Targeted nucleotide exchange in the CAG repeat region of the human HD gene

Targeted nucleotide exchange in bovine myostatin gene

The myostatin gene, known as Growth Differentiation Factor 8 (GDF8), located at chromosome 2 (BTA2) in cattle, is specifically expressed during embryo development and in the adult skeletal muscle. Molecular analysis of this gene reveals the presence of three exons and two introns. Several cattle breeds, such as Piedmontese, Belgian Blue, Blond'Aquitaine, among others, show polymorphisms in this gene, which are directly related to double muscling phenotype. Piedmontese cattle shows a nucleotide transition G --> A (G938A) at exon 3, resulting in the substitution of cysteine to tyrosine, leading to a protein structure change, which determines myostatin inactivation and consequent muscular hypertrophy. The objective of this work was to implant the polymorphism G938A, naturally existent in Piedmontese breed, into in vitro propagated foetal myoblasts, from Nellore cattle. Single strand DNA (ssDNA) oligonucleotides were used to direct the same nucleotidic transition (G938A) to exon 3. Two transfection protocols (cationic lipid solution and electroporation) were tested and, 48 hours after transfection, RNA and DNA were extracted from myoblasts. Reverse transcription and polymerase chain reaction (PCR) were performed, using primers flanking the mutation region. The PCR products were cloned and analyzed by DNA sequencing, and it was possible to detect the nucleotidic CT transition at position 938, in the electroporated myoblasts. The existence of a positive signal in the transfection indicates that ssDNA oligonucleotides can be used to introduce this point mutation in specific functional gene sites.

Site-specific strand bias in gene correction using single-stranded oligonucleotides

Targeted gene editing mediated by chimeric RNA-DNA oligonucleotides (RDOs) or single-stranded oligo-deoxyribonucleotides (ssODNs) has been demonstrated in a wide variety of cell types both in vitro and in vivo. In this study we investigated the correlation between the polarity of the used oligonucleotides and the obtained correction frequency in targeted ssODN-mediated correction of two G>A mutations (introduced at positions 659 and 1567, respectively) in an episomal beta-galactosidase gene. At position 659 the highest correction efficiency was observed using an ssODN complementary to the transcribed strand of the target gene. In contrast, at position 1567 the highest correction frequency was observed using an ssODN complementary to the nontranscribed strand of the target gene. It has been reported that site-specific gene editing mediated by ssODNs targeting the nontranscribed strand of the target gene results in a higher gene editing frequency, and it has been suggested that steric hindrance or displacement of ssODNs by traversing transcription complexes prevents efficient targeting of the transcribed strand. However, the results of the present study demonstrate that occupancy by transcriptional complexes alone does not dictate strand bias in ssODN-mediated gene editing, and that the sequences surrounding the targeted nucleotide may profoundly influence strand bias. This finding has important implications for the design of optimal ssODNs for targeted editing of a given nucleotide sequence.

Concurrent targeted exchange of three bases in mammalian hprt by oligonucleotides

The repair of point mutations in hprt gene by single-stranded oligonucleotides represents a model to test targeted nucleotide exchange. We studied the concurrent nucleotide exchange of two or three nucleotides in the hprt deficient hamster cell line V79-151. The used oligonucleotides resulted in mismatches at two (151, 159) or three (151, 144, and 159) hprt positions. The hprt point mutation at position 151 was repaired in about 2/10(6) cells as shown by hprt sequencing in clones surviving HAT selection. The second nucleotide exchange at hprt position 159 was found in 7% of these HAT selected clones. Using oligonucleotides resulting in three mismatches, 29% of the clones showed nucleotide exchanges at the two hprt positions (151, 144) and about 4% at three positions (151, 144, and 159). These results indicate that single-stranded oligonucleotides can generate two or three nucleotide exchanges in a mammalian chromosomal gene.