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Y Prasad

Publications and source records attributed to Y Prasad.

5 recordsLinked to original sources

CNS-Specific Ribozyme Expression

Targeted genetic deletion is a powerful tool for analysis of gene function, but the standard approaches carry certain inescapable disadvantages. First, deletion is ubiquitous; tissue-specific knockout cannot be obtained. Second, temporal regulation of depletion is unattainable; the deleted functions are absent throughout the animal's development. As a consequence, during ontogeny, other gene products may be able to compensate, filling the functional gap. Furthermore bifunctional proteins exist that fulfill one role during development and another in the mature organism; deletion will remove the early function and, if this is lethal, the later function will remain undetected. Third, if genes utilize alternative splicing to control protein expression, it is difficult to target one spliced mRNA while leaving intact its related, but different, siblings. We review how these problems may be circumvented using ribozymes to diminish gene expression in a tissue-specific and temporally regulated manner and provide guidelines for the design and delivery of active ribozymes in vivo. Such methods may be particularly useful for analysis of genes involved in ontogeny and function of the central nervous system, in which individual genes may be expressed with alternative splicing patterns, or at differentially regulated levels, at different stages of CNS development.

Journal Article

Evidence that alternate foldings of the hepatitis delta RNA confer varying rates of self-cleavage.

The pentapurine sequence GGAGA, located between 80 and 84 nucleotides downstream of the cleavage site in the self-cleaving antigenomic RNA of hepatitis delta virus, is necessary for highly efficient cleavage and for stability in up to 20 M formamide. Yet much of the cleavage activity lost upon its removal from the 3' end of an 84-nucleotide RNA can be restored by elongation of the 5' end of the RNA with the polypyrimidine sequence found in the virus. We propose that this sequence alteration causes a refolding of the RNA, resulting in a "structural compensation" of the active core of the molecule. Restoration of the self-cleavage activity did not restore the ability to cleave in high concentrations of formamide. Deletion mutagenesis was carried out and supported the alternate RNA folding. The ability to assume more than one active conformation and for one RNA structure to compensate for another in supporting ribozyme activity may be unique to RNA enzymes and could be a useful adaptation in viruses or in prebiotic RNAs.

Base Sequence

Deriving a 67-nucleotide trans-cleaving ribozyme from the hepatitis delta virus antigenomic RNA.

RNAs derived from the genomic and antigenomic hepatitis delta virus are capable of self-cleavage, and thus have the potential for serving as ribozymes in a trans-cleaving reaction. Because the catalytic core of such an enzymatic RNA was not evident from phylogenetic data, we took a step-wise approach to identifying the core, reducing the RNA in size, and characterizing various properties for each size class. Thus, a 186-nucleotide antigenomic RNA (termed Ag180) was found to be capable of cleaving well in 20 M formamide (Smith and Dinter-Gottlieb, 1991), and this unusual stability in formamide was lost by reducing the 3' end of the molecule, leaving a 140-nucleotide RNA (Ag 140). Both RNAs showed only intramolecular cleavage at a wide range of concentrations, and a number of conformers could be seen in the Ag140 RNA, some of which were resistant to cleavage at 37 degrees C. Since Ag140 could not cleave in 20 M formamide, the 5' and 3' termini of Ag180 were truncated and produced Ag5-84, which cleaved to 100% at 37 degrees C in less than 0.25 min. Internal deletions of the Stem IV region resulted in Ag5-73, still capable of efficient cleavage, although with a lessened stability in formamide. A trans-cleaving enzyme-substrate pair was finally derived from this RNA, and it consisted of a 67-nucleotide enzyme that cleaved a 13-nucleotide RNA substrate.

Base Sequence