title: Molecular beacon sequence design algorithm.
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.
authors.affiliation: Vanderbilt University, Nashville, TN, USA. tmonroe@lsu.edu
authors.forename: W Todd
authors.initials: WT
authors.lastname: Monroe
authors.forename: Frederick R
authors.initials: FR
authors.lastname: Haselton
mesh_terms: D000465:Algorithms; D001483:Base Sequence; D020650:Combinatorial Chemistry Techniques; D017076:Computer-Aided Design; D015342:DNA Probes / Q000138:chemical synthesis / Q000737:chemistry*; D030561:Databases, Nucleic Acid; D004867:Equipment Design / Q000379:methods; D005453:Fluorescence; D020407:Internet; D015336:Molecular Probe Techniques; D008969:Molecular Sequence Data; D009841:Oligonucleotides / Q000032:analysis; D016415:Sequence Alignment / Q000379:methods; D017422:Sequence Analysis, DNA / Q000295:instrumentation / Q000379:methods; D012984:Software
chemical_list: D015342:DNA Probes; D009841:Oligonucleotides