Primer annealing

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  • The term DNA sequencing refers to methods for determining the order of the nucleotides bases adenine,guanine,cytosine and thymine in a molecule of DNA. The first DNA sequence were obtained by academic researchers,using laboratories methods based on 2- dimensional chromatography in the early 1970s. By the development of dye based sequencing method with automated analysis,DNA sequencing has become easier and faster.

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  • Automated DNA sequencing is a core research tool used by almost every research biochemistry lab. It is used to determine the sequence of DNA, or the genetic code, that serves as the blueprint of life for every organism on Earth.

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  • The utility of primer pairs in SCoTs was advocated by Gorji et al. (2011). SCoT markers are generally reproducible, and it is suggested that primer length and annealing temperature are not the sole factors determining reproducibility (Gorji et al., 2011). They are dominant markers, however, while a number of co-dominant markers are also generated during amplification, and thus they could be used for genetic diversity analysis (Collard & Mackill, 2009b). This has been validated through study of genetic diversity among rice varieties (Collard & Mackill, 2009b).

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  • Molecular markers from the transcribed region of the genome can offer potential for various applications in plant genotyping as they reveal polymorphisms that might be directly related to gene function. A novel marker system called Start Codon Targeted Polymorphism (SCoT) was described by Collard & Mackill (2009b), based on the observation that the short conserved regions of plant genes are surrounded by the ATG translation start codon (Sawant et al., 1999). The technique uses single primers designed to anneal to the flanking regions of the ATG initiation codon on both DNA strands.

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