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According to the principles of GenomeLab™ GeXP Genetic Analysis System, we designed 20 pairs of multiplex gene-specific primer with a tag for the 20 genes in S. cerevisiae strain W303-1A and 1 pair of universal primer by using Beacon Designer 2.0 software (Bio-Rad, USA) (Table S1).
Two microliters of the eluted DNA were used for reamplification with the GC-clamped primer by using the conditions described above and the PCR products generated were checked by DGGE.
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In this study we have characterized antibiotic resistance gene cassette arrays in class 1 integrons that could not be amplified using standard PCR primers, by using primer pairs that target the intI1 gene and IS26.
The method detailed in our work avoids the use of any HIV sequence specific primers by using a combination of oligodT and random hexamers that prime throughout the genome.
For 4 of the 5 genes (exception rpoC gene), their fragments could be sequenced directly in both directions with the PCR primers by using the ABI prism 3130xl instrument.
We designed other primers by using PyroMark Assay Design 2.0 (Qiagen, Germany).
Amplification products were separated from unused primers by using QIAquick 96 PCR purification cartridges (Qiagen, with modified binding and wash buffers).
A primer compatibility test was performed for all the primers by using the software developed in our laboratory [ 4, 45] to avoid primer-primer interactions during multiplex PCR.
Nucleotide sequences of PCR products were determined with PCR primers by using an automated DNA sequencer (ABI Prism 377A; Perkin-Elmer Applied Biosystems, Foster City, CA, USA).
These results indicate that designing PCR primers by using a lacZ consensus sequence as a target might widen the spectrum of coliform detection.
AqGATA gene fragments were amplified with gene specific primers, by using complimentary DNA from mixed developmental stages as a PCR template.
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