Coupling molecular beacons to barcoded metal nanowires for multiplexed, sealed chamber DNA bioassays.

Coupling molecular beacons to barcoded metal nanowires for multiplexed, sealed chamber DNA bioassays. Research Abstract Details 

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Coupling molecular beacons to barcoded metal nanowires for multiplexed, sealed chamber DNA bioassays. Abstract Text:

Rebecca L Stoermer,Kristin B Cederquist,Sean K McFarland,Michael Y Sha,Sharron G Penn,Christine D Keating,

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 DeltaG of folding in 500 mM buffered NaCl of approximately -4 kcal/mol performed better than those with DeltaG > -2 or < -6 kcal/mol. Buffered 300-500 mM NaCl was selected after comparison of several buffers previously reported for similar types of assays, and 200-500 mM NaCl was found to be the optimal ionic strength for the hybridization temperatures (25 and 50 degrees C) and probe designs used here. Target binding to the surface as a function of solution concentration fit a Sips isotherm with Kd = 1.7 +/- 0.3 nM. The detection limit was approximately 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.

Coupling molecular beacons to barcoded metal nanowires for multiplexed, sealed chamber DNA bioassays. Publishing Authors By Initials

RL Stoermer,KB Cederquist,SK McFarland,MY Sha,SG Penn,CD Keating,

For similar natural sciences: physics: thermodynamics research abstracts see: natural sciences: physics: thermodynamics research

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Coupling molecular beacons to barcoded metal nanowires for multiplexed, sealed chamber DNA bioassays. Journal Published:

PUBLICATION TYPE: Research Support, U.S. Gov't,

Journal: Journal of the American Chemical Society

VOLUME: 128

Page Numbers: 16892-903

Journal Abbreviation: J. Am. Chem. Soc.

ISSN: 0002-7863

DAY: 27

MONTH: Dec

YEAR: 2006

Coupling molecular beacons to barcoded metal nanowires for multiplexed, sealed chamber DNA bioassays. Information

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LANGUAGE: eng

NlmUniqueID: 7503056

Coupling molecular beacons to barcoded metal nanowires for multiplexed, sealed chamber DNA bioassays. Keywords Mesh Terms:

KEYWORDS: Thermodynamics

MESH TERMS: chemistry

Chemical & Substance for Abstract: Coupling molecular beacons to barcoded metal nanowires for multiplexed, sealed chamber DNA bioassays. Information

Substance Name: Sodium Chloride

Registry Number: 7647-14-5

Grant and Affiliation Information for Coupling molecular beacons to barcoded metal nanowires for multiplexed, sealed chamber DNA bioassays.

AFFILIATION: Department of Chemistry, Pennsylvania State University, University Park, PA 16802, USA.

Country: United States

AGENCY: United States NIBIB

GRANT: R01 EB 000268

ACRONYM: EB

MEDLINETA: J Am Chem Soc

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