Closed-tube human leukocyte antigen DQA1∗05 genotyping assay based on switchable lanthanide luminescence probes

Lehmusvuori, Ari; Ilonen, Jorma; Soukka, Tero

doi:10.1016/j.ab.2014.07.029

Cited by 3 publications

(2 citation statements)

References 31 publications

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“…Targets of interest include specific sequences of genomic DNA, protein-coding mRNA, and regulatory RNA such as microRNA, among others. − Oligonucleotide probes are almost exclusively used for these assays because of their inherently selective and high-affinity binding to complementary sequences and the widely available chemical synthesis of oligonucleotide probes with modifications such as unnatural bases and backbones, linkers, and fluorescent dyes. , Fluorescence-based hybridization assays with oligonucleotide probes, including those utilizing Förster resonance energy transfer (FRET), , are among the most popular assay formats because they offer high sensitivity, multiplexing capability, multimodal detection (e.g., intensity, lifetime, polarization), and measurement-at-a-distance. Nonetheless, these assays have often been limited by the shortcomings of fluorescent dyes, prompting the development of assays with novel or nontraditional luminescent materials such as fluorescent polymers, , quantum dots, , metal nanoclusters, , upconversion nanoparticles , luminescent lanthanide complexes (LLCs), − and combinations of these materials. , These materials can either replace fluorescent dyes or be used in tandem with dyes to enhance assay capabilities.…”

mentioning

confidence: 99%

Time-Resolved Nucleic Acid Hybridization Beacons Utilizing Unimolecular and Toehold-Mediated Strand Displacement Designs

Massey

Ancona²,

Medintz³

et al. 2015

Anal. Chem.

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Nucleic acid hybridization probes are sought after for numerous assay and imaging applications. These probes are often limited by the properties of fluorescent dyes, prompting the development of new probes where dyes are paired with novel or nontraditional luminescent materials. Luminescent terbium complexes are an example of such a material, and these complexes offer several unique spectroscopic advantages. Here, we demonstrate two nonstem-loop designs for light-up nucleic acid hybridization beacons that utilize time-resolved Förster resonance energy transfer (TR-FRET) between a luminescent Lumi4-Tb cryptate (Tb) donor and a fluorescent reporter dye, where time-resolved emission from the dye provides an analytical signal. Both designs are based on probe oligonucleotides that are labeled at their opposite termini with Tb and a fluorescent reporter dye. In one design, a probe is partially blocked with a quencher dye-labeled oligonucleotide, and target hybridization is signaled through toehold-mediated strand displacement and loss of a competitive FRET pathway. In the other design, the intrinsic folding properties of an unblocked probe are utilized in combination with a temporal mechanism for signaling target hybridization. This temporal mechanism is based on a recently elucidated "sweet spot" for TR-FRET measurements and exploits distance control over FRET efficiencies to shift the Tb lifetime within or outside the time-gated detection window for measurements. Both the blocked and unblocked beacons offer nanomolar (femtomole) detection limits, response times on the order of minutes, multiplexing through the use of different reporter dyes, and detection in complex matrices such as serum and blood. The blocked beacons offer better mismatch selectivity, whereas the unblocked beacons are simpler in design. The temporal mechanism of signaling utilized with the unblocked beacons also plays a significant role with the blocked beacons and represents a new and effective strategy for developing FRET probes for bioassays.

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mentioning

confidence: 99%

Time-Resolved Nucleic Acid Hybridization Beacons Utilizing Unimolecular and Toehold-Mediated Strand Displacement Designs

Massey

Ancona²,

Medintz³

et al. 2015

Anal. Chem.

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“…DNA was extracted from 100 µl of sample using a QIAamp DNA Blood Mini kit (51104, Qiagen) following the manufacturer's protocol. HLA-DQB1 and HLA-DQA1 typing was performed at the Immunogenetics Laboratory at the University of Turku, and the method was based on an asymmetrical PCR and a subsequent hybridization of allele-specific probes, as previously described 75,76 .…”

Section: Articlementioning

confidence: 99%

Transcriptomic analysis of intestine following administration of a transglutaminase 2 inhibitor to prevent gluten-induced intestinal damage in celiac disease

Dotsenko,

Tewes,

Hils

et al. 2024

Nat Immunol

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Transglutaminase 2 (TG2) plays a pivotal role in the pathogenesis of celiac disease (CeD) by deamidating dietary gluten peptides, which facilitates antigenic presentation and a strong anti-gluten T cell response. Here, we elucidate the molecular mechanisms underlying the efficacy of the TG2 inhibitor ZED1227 by performing transcriptional analysis of duodenal biopsies from individuals with CeD on a long-term gluten-free diet before and after a 6-week gluten challenge combined with 100 mg per day ZED1227 or placebo. At the transcriptome level, orally administered ZED1227 effectively prevented gluten-induced intestinal damage and inflammation, providing molecular-level evidence that TG2 inhibition is an effective strategy for treating CeD. ZED1227 treatment preserved transcriptome signatures associated with mucosal morphology, inflammation, cell differentiation and nutrient absorption to the level of the gluten-free diet group. Nearly half of the gluten-induced gene expression changes in CeD were associated with the epithelial interferon-γ response. Moreover, data suggest that deamidated gluten-induced adaptive immunity is a sufficient step to set the stage for CeD pathogenesis. Our results, with the limited sample size, also suggest that individuals with CeD might benefit from an HLA-DQ2/HLA-DQ8 stratification based on gene doses to maximally eliminate the interferon-γ-induced mucosal damage triggered by gluten.

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Tri-SNP polymorphism in the intron of HLA-DRA1 affects type 1 diabetes susceptibility in the Finnish population

et al. 2021

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Closed-tube human leukocyte antigen DQA1∗05 genotyping assay based on switchable lanthanide luminescence probes

Cited by 3 publications

References 31 publications

Time-Resolved Nucleic Acid Hybridization Beacons Utilizing Unimolecular and Toehold-Mediated Strand Displacement Designs

Time-Resolved Nucleic Acid Hybridization Beacons Utilizing Unimolecular and Toehold-Mediated Strand Displacement Designs

Transcriptomic analysis of intestine following administration of a transglutaminase 2 inhibitor to prevent gluten-induced intestinal damage in celiac disease

Tri-SNP polymorphism in the intron of HLA-DRA1 affects type 1 diabetes susceptibility in the Finnish population

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