DNA hybridization and discrimination of single-nucleotide mismatches using chip-based microbead arrays

Mehnaaz F. Ali, Romy Kirby, Adrian P. Goodey, Marc D. Rodriguez, Andrew D. Ellington, Dean P. Neikirk, John McDevitt

Research output: Contribution to journalArticle

Abstract

The development of a chip-based sensor array composed of individually addressable agarose microbeads has been demonstrated for the rapid detection of DNA oligonucleotides. Here, a "plug and play" approach allows for the simple incorporation of various biotinylated DNA capture probes into the bead-microreactors, which are derivatized in each case with avidin docking sites. The DNA capture probe containing microbeads are selectively arranged in micromachined cavities localized on silicon wafers. The microcavities possess trans-wafer openings, which allow for both fluid flow through the microreactors/analysis chambers and optical access to the chemically sensitive microbeads. Collectively, these features allow the identification and quantitation of target DNA analytes to occur in near real time using fluorescence changes that accompany binding of the target sample. The unique three-dimensional microenvironment within the agarose bead and the microfluidics capabilities of the chip structure afford a fully integrated package that fosters rapid analyses of solutions containing complex mixtures of DNA oligomers. These analyses can be completed at room temperature through the use of appropriate hybridization buffers. For applications requiring analysis of ≤102 different DNA sequences, the hybridization times and point mutation selectivity factors exhibited by this bead array method exceed in many respects the operational characteristics of the commonly utilized planar DNA chip technologies. The power and utility of this microbead array DNA detection methodology is demonstrated here for the analysis of fluids containing a variety of similar 18-base oligonucleotides. Hybridization times on the order of minutes with point mutation selectivity factors greater than 10 000 and limit of detection values of ∼10-13 M are obtained readily with this microbead array system.

Original languageEnglish (US)
Pages (from-to)4732-4739
Number of pages8
JournalAnalytical Chemistry
Volume75
Issue number18
DOIs
StatePublished - Sep 15 2003

Fingerprint

Nucleotides
DNA
DNA Probes
Oligonucleotides
Sepharose
Microcavities
Avidin
DNA sequences
Sensor arrays
Complex Mixtures
Silicon wafers
Oligomers
Microfluidics
Flow of fluids
Buffers
Fluorescence
Fluids
Temperature

ASJC Scopus subject areas

  • Analytical Chemistry

Cite this

Ali, M. F., Kirby, R., Goodey, A. P., Rodriguez, M. D., Ellington, A. D., Neikirk, D. P., & McDevitt, J. (2003). DNA hybridization and discrimination of single-nucleotide mismatches using chip-based microbead arrays. Analytical Chemistry, 75(18), 4732-4739. https://doi.org/10.1021/ac034106z

DNA hybridization and discrimination of single-nucleotide mismatches using chip-based microbead arrays. / Ali, Mehnaaz F.; Kirby, Romy; Goodey, Adrian P.; Rodriguez, Marc D.; Ellington, Andrew D.; Neikirk, Dean P.; McDevitt, John.

In: Analytical Chemistry, Vol. 75, No. 18, 15.09.2003, p. 4732-4739.

Research output: Contribution to journalArticle

Ali, MF, Kirby, R, Goodey, AP, Rodriguez, MD, Ellington, AD, Neikirk, DP & McDevitt, J 2003, 'DNA hybridization and discrimination of single-nucleotide mismatches using chip-based microbead arrays', Analytical Chemistry, vol. 75, no. 18, pp. 4732-4739. https://doi.org/10.1021/ac034106z
Ali MF, Kirby R, Goodey AP, Rodriguez MD, Ellington AD, Neikirk DP et al. DNA hybridization and discrimination of single-nucleotide mismatches using chip-based microbead arrays. Analytical Chemistry. 2003 Sep 15;75(18):4732-4739. https://doi.org/10.1021/ac034106z
Ali, Mehnaaz F. ; Kirby, Romy ; Goodey, Adrian P. ; Rodriguez, Marc D. ; Ellington, Andrew D. ; Neikirk, Dean P. ; McDevitt, John. / DNA hybridization and discrimination of single-nucleotide mismatches using chip-based microbead arrays. In: Analytical Chemistry. 2003 ; Vol. 75, No. 18. pp. 4732-4739.
@article{ff19962c6aba44f487771bd28d873b38,
title = "DNA hybridization and discrimination of single-nucleotide mismatches using chip-based microbead arrays",
abstract = "The development of a chip-based sensor array composed of individually addressable agarose microbeads has been demonstrated for the rapid detection of DNA oligonucleotides. Here, a {"}plug and play{"} approach allows for the simple incorporation of various biotinylated DNA capture probes into the bead-microreactors, which are derivatized in each case with avidin docking sites. The DNA capture probe containing microbeads are selectively arranged in micromachined cavities localized on silicon wafers. The microcavities possess trans-wafer openings, which allow for both fluid flow through the microreactors/analysis chambers and optical access to the chemically sensitive microbeads. Collectively, these features allow the identification and quantitation of target DNA analytes to occur in near real time using fluorescence changes that accompany binding of the target sample. The unique three-dimensional microenvironment within the agarose bead and the microfluidics capabilities of the chip structure afford a fully integrated package that fosters rapid analyses of solutions containing complex mixtures of DNA oligomers. These analyses can be completed at room temperature through the use of appropriate hybridization buffers. For applications requiring analysis of ≤102 different DNA sequences, the hybridization times and point mutation selectivity factors exhibited by this bead array method exceed in many respects the operational characteristics of the commonly utilized planar DNA chip technologies. The power and utility of this microbead array DNA detection methodology is demonstrated here for the analysis of fluids containing a variety of similar 18-base oligonucleotides. Hybridization times on the order of minutes with point mutation selectivity factors greater than 10 000 and limit of detection values of ∼10-13 M are obtained readily with this microbead array system.",
author = "Ali, {Mehnaaz F.} and Romy Kirby and Goodey, {Adrian P.} and Rodriguez, {Marc D.} and Ellington, {Andrew D.} and Neikirk, {Dean P.} and John McDevitt",
year = "2003",
month = "9",
day = "15",
doi = "10.1021/ac034106z",
language = "English (US)",
volume = "75",
pages = "4732--4739",
journal = "Analytical Chemistry",
issn = "0003-2700",
publisher = "American Chemical Society",
number = "18",

}

TY - JOUR

T1 - DNA hybridization and discrimination of single-nucleotide mismatches using chip-based microbead arrays

AU - Ali, Mehnaaz F.

AU - Kirby, Romy

AU - Goodey, Adrian P.

AU - Rodriguez, Marc D.

AU - Ellington, Andrew D.

AU - Neikirk, Dean P.

AU - McDevitt, John

PY - 2003/9/15

Y1 - 2003/9/15

N2 - The development of a chip-based sensor array composed of individually addressable agarose microbeads has been demonstrated for the rapid detection of DNA oligonucleotides. Here, a "plug and play" approach allows for the simple incorporation of various biotinylated DNA capture probes into the bead-microreactors, which are derivatized in each case with avidin docking sites. The DNA capture probe containing microbeads are selectively arranged in micromachined cavities localized on silicon wafers. The microcavities possess trans-wafer openings, which allow for both fluid flow through the microreactors/analysis chambers and optical access to the chemically sensitive microbeads. Collectively, these features allow the identification and quantitation of target DNA analytes to occur in near real time using fluorescence changes that accompany binding of the target sample. The unique three-dimensional microenvironment within the agarose bead and the microfluidics capabilities of the chip structure afford a fully integrated package that fosters rapid analyses of solutions containing complex mixtures of DNA oligomers. These analyses can be completed at room temperature through the use of appropriate hybridization buffers. For applications requiring analysis of ≤102 different DNA sequences, the hybridization times and point mutation selectivity factors exhibited by this bead array method exceed in many respects the operational characteristics of the commonly utilized planar DNA chip technologies. The power and utility of this microbead array DNA detection methodology is demonstrated here for the analysis of fluids containing a variety of similar 18-base oligonucleotides. Hybridization times on the order of minutes with point mutation selectivity factors greater than 10 000 and limit of detection values of ∼10-13 M are obtained readily with this microbead array system.

AB - The development of a chip-based sensor array composed of individually addressable agarose microbeads has been demonstrated for the rapid detection of DNA oligonucleotides. Here, a "plug and play" approach allows for the simple incorporation of various biotinylated DNA capture probes into the bead-microreactors, which are derivatized in each case with avidin docking sites. The DNA capture probe containing microbeads are selectively arranged in micromachined cavities localized on silicon wafers. The microcavities possess trans-wafer openings, which allow for both fluid flow through the microreactors/analysis chambers and optical access to the chemically sensitive microbeads. Collectively, these features allow the identification and quantitation of target DNA analytes to occur in near real time using fluorescence changes that accompany binding of the target sample. The unique three-dimensional microenvironment within the agarose bead and the microfluidics capabilities of the chip structure afford a fully integrated package that fosters rapid analyses of solutions containing complex mixtures of DNA oligomers. These analyses can be completed at room temperature through the use of appropriate hybridization buffers. For applications requiring analysis of ≤102 different DNA sequences, the hybridization times and point mutation selectivity factors exhibited by this bead array method exceed in many respects the operational characteristics of the commonly utilized planar DNA chip technologies. The power and utility of this microbead array DNA detection methodology is demonstrated here for the analysis of fluids containing a variety of similar 18-base oligonucleotides. Hybridization times on the order of minutes with point mutation selectivity factors greater than 10 000 and limit of detection values of ∼10-13 M are obtained readily with this microbead array system.

UR - http://www.scopus.com/inward/record.url?scp=0141705552&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=0141705552&partnerID=8YFLogxK

U2 - 10.1021/ac034106z

DO - 10.1021/ac034106z

M3 - Article

C2 - 14674448

AN - SCOPUS:0141705552

VL - 75

SP - 4732

EP - 4739

JO - Analytical Chemistry

JF - Analytical Chemistry

SN - 0003-2700

IS - 18

ER -