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Molecular beacon sequence design algorithm.

W Todd Monroe·Frederick R Haselton
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Abstract

A method based on Web-based tools is presented to design optimally functioning molecular beacons. Molecular beacons, fluorogenic hybridization probes, are a powerful tool for the rapid and specific detection of a particular nucleic acid sequence. However, their synthesis costs can be considerable. Since molecular beacon performance is based on its sequence, it is imperative to rationally design an optimal sequence before synthesis. The algorithm presented here uses simple Microsoft Excel formulas and macros to rank candidate sequences. This analysis is carried out using mfold structural predictions along with other free Web-based tools. For smaller laboratories where molecular beacons are not the focus of research, the public domain algorithm described here may be usefully employed to aid in molecular beacon design.

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AlgorithmsBase SequenceCombinatorial Chemistry TechniquesComputer-Aided DesignDNA ProbesDatabases, Nucleic AcidEquipment DesignFluorescenceInternetMolecular Probe TechniquesMolecular Sequence DataOligonucleotidesSequence AlignmentSequence Analysis, DNASoftwareEvaluation StudyResearch Support, U.S. Gov't, Non-P.H.S.Research Support, U.S. Gov't, P.H.S.Technical ReportJournal Article

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W Todd Monroe, Frederick R Haselton. 2003. Molecular beacon sequence design algorithm.. https://doi.org/10.2144/03341st02

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