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Genomics is the science of genomes: it is the study of all the genetic material of an organism. In humans, the genome consists of information carried in 23 pairs of chromosomes in the nucleus, as well as mitochondrial DNA. In genomics, both coding and non-coding DNA is sequenced and analyzed. Genomics allows a better understanding of all living things, their evolution, and their diversity. It has a myriad of uses: for example, to build phylogenetic trees, to improve productivity and...
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A partial fraction is a component of a rational expression represented as the sum of simpler fractions. When a rational function is expressed as a ratio of two polynomials, it can often be decomposed into a sum of fractions whose denominators are simpler polynomials, typically linear or irreducible quadratic factors. This process is called partial fraction decomposition, and it is used to simplify complex expressions for integration, solving equations, or analysis.Partial fraction decomposition...
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While every living organism has a genome of some kind (be it RNA, or DNA), there is considerable variation in the sizes of these blueprints. One major factor that impacts genome size is whether the organism is prokaryotic or eukaryotic. In prokaryotes, the genome contains little to no non-coding sequence, such that genes are tightly clustered in groups or operons sequentially along the chromosome. Conversely, the genes in eukaryotes are punctuated by long stretches of non-coding sequence.
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Genome-wide Gene Deletions in Streptococcus sanguinis by High Throughput PCR
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Stepwise partially overlapping primer-based PCR for genome walking.

Kunpeng Chang1, Qiong Wang1, Xiaofei Shi2

  • 1State Key Laboratory of Food Science and Technology, Sino-German Joint Research Institute, Nanchang University, Nanchang, 330047, Jiangxi, China.

AMB Express
|May 11, 2018
PubMed
Summary
This summary is machine-generated.

A novel stepwise partially overlapping primer-based PCR (SWPOP-PCR) method efficiently isolates unknown flanking DNA regions. This technique enhances specificity and yield for applications in microbial and plant genomics.

Keywords:
Genome walkingPCRPartially overlapping primergadA locushyg

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Area of Science:

  • Molecular Biology
  • Genomics
  • Biotechnology

Background:

  • Isolating unknown flanking DNA regions is crucial for gene characterization and genome analysis.
  • Traditional methods can suffer from low efficiency and nonspecific amplification.

Purpose of the Study:

  • To develop a novel PCR-based method for efficient isolation of flanking unknown DNA regions.
  • To enhance specificity and reduce nonspecific amplification in DNA isolation.

Main Methods:

  • Developed a stepwise partially overlapping primer-based PCR (SWPOP-PCR) method.
  • Utilized three rounds of nested PCR with specific primer pairs.
  • Employed SWPOP primers with a 10 bp partial overlap for selective annealing at low temperatures.

Main Results:

  • SWPOP-PCR successfully isolated flanking DNA sequences for the glutamate decarboxylase gene (gadA) in Lactobacillus brevis NCL912.
  • The method also obtained sequences for the hygromycin gene (hyg) integrated in rice.
  • Demonstrated preferential synthesis of target products and inhibition of nonspecific amplification.

Conclusions:

  • SWPOP-PCR is an effective technique for isolating flanking unknown DNA regions.
  • The method offers improved specificity and efficiency compared to conventional approaches.
  • Applicable to diverse genomic research in bacteria and plants.