rna Cleavage ◽  
Dna And Rna

scholarly journals Intracellular RNA cleavage by the hairpin ribozyme

1998 ◽  
Vol 26 (15) ◽  
pp. 3494-3504 ◽  
Author(s):  
A. Seyhan
Keyword(s):  
Rna Cleavage ◽  
Hairpin Ribozyme

scholarly journals The influence of junction conformation on RNA cleavage by the hairpin ribozyme in its natural junction form

RNA ◽  
1999 ◽  
Vol 5 (2) ◽  
pp. 180-187 ◽  
Author(s):  
JAMES B. THOMSON ◽  
DAVID M.J. LILLEY
Keyword(s):  
Rna Cleavage ◽  
Hairpin Ribozyme
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