ArticleBMC biotechnology2010
A novel FRET pair for detection of parallel DNA triplexes by the LightCycler.
Article in BMC biotechnology, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 8 papers.
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Who cites it
8 citing papers in PubMed.
- Coupling pH-Responsive Dyes to Agarose Hydrogels for Monitoring Metabolic States of Encapsulated Phototrophic Microbial Consortia.ACS applied bio materials · 2025Article
- Targeting triple-negative breast cancer cells with a β1-integrin binding aptamer.Molecular therapy. Nucleic acids · 2023Article
- Modulation of DNA structure formation using small molecules.Biochimica et biophysica acta. Molecular cell research · 2019Review
- A tunable assay for modulators of genome-destabilizing DNA structures.Nucleic acids research · 2019Article
- Measuring thermodynamic details of DNA hybridization using fluorescence.Biopolymers · 2011Article
- Increasing the analytical sensitivity by oligonucleotides modified with para- and ortho-twisted intercalating nucleic acids--TINA.PloS one · 2011Article
- Optimal design of parallel triplex forming oligonucleotides containing Twisted Intercalating Nucleic Acids--TINA.Nucleic acids research · 2010Article
- Fluorescent triplex-forming DNA oligonucleotides labeled with a thiazole orange dimer unit.Artificial DNA, PNA & XNAArticle
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10 authors.
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Abstract
backgroundMelting temperature of DNA structures can be determined on the LightCycler using quenching of FAM. This method is very suitable for pH independent melting point (Tm) determination performed at basic or neutral pH, as a high throughput alternative to UV absorbance measurements. At acidic pH quenching of FAM is not very suitable, since the fluorescence of FAM is strongly pH dependent and drops with acidic pH.Hoogsteen based parallel triplex helix formation requires protonation of cytosines in the triplex forming strand. Therefore, nucleic acid triplexes show strong pH dependence and are stable only at acidic pH. This led us to establish a new pH independent fluorophore based measuring system on the LightCycler for thermal stability studies of parallel triplexes.
resultsA novel LightCycler FRET pair labelled with ATTO495 and ATTO647N was established for parallel triplex detection with antiparallel duplex as a control for the general applicability of these fluorophores for Tm determination. The ATTO fluorophores were pH stable from pH 4.5 to 7.5. Melting of triplex and duplex structures were accompanied by a large decrease in fluorescence intensity leading to well defined Tm and high reproducibility. Validation of Tm showed low intra- and inter-assay coefficient of variation; 0.11% and 0.14% for parallel triplex and 0.19% and 0.12% for antiparallel duplex. Measurements of Tm and fluorescence intensity over time and multiple runs showed great time and light stability of the ATTO fluorophores. The variance on Tm determinations was significant lower on the LightCycler platform compared to UV absorbance measurements, which enable discrimination of DNA structures with very similar Tm. Labelling of DNA probes with ATTO fluorophore increased Tm of antiparallel duplexes significantly, but not Tm of parallel triplexes.
conclusionsWe have established a novel pH independent FRET pair with high fluorescence signals on the LightCycler platform for both antiparallel duplex and parallel triplex formation. The method has been thoroughly validated, and is characterized by an excellent accuracy and reproducibility. This FRET pair is especially suitable for DeltaTm and Tm determinations of pH dependent parallel triplex formation.
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