Determination of Repeat Numbers of (CA)n in Mitochondrial D-loop using Polymerase Chain Reaction-single Strand Conformational Polymorphism (PCR-SSCP)

Kim, Joo-Young; Kim, Dae-Kwang

doi:10.11637/kjpa.2018.31.3.77

Cited by 1 publication

(1 citation statement)

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“…8,9 It is worth mentioning that in addition to being valuable for the determination of intraspecies variation, 10 both techniques have been employed in species identification and differentiation. Furthermore, both techniques have been used to differentiate many organisms to species level by the amplification of a conserved region of the mitochondrial D-loop, 11,12 ribosomal regions, 13,14 or other genetic loci. 15,16 However, although PCR-SSCP can be applied to any gene in any organism, PCR-RFLP has less spectrum superiority.…”

Section: Introductionmentioning

confidence: 99%

Exploring the Potential and Limitations of PCR-RFLP and PCR-SSCP for SNP Detection: A Review

Hashim

Al-Shuhaib

2019

J Apple Biotechnol Rep

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Polymerase chain reaction-single-strand conformation polymorphism (PCR-SSCP) and PCR-restriction fragment length polymorphism (PCR-RFLP) are two independent methods used in the post-amplification genotyping of DNA variations. Both techniques are used in a wide range of screening applications to characterize single nucleotide polymorphisms (SNPs). The PCR-SSCP enables the identification of a potentially causative unknown SNP that could not be identified by PCR-RFLP. However, because complicated steps are not required to perform PCR-RFLP, it is used in many applications. On the other hand, PCR-RFLP is easier to process in terms of time and handover experience, the detection of a particular unknown SNP by PCR-SSCP has further chances. The simplicity of PCR-RFLP does not mean that it is better than PCR-SSCP. The reason is the limited ability of PCR-RFLP to detect nucleotide variations, which often go undetected because each restriction enzyme (RE) scans only a few recognition sequences, and other sequences are ignored. Furthermore, the efficacy of PCR-SSCP is sometimes hindered by many optimizations and also lack of experience. As PCR-SSCP allows other sequences within an amplicon to be separated and characterized, the choice between PCR-RFLP and PCR-SSCP is largely dependent on the reason for each genotyping experiment. This review provides a useful guide for comparing PCR-RFLP and PCR-SSCP in terms of their concepts, efficiency, ease of use, interpretation, and sensitivity as well as several other parameters. The comparison is extended to the practical applications of both techniques in terms of their utilization in molecular diagnostics and related applications.

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