Abstract
The majority of studies employing short tandem repeats (STRs) require investigation of several of these genetic markers. As such, we demonstrate the feasibility of the trinucleotide threading (TnT) approach for scalable analysis of STRs. The TnT method represents a parallel amplification alternative that addresses the obstacles associated with multiplex PCR. In this study, analysis of the STR fragments was performed with capillary gel electrophoresis; however, it should be possible to combine our approach with the massive 454 sequencing platform to considerably increase the number of targeted STRs.
Highlights
Microsatellites, or short tandem repeats (STRs), are abundant 1–6 bp nucleotide motifs repeated in a tandem fashion in genomes from all classes of organisms, ranging from prokaryotes to eukaryotes [1,2]
As trinucleotide threading (TnT) has been shown to amplify desired DNA regions, it could address the inherent limitations of multiplex PCR and, enable larger STR sets to be amplified in a parallel fashion
The three markers – TPOX, CSF1PO and D18S51 – were chosen among the ones of the FBI Combined DNA Index System (CODIS) set and represent tetra-repeats assembled of A, G and T nucleotides
Summary
Microsatellites, or short tandem repeats (STRs), are abundant 1–6 bp nucleotide motifs repeated in a tandem fashion in genomes from all classes of organisms, ranging from prokaryotes to eukaryotes [1,2]. The most widely employed method involves PCR amplification and fragment analysis by gel electrophoresis. In this proof-of-concept study, three markers from the FBI CODIS set were assayed with TnT to evaluate this approach for parallel amplification of STRs. Results and Discussion
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