Live-cell PCR and one-step purification streamline DNA engineering

Improved live-cell PCR method for detection of organophosphates degrading opd genes and applications

Organophosphates are becoming an emerging pollutant due to their various applications, particularly as pesticides. In this study, an improved Colony (Live-cell) PCR method was developed for the detection of opd genes from bacteria encoding the organophosphate hydrolase enzymes capable of degrading various organophosphates. The improved method does not require pre-heating or pre-lysis of bacterial cells as essential in the conventional colony PCR. The reaction volume was scaled down to 10 µl by optimizing the PCR buffer and amplification conditions. The improved method was used for Gram positive and negative bacteria, glycerol stocks, liquid cultures, recombinant and mutant strains. Also, 16S rRNA gene was amplified from unknown environmental isolates and known E. coli strains. The amplified opd and 16S rRNA genes from the improved colony PCR method and by conventional PCR were sequenced, and similar results were obtained from both techniques. Thus, the improved method can be further explored in molecular biology or during biomarker studies. KEY POINTS: • Improved colony PCR method was developed for screening of opd genes from bacteria. • Method was validated for Gram positive/negative bacteria from solid as well as liquid media. • The improved method was rapid, efficient, and can be applied under various conditions.

DNA gap repair in Escherichia coli for multiplex site-directed mutagenesis

Site-directed mutagenesis allows the generation of novel DNA sequences that can be used for a variety of important applications such as the functional analysis of genetic variants. To overcome the limitations of existing site-directed mutagenesis approaches, we explored in vivo DNA gap repair. We found that site-specific mutations in plasmid DNA can be generated in Escherichia coli using mutant single-stranded oligonucleotides to target PCR-derived linear double-stranded plasmid DNA. We called this method DeGeRing, and we characterized its advantages, including non-biased multiplex mutagenesis, over existing site-directed mutagenesis methods such as recombineering (recombination-mediated genetic engineering), single DNA break repair (SDBR, introduced by W. Mandecki), and QuikChange (Agilent Technologies, La Jolla, CA). We determined the efficiency of DeGeRing to induce site-directed mutations with and without a phenotype in three K-12 E coli strains using multiple single-stranded oligonucleotides containing homological and heterological parts of various sizes. Virtual lack of background made the isolation of mutants with frequencies up to 10^-6 unnecessary. Our data show that endogenous DNA gap repair in E coli supports efficient multiplex site-directed mutagenesis. DeGeRing might facilitate the generation of mutant DNA sequences for protein engineering and the functional analysis of genetic variants in reverse genetics.