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For gene therapy of inherited diseases, targeted integration͞gene repair through homologous recombination (HR) between exogenous and chromosomal DNA would be an ideal strategy to avoid potentially serious problems of random integration such as cellular transformation and gene silencing. Efficient sequence-specific modification of chromosomes by HR would also advance both biological studies and therapeutic applications of a variety of stem cells. Toward these goals, we developed an improved strategy of adenoviral vector (AdV)-mediated HR and examined its ability to correct an insertional mutation in the hypoxanthine phosphoribosyl transferase (Hprt) locus in male mouse ES cells. The efficiency of HR was compared between four types of AdVs that contained various lengths of homologies at the Hprt locus and with various multiplicities of infections. The frequency of HR with helperdependent AdVs (HD AdVs) with an 18.6-kb homology reached 0.2% per transduced cell at a multiplicity of infection of 10 genomes per cell. Detection of random integration at DNA levels by PCR revealed extremely high efficiency of 5% per cell. We also isolated and characterized chromosomal sites where HD AdVs integrated in a random manner. In contrast to retroviral, lentiviral, and adeno-associated viral vectors, which tend to integrate into genes, the integration sites of AdV was distributed randomly inside and outside genes. These findings suggest that HR mediated by HD AdVs is efficient and relatively safe and might be a new viable option for ex vivo gene therapy as well as a tool for chromosomal manipulation of a variety of stem cells.gene therapy ͉ homologous recombination ͉ hypoxanthine phosphoribosyl transferase
For gene therapy of inherited diseases, targeted integration͞gene repair through homologous recombination (HR) between exogenous and chromosomal DNA would be an ideal strategy to avoid potentially serious problems of random integration such as cellular transformation and gene silencing. Efficient sequence-specific modification of chromosomes by HR would also advance both biological studies and therapeutic applications of a variety of stem cells. Toward these goals, we developed an improved strategy of adenoviral vector (AdV)-mediated HR and examined its ability to correct an insertional mutation in the hypoxanthine phosphoribosyl transferase (Hprt) locus in male mouse ES cells. The efficiency of HR was compared between four types of AdVs that contained various lengths of homologies at the Hprt locus and with various multiplicities of infections. The frequency of HR with helperdependent AdVs (HD AdVs) with an 18.6-kb homology reached 0.2% per transduced cell at a multiplicity of infection of 10 genomes per cell. Detection of random integration at DNA levels by PCR revealed extremely high efficiency of 5% per cell. We also isolated and characterized chromosomal sites where HD AdVs integrated in a random manner. In contrast to retroviral, lentiviral, and adeno-associated viral vectors, which tend to integrate into genes, the integration sites of AdV was distributed randomly inside and outside genes. These findings suggest that HR mediated by HD AdVs is efficient and relatively safe and might be a new viable option for ex vivo gene therapy as well as a tool for chromosomal manipulation of a variety of stem cells.gene therapy ͉ homologous recombination ͉ hypoxanthine phosphoribosyl transferase
Understanding and manipulation of the forces assembling DNA/ RNA helices have broad implications for biology, medicine, and physics. One subject of significance is the attractive force between dsDNA mediated by polycations of valence ≥3. Despite extensive studies, the physical origin of the "like-charge attraction" remains unsettled among competing theories. Here we show that triplestrand DNA (tsDNA), a more highly charged helix than dsDNA, is precipitated by alkaline-earth divalent cations that are unable to condense dsDNA. We further show that our observation is general by examining several cations (Mg 2þ , Ba 2þ , and Ca 2þ ) and two distinct tsDNA constructs. Cation-condensed tsDNA forms ordered hexagonal arrays that redissolve upon adding monovalent salts. Forces between tsDNA helices, measured by osmotic stress, follow the form of hydration forces observed with condensed dsDNA. Probing a well-defined system of point-like cations and tsDNAs with more evenly spaced helical charges, the counterintuitive observation that the more highly charged tsDNA (vs. dsDNA) is condensed by cations of lower valence provides new insights into theories of polyelectrolytes and the biological and pathological roles of tsDNA. Cations and tsDNAs also hold promise as a model system for future studies of DNA-DNA interactions and electrostatic interactions in general.DNA condensation | small angle X-ray diffraction H ighly charged DNA helices naturally repel each other under physiological conditions (1). However, cations of valence ≥3 very effectively condense DNA at micromolar concentrations (2). The most studied systems are the condensation of dsDNA with cobalt 3þ hexammine and the biogenic polyamines (spermidine 3þ and spermine 4þ ), whereas polymer-based cations are being exploited as DNA packaging agents for gene delivery (3). In contrast, nonspecifically interacting monovalent and divalent cations [i.e., excluding base-coordinating transition-metal ions (4) such as Mn 2þ , Ni 2þ , and Cu 2þ ], even at molar concentrations, do not condense dsDNA from dilute solution (2). The prominent role of cation valence has promoted electrostatic interaction as the primary candidate to explain this multivalent cation mediated DNA-DNA attraction (1). Whereas it is clear that further considerations must be made beyond the mean field PoissonBoltzmann (PB) treatment, which always predicts like-charge repulsion, the physical basis for DNA condensation is still under intensive debate (5).The multifaceted nature of DNA-ion interactions and of possible DNA-ion-DNA correlations between apposing helices has led to theories that differ greatly in starting assumptions. For instance, counterions have been treated either as continuous ionic "clouds" or as discrete point-like cations of finite radius; the DNA helix has been modeled as a continuously charged rod or to have discretely charged phosphates placed on a helical path around a smooth rod. As a result, a number of competing theories have been proposed to explain cation mediated DNA-DNA attraction....
SummaryThe correction of an inactivated hygromycin-resistance and enhanced green fluorescent protein (Hyg-EGFP) fusion gene by a several hundred-base single-stranded (ss) DNA fragment has been reported. In this study, the effectiveness of this type of gene correction was examined for various positions in the rpsL gene. Sense and antisense ss DNA fragments were prepared, and the gene correction efficiencies were determined by co-introduction of the target plasmid containing the gene with the ss DNA fragments. The gene correction efficiency varied (0.8-9.3%), depending on target positions and sense/antisense strands. Sense ss DNA fragments corrected the target gene with equal or higher efficiencies as compared to their antisense counterparts. The target positions corrected with high efficiency by the sense fragments also tended to be corrected efficiently by the antisense fragments. These results suggest that the sense ss DNA fragments are useful for the correction of mutated genes. The variation in the correction efficiency may depend on the sequence of the target position in double-stranded DNA.Key Words: gene correction; single-stranded DNA fragment; nucleic acid therapeutics; genetic engineering; rpsL gene. 3Gene correction (nucleotide sequence conversion), by which a mutated gene is converted to one with the normal (or desired) sequence, is an attractive strategy for gene therapy (1-10). Disruption of a gene involved in maintenance of a disease could be conducted with this technology. The corrected genes can be expressed under the control of their authentic regulatory elements. Moreover, gain-of-function or dominant mutations, such as activated oncogenes, could be suitable subjects for the gene correction strategy. Various kinds of devices, such as ss oligonucleotides, triplex-forming oligonucleotides, and heat-denatured, 400-800 bp ds PCR fragments, have been examined as nucleic acid tools for gene correction (1-10).Previously, it was reported that a several hundred-base ss DNA fragment containing the sense sequence, prepared by restriction enzyme digestions of ss phagemid DNA, corrected an inactivated episomal Hyg-EGFP fusion gene with higher gene correction efficiency, in comparison with the conventional PCR fragment (11). In contrast, the correction with the ss DNA fragment containing the antisense sequence was less efficient than that with the sense ss DNA fragment.These results raised the questions of whether ss DNA fragments could be used to correct different target sequences and whether sense fragments are more efficient than the corresponding antisense fragments for other target sequences. In this study, we chose the rpsL (bacterial streptomycin-resistance) gene as the target gene. The gene encodes the S12 protein, one of the small subunit proteins of the E. coli ribosome. Specific mutations at various positions in the rpsL gene confer streptomycin-resistant phenotype (strA) to bacteria. The E. coli strA strain harboring the plasmid with the wild-type rpsL gene exhibits the streptomycin-sensitive phe...
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