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Stem-loop oligonucleotides as tools for labelling double-stranded DNA.

Bénédicte Géron-Landre·Thibaut Roulon·Christophe Escudé
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Abstract

We report on a sequence-specific double-stranded DNA labelling strategy in which a stem-loop triplex forming oligonucleotide (TFO) is able to encircle its DNA target. Ligation of this TFO to either a short hairpin oligonucleotide or a long double-stranded DNA fragment leads to the formation of a topological complex. This process requires the hybridization of both extremities of the TFO to each other on a few base pairs. The effects of different factors on the formation of these complexes have been investigated. Efficient complex formation was observed using both GT or TC TFOs. The stem-loop structure enhances the specificity of the complex. The topologically linked TFO remains associated with its target even under conditions that do not favour triple-helix formation. This approach is sufficiently sensitive for detection of a 20-bp target sequence at the subfemtomolar level. This study provides new insights into the mechanics and properties of stem-loop TFOs and their complexes with double-stranded DNA targets. It emphasizes the interest of such molecules in the development of new tools for the specific labelling of short DNA sequences.

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AT Rich SequenceBase SequenceDNADNA, CircularElectrophoresis, Agar GelGC Rich SequenceIsotope LabelingMolecular Sequence DataNucleic Acid ConformationNucleic Acid HybridizationOligonucleotide ProbesPlasmidsStaining and LabelingJournal ArticleResearch Support, Non-U.S. Gov't

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Bénédicte Géron-Landre, Thibaut Roulon, Christophe Escudé. 2005. Stem-loop oligonucleotides as tools for labelling double-stranded DNA.. https://doi.org/10.1111/j.1742-4658.2005.04932.x

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