ArticleRNA (New York, N.Y.)2005
Functional characterization of the SOFA delta ribozyme.
Article in RNA (New York, N.Y.), 2005. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 papers.
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Who cites it
14 citing papers in PubMed.
- Design and testing of Hepatitis Delta Ribozymes for suppression of Chikungunya virus infection in cell cultures.Medical research archives · 2024Article
- Topological constraints of structural elements in regulation of catalytic activity in HDV-like self-cleaving ribozymes.Scientific reports · 2016Article
- Effective inhibition of HIV-1 production by short hairpin RNAs and small interfering RNAs targeting a highly conserved site in HIV-1 Gag RNA is optimized by evaluating alternative length formats.Antimicrobial agents and chemotherapy · 2015Article
- A Conserved Target Site in HIV-1 Gag RNA is Accessible to Inhibition by Both an HDV Ribozyme and a Short Hairpin RNA.Molecular therapy. Nucleic acids · 2014Article
- Prospects for nucleic acid-based therapeutics against hepatitis C virus.World journal of gastroenterology · 2013Review
- Silencing of amyloid precursor protein expression using a new engineered delta ribozyme.International journal of Alzheimer's disease · 2012Article
- Selection of the most potent specific on/off adaptor-hepatitis delta virus ribozymes for use in gene targeting.Nucleic acid therapeutics · 2011Article
- Molecular Validation of PACE4 as a Target in Prostate Cancer.Translational oncology · 2011Article
- Article
- Modulating RNA structure and catalysis: lessons from small cleaving ribozymes.Cellular and molecular life sciences : CMLS · 2009Review
- Development of an isoform-specific gene suppression system: the study of the human Pax-5B transcriptional element.Nucleic acids research · 2008Article
- A modern mode of activation for nucleic acid enzymes.PloS one · 2007Article
- RiboSubstrates: a web application addressing the cleavage specificities of ribozymes in designated genomes.BMC bioinformatics · 2006Article
- Gene targeting in the Gram-Positive bacterium Lactococcus lactis, using various delta ribozymes.Applied and environmental microbiology · 2006Article
Corrections and comments
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Authors and funding
3 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Molecular engineering has led to the development of a novel target-dependent riboswitch that increases deltaribozyme fidelity. This delta ribozyme possesses a specific on/off adapter (SOFA) that switches the cleavage activity from off (a "safety lock") to on solely in the presence of the desired RNA substrate. In this report, we investigate the influence of both the structure and the sequence of each domain of the SOFA module. Analysis of the cleavage activity, using a large collection of substrates and SOFA-ribozyme mutants, together with RNase H probing provided several insights into the nature of the sequence and the optimal design of each domain of the SOFA module. For example, we determined that (1) the optimal size of the blocker sequence, which keeps the ribozyme off in the absence of the substrate, is 4 nucleotides (nt); (2) a single nucleotide difference between the substrate and the biosensor domain, which is responsible for the initial binding of the substrate that subsequently switches the SOFA-ribozyme on, is sufficient to cause non-recognition of the appropriate substrate; (3) the stabilizer, which joins the 5' and 3' ends of the SOFA-ribozyme, plays only a structural role; and (4) the optimal spacer sequence, which serves to separate the binding regions of the biosensor and catalytic domain of the ribozyme on the substrate, is from 1 to 5 nt long. Together, these data should facilitate the design of more efficient SOFA-ribozymes with significant potential for many applications in gene-inactivation systems.
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