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

摘要

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 DELTA G of folding in 500 mM buffered NaCI of approximately -4 kcal/mol performed better than those with DELTA G > -2 or < -6 kcal/mol.Buffered 300-500 mM NaCI was selected after comparison of several buffers previously reported for similar types of assays,and 200-500 mM NaCI was found to be the optimal ionic strength for the hybridization temperatures (25 and 50 deg C) and probe designs used here.Target binding to the surface as a function of solution concentration fit a Sips isotherm with K_d = 1.7 +- 0.3 nM.The detection limit was approx 100 pM,limited by incomplete quenching.Single base mismatches could be discriminated from fully complementary targets.Oligonucleotide target sequences specific for human immunodeficiency,hepatitis C,and severe acute respiratory viruses were assayed simultaneously in a no-wash,sealed chamber,multiplexed experiment in which each of three probe sequences was attached to a different pattern of encoded nanowires.Finally,we demonstrated that probe-coated nanowires retain their selectivity and sensitivity in a triplexed assay after storage for over 3 months.