Time-Resolved Förster Resonance Energy Transfer Analysis of Single-Nucleotide Polymorphisms: Towards Molecular Typing of Genes on Non-Purified and Non-PCR-Amplified DNA

Luca Nardo, Nicola Camera, Edoardo Totè, Maria Bondani, Roberto S. Accolla, Giovanna Tosi


Quantitative assessment of the fluorescence resonance energy transfer (FRET) efficiency between chromophores labeling the opposite ends of gene-specific oligonucleotide probes is a powerful tool to detect DNA polymorphisms with single-nucleotide resolution. The FRET efficiency can be most conveniently quantified by applying a time-resolved fluorescence analysis methodology, time-correlated single-photon counting. Recently, we probed by such technique the highly polymorphic DQB1 human gene. Namely, by using a single oligonucleotide probe and acting on non-amplified DNA samples contained in untreated cell extracts, we demonstrated the ability of pursuing unambiguous recognition of subjects bearing the homozygous DQB1-0201 genotype by exploiting the subtle, yet statistically significant, structural differences between the duplex formed by the probe with DQB1-0201 on the one end and duplexes formed with any of the other alleles, on the other end. The relevance of homozygous DQB1-0201 genotype recognition reseeds in the fact that the latter is overexpressed in subjects affected by insulin-dependent diabetes mellitus in north-eastern Italy.

In this article we review our preceding achievements and report on additional in-vitro experiments aimed at characterizing the duplexes obtained by annealing of the DQB1 allelic variants with a second oligonucleotide probe, with the final scope to achieve full genotyping of DQB1 on raw DNA samples by means of cross-combination of the FRET responses of both probes.

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DOI: https://doi.org/10.5539/jmbr.v3n1p15


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