Coupling molecular beacons to barcoded metal nanowires for multiplexed, sealed chamber DNA bioassays.
Identifieur interne : 001810 ( Ncbi/Checkpoint ); précédent : 001809; suivant : 001811Coupling molecular beacons to barcoded metal nanowires for multiplexed, sealed chamber DNA bioassays.
Auteurs : Rebecca L. Stoermer [États-Unis] ; Kristin B. Cederquist ; Sean K. Mcfarland ; Michael Y. Sha ; Sharron G. Penn ; Christine D. KeatingSource :
- Journal of the American Chemical Society [ 0002-7863 ] ; 2006.
Descripteurs français
- KwdFr :
- ADN viral (analyse), Argent (), Chlorure de sodium (), Concentration osmolaire, Hepacivirus (), Humains, Métaux (), Nanostructures (), Or (), Propriétés de surface, Sensibilité et spécificité, Sondes moléculaires (), Techniques de sonde moléculaire (instrumentation), Thermodynamique, VIH (Virus de l'Immunodéficience Humaine) (), Virus du SRAS ().
- MESH :
- analyse : ADN viral.
- Argent, Chlorure de sodium, Concentration osmolaire, Hepacivirus, Humains, Métaux, Nanostructures, Or, Propriétés de surface, Sensibilité et spécificité, Sondes moléculaires, Techniques de sonde moléculaire, Thermodynamique, VIH (Virus de l'Immunodéficience Humaine), Virus du SRAS.
English descriptors
- KwdEn :
- DNA, Viral (analysis), Gold (chemistry), HIV (chemistry), Hepacivirus (chemistry), Humans, Metals (chemistry), Molecular Probe Techniques (instrumentation), Molecular Probes (chemistry), Nanostructures (chemistry), Osmolar Concentration, SARS Virus (chemistry), Sensitivity and Specificity, Silver (chemistry), Sodium Chloride (chemistry), Surface Properties, Thermodynamics.
- MESH :
- chemical , analysis : DNA, Viral.
- chemical , chemistry : Gold, Metals, Molecular Probes, Silver, Sodium Chloride.
- chemistry : HIV, Hepacivirus, Nanostructures, SARS Virus.
- instrumentation : Molecular Probe Techniques.
- Humans, Osmolar Concentration, Sensitivity and Specificity, Surface Properties, Thermodynamics.
Abstract
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.
DOI: 10.1021/ja0658261
PubMed: 17177440
Affiliations:
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Stoermer</name><affiliation wicri:level="4"><nlm:affiliation>Department of Chemistry, Pennsylvania State University, University Park, PA 16802, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Chemistry, Pennsylvania State University, University Park, PA 16802</wicri:regionArea><placeName><region type="state">Pennsylvanie</region><settlement type="city">University Park (Pennsylvanie)</settlement></placeName><orgName type="university">Université d'État de Pennsylvanie</orgName></affiliation></author><author><name sortKey="Cederquist, Kristin B" sort="Cederquist, Kristin B" uniqKey="Cederquist K" first="Kristin B" last="Cederquist">Kristin B. Cederquist</name></author><author><name sortKey="Mcfarland, Sean K" sort="Mcfarland, Sean K" uniqKey="Mcfarland S" first="Sean K" last="Mcfarland">Sean K. Mcfarland</name></author><author><name sortKey="Sha, Michael Y" sort="Sha, Michael Y" uniqKey="Sha M" first="Michael Y" last="Sha">Michael Y. Sha</name></author><author><name sortKey="Penn, Sharron G" sort="Penn, Sharron G" uniqKey="Penn S" first="Sharron G" last="Penn">Sharron G. Penn</name></author><author><name sortKey="Keating, Christine D" sort="Keating, Christine D" uniqKey="Keating C" first="Christine D" last="Keating">Christine D. 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Stoermer</name><affiliation wicri:level="4"><nlm:affiliation>Department of Chemistry, Pennsylvania State University, University Park, PA 16802, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Chemistry, Pennsylvania State University, University Park, PA 16802</wicri:regionArea><placeName><region type="state">Pennsylvanie</region><settlement type="city">University Park (Pennsylvanie)</settlement></placeName><orgName type="university">Université d'État de Pennsylvanie</orgName></affiliation></author><author><name sortKey="Cederquist, Kristin B" sort="Cederquist, Kristin B" uniqKey="Cederquist K" first="Kristin B" last="Cederquist">Kristin B. Cederquist</name></author><author><name sortKey="Mcfarland, Sean K" sort="Mcfarland, Sean K" uniqKey="Mcfarland S" first="Sean K" last="Mcfarland">Sean K. Mcfarland</name></author><author><name sortKey="Sha, Michael Y" sort="Sha, Michael Y" uniqKey="Sha M" first="Michael Y" last="Sha">Michael Y. Sha</name></author><author><name sortKey="Penn, Sharron G" sort="Penn, Sharron G" uniqKey="Penn S" first="Sharron G" last="Penn">Sharron G. Penn</name></author><author><name sortKey="Keating, Christine D" sort="Keating, Christine D" uniqKey="Keating C" first="Christine D" last="Keating">Christine D. Keating</name></author></analytic><series><title level="j">Journal of the American Chemical Society</title><idno type="ISSN">0002-7863</idno><imprint><date when="2006" type="published">2006</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>DNA, Viral (analysis)</term><term>Gold (chemistry)</term><term>HIV (chemistry)</term><term>Hepacivirus (chemistry)</term><term>Humans</term><term>Metals (chemistry)</term><term>Molecular Probe Techniques (instrumentation)</term><term>Molecular Probes (chemistry)</term><term>Nanostructures (chemistry)</term><term>Osmolar Concentration</term><term>SARS Virus (chemistry)</term><term>Sensitivity and Specificity</term><term>Silver (chemistry)</term><term>Sodium Chloride (chemistry)</term><term>Surface Properties</term><term>Thermodynamics</term></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>ADN viral (analyse)</term><term>Argent ()</term><term>Chlorure de sodium ()</term><term>Concentration osmolaire</term><term>Hepacivirus ()</term><term>Humains</term><term>Métaux ()</term><term>Nanostructures ()</term><term>Or ()</term><term>Propriétés de surface</term><term>Sensibilité et spécificité</term><term>Sondes moléculaires ()</term><term>Techniques de sonde moléculaire (instrumentation)</term><term>Thermodynamique</term><term>VIH (Virus de l'Immunodéficience Humaine) ()</term><term>Virus du SRAS ()</term></keywords><keywords scheme="MESH" type="chemical" qualifier="analysis" xml:lang="en"><term>DNA, Viral</term></keywords><keywords scheme="MESH" type="chemical" qualifier="chemistry" xml:lang="en"><term>Gold</term><term>Metals</term><term>Molecular Probes</term><term>Silver</term><term>Sodium Chloride</term></keywords><keywords scheme="MESH" qualifier="analyse" xml:lang="fr"><term>ADN viral</term></keywords><keywords scheme="MESH" qualifier="chemistry" xml:lang="en"><term>HIV</term><term>Hepacivirus</term><term>Nanostructures</term><term>SARS Virus</term></keywords><keywords scheme="MESH" qualifier="instrumentation" xml:lang="en"><term>Molecular Probe Techniques</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Humans</term><term>Osmolar Concentration</term><term>Sensitivity and Specificity</term><term>Surface Properties</term><term>Thermodynamics</term></keywords><keywords scheme="MESH" xml:lang="fr"><term>Argent</term><term>Chlorure de sodium</term><term>Concentration osmolaire</term><term>Hepacivirus</term><term>Humains</term><term>Métaux</term><term>Nanostructures</term><term>Or</term><term>Propriétés de surface</term><term>Sensibilité et spécificité</term><term>Sondes moléculaires</term><term>Techniques de sonde moléculaire</term><term>Thermodynamique</term><term>VIH (Virus de l'Immunodéficience Humaine)</term><term>Virus du SRAS</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">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.</div></front></TEI><affiliations><list><country><li>États-Unis</li></country><region><li>Pennsylvanie</li></region><settlement><li>University Park (Pennsylvanie)</li></settlement><orgName><li>Université d'État de Pennsylvanie</li></orgName></list><tree><noCountry><name sortKey="Cederquist, Kristin B" sort="Cederquist, Kristin B" uniqKey="Cederquist K" first="Kristin B" last="Cederquist">Kristin B. Cederquist</name><name sortKey="Keating, Christine D" sort="Keating, Christine D" uniqKey="Keating C" first="Christine D" last="Keating">Christine D. Keating</name><name sortKey="Mcfarland, Sean K" sort="Mcfarland, Sean K" uniqKey="Mcfarland S" first="Sean K" last="Mcfarland">Sean K. Mcfarland</name><name sortKey="Penn, Sharron G" sort="Penn, Sharron G" uniqKey="Penn S" first="Sharron G" last="Penn">Sharron G. Penn</name><name sortKey="Sha, Michael Y" sort="Sha, Michael Y" uniqKey="Sha M" first="Michael Y" last="Sha">Michael Y. Sha</name></noCountry><country name="États-Unis"><region name="Pennsylvanie"><name sortKey="Stoermer, Rebecca L" sort="Stoermer, Rebecca L" uniqKey="Stoermer R" first="Rebecca L" last="Stoermer">Rebecca L. Stoermer</name></region></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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