title: Full genotyping of a highly polymorphic human gene trait by time-resolved fluorescence resonance energy transfer.
abstract: The ability of detecting the subtle variations occurring, among different individuals, within specific DNA sequences encompassed in highly polymorphic genes discloses new applications in genomics and diagnostics. DQB1 is a gene of the HLA-II DQ locus of the Human Leukocyte Antigens (HLA) system. The polymorphisms of the trait of the DQB1 gene including codons 52-57 modulate the susceptibility to a number of severe pathologies. Moreover, the donor-receiver tissue compatibility in bone marrow transplantations is routinely assessed through crossed genotyping of DQB and DQA. For the above reasons, the development of rapid, reliable and cost-effective typing technologies of DQB1 in general, and more specifically of the codons 52-57, is a relevant although challenging task. Quantitative assessment of the fluorescence resonance energy transfer (FRET) efficiency between chromophores labelling the opposite ends of gene-specific oligonucleotide probes has proven to be a powerful tool to type DNA polymorphisms with single-nucleotide resolution. The FRET efficiency can be most conveniently quantified by applying a time-resolved fluorescence analysis methodology, i.e. time-correlated single-photon counting, which allows working on very diluted template specimens and in the presence of fluorescent contaminants. Here we present a full in-vitro characterization of the fluorescence responses of two probes when hybridized to oligonucleotide mixtures mimicking all the possible genotypes of the codons 52-57 trait of DQB1 (8 homozygous and 28 heterozygous). We show that each genotype can be effectively tagged by the combination of the fluorescence decay constants extrapolated from the data obtained with such probes.
authors.affiliation: Department of Science and High Technology, University of Insubria, Como, Italy.
authors.forename: Edoardo
authors.initials: E
authors.lastname: Totè
authors.affiliation: Department of Science and High Technology, University of Insubria, Como, Italy.
authors.forename: Marco
authors.initials: M
authors.lastname: Lamperti
authors.affiliation: C. N. R. (Consiglio Nazionale delle Ricerche), Institute for Photonics and Nanotechnology, Como, Italy.
authors.forename: Maria
authors.initials: M
authors.lastname: Bondani
authors.affiliation: Department of Health Sciences, University of Milan Bicocca, Monza, Italy.
authors.forename: Domenico
authors.initials: D
authors.lastname: Salerno
authors.affiliation: Department of Health Sciences, University of Milan Bicocca, Monza, Italy.
authors.forename: Valeria
authors.initials: V
authors.lastname: Cassina
authors.affiliation: Department of Health Sciences, University of Milan Bicocca, Monza, Italy.
authors.forename: Luca
authors.initials: L
authors.lastname: Nardo
mesh_terms: D000483:Alleles; D016026:Bone Marrow Transplantation; D031541:Fluorescence Resonance Energy Transfer / Q000379:methods*; D005838:Genotype; D060005:Genotyping Techniques / Q000379:methods*; D059866:HLA-DQ beta-Chains / Q000235:genetics*; D006801:Humans; D009841:Oligonucleotides / Q000235:genetics; D010641:Phenotype; D020641:Polymorphism, Single Nucleotide / Q000235:genetics
chemical_list: D059866:HLA-DQ beta-Chains; C069051:HLA-DQB1 antigen; D009841:Oligonucleotides