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Molecular beacon sequence design algorithm.

Monroe WT, Haselton FR
Biotechniques. 2003 34 (1): 68-70, 72-3

PMID: 12545542 · DOI:10.2144/03341st02

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.

MeSH Terms (15)

Algorithms Base Sequence Combinatorial Chemistry Techniques Computer-Aided Design Databases, Nucleic Acid DNA Probes Equipment Design Fluorescence Internet Molecular Probe Techniques Molecular Sequence Data Oligonucleotides Sequence Alignment Sequence Analysis, DNA Software

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