Coupling Molecular Beacons to Barcoded Metal Nanowires for Multiplexed, Sealed Chamber DNA Bioassays

We have combined molecular beacon (MB) probes with barcoded metal nanowires to enable no-wash, sealed chamber, multiplexed detection of nucleic acids. Probe design and experimental parameters important in nanowire-based MB assays are discussed. Loop regions of 24 bases and 5 base pair stem regions i...

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Bibliographic Details
Published in:Journal of the American Chemical Society 2006-12, Vol.128 (51), p.16892-16903
Main Authors: Stoermer, Rebecca L, Cederquist, Kristin B, McFarland, Sean K, Sha, Michael Y, Penn, Sharron G, Keating, Christine D
Format: Article
Language:English
Subjects:
Analytical, structural and metabolic biochemistry
Biological and medical sciences
Carbohydrates. Nucleosides and nucleotides
Chemistry
Dna, deoxyribonucleoproteins
DNA, Viral - analysis
Exact sciences and technology
Fundamental and applied biological sciences. Psychology
General and physical chemistry
Gold - chemistry
Hepacivirus - chemistry
HIV - chemistry
Humans
Metals - chemistry
Molecular Probe Techniques - instrumentation
Molecular Probes - chemistry
Nanostructures - chemistry
Nucleic acids
Nucleosides, nucleotides and oligonucleotides
Organic chemistry
Osmolar Concentration
Preparations and properties
Sensitivity and Specificity
Severe acute respiratory syndrome-related coronavirus - chemistry
Silver - chemistry
Sodium Chloride - chemistry
Surface Properties
Thermodynamics
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Summary:We have combined molecular beacon (MB) probes with barcoded metal nanowires to enable no-wash, sealed chamber, multiplexed detection of nucleic acids. Probe design and experimental parameters important in nanowire-based MB assays are discussed. Loop regions of 24 bases and 5 base pair stem regions in the beacon probes gave optimal performance. Our results suggest that thermodynamic predictions for secondary structure stability of solution-phase MB can guide probe design for nanowire-based assays. Dengue virus-specific probes with predicted solution-phase ΔG of folding in 500 mM buffered NaCl of approximately −4 kcal/mol performed better than those with ΔG > −2 or
ISSN:0002-7863
1520-5126
DOI:10.1021/ja0658261