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Oligodeoxyribonucleotide probe accessibility on a three-dimensional DNA microarray surface and the effect of hybridization time on the accuracy of expression ratios

BACKGROUND: DNA microarrays are now routinely used to monitor the transcript levels of thousands of genes simultaneously. However, the array fabrication method, hybridization conditions, and oligodeoxyribonucleotide probe length can impact the performance of a DNA microarray platform. RESULTS: We de...

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Autores principales: Dorris, David R, Nguyen, Allen, Gieser, Linn, Lockner, Randall, Lublinsky, Anna, Patterson, Marcus, Touma, Edward, Sendera, Timothy J, Elghanian, Robert, Mazumder, Abhijit
Formato: Texto
Lenguaje:English
Publicado: BioMed Central 2003
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC165584/
https://www.ncbi.nlm.nih.gov/pubmed/12801425
http://dx.doi.org/10.1186/1472-6750-3-6
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author Dorris, David R
Nguyen, Allen
Gieser, Linn
Lockner, Randall
Lublinsky, Anna
Patterson, Marcus
Touma, Edward
Sendera, Timothy J
Elghanian, Robert
Mazumder, Abhijit
author_facet Dorris, David R
Nguyen, Allen
Gieser, Linn
Lockner, Randall
Lublinsky, Anna
Patterson, Marcus
Touma, Edward
Sendera, Timothy J
Elghanian, Robert
Mazumder, Abhijit
author_sort Dorris, David R
collection PubMed
description BACKGROUND: DNA microarrays are now routinely used to monitor the transcript levels of thousands of genes simultaneously. However, the array fabrication method, hybridization conditions, and oligodeoxyribonucleotide probe length can impact the performance of a DNA microarray platform. RESULTS: We demonstrate solution-phase hybridization behavior of probe:target interactions by showing a strong correlation between the effect of mismatches in probes attached to a three dimensional matrix of a microarray and solution-based, thermodynamic duplex melting studies. The effects of mismatches in the probes attached to the microarray also demonstrate that most, if not all, of the oligodeoxyribonucleotide is available for hybridization. Kinetic parameters were also investigated. As anticipated, hybridization signals increased in a transcript concentration-dependent manner, and mismatch specificity increased with hybridization time. Unexpectedly, hybridization time increased the accuracy of fold changes by relieving the compression observed in expression ratios, and this effect may be more dramatic for larger fold changes. CONCLUSIONS: Taken together, these studies demonstrate that a three-dimensional surface may enable use of shorter oligodeoxyribonucleotide probes and that hybridization time may be critical in improving the accuracy of microarray data.
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spelling pubmed-1655842003-07-16 Oligodeoxyribonucleotide probe accessibility on a three-dimensional DNA microarray surface and the effect of hybridization time on the accuracy of expression ratios Dorris, David R Nguyen, Allen Gieser, Linn Lockner, Randall Lublinsky, Anna Patterson, Marcus Touma, Edward Sendera, Timothy J Elghanian, Robert Mazumder, Abhijit BMC Biotechnol Research Article BACKGROUND: DNA microarrays are now routinely used to monitor the transcript levels of thousands of genes simultaneously. However, the array fabrication method, hybridization conditions, and oligodeoxyribonucleotide probe length can impact the performance of a DNA microarray platform. RESULTS: We demonstrate solution-phase hybridization behavior of probe:target interactions by showing a strong correlation between the effect of mismatches in probes attached to a three dimensional matrix of a microarray and solution-based, thermodynamic duplex melting studies. The effects of mismatches in the probes attached to the microarray also demonstrate that most, if not all, of the oligodeoxyribonucleotide is available for hybridization. Kinetic parameters were also investigated. As anticipated, hybridization signals increased in a transcript concentration-dependent manner, and mismatch specificity increased with hybridization time. Unexpectedly, hybridization time increased the accuracy of fold changes by relieving the compression observed in expression ratios, and this effect may be more dramatic for larger fold changes. CONCLUSIONS: Taken together, these studies demonstrate that a three-dimensional surface may enable use of shorter oligodeoxyribonucleotide probes and that hybridization time may be critical in improving the accuracy of microarray data. BioMed Central 2003-06-11 /pmc/articles/PMC165584/ /pubmed/12801425 http://dx.doi.org/10.1186/1472-6750-3-6 Text en Copyright © 2003 Dorris et al; licensee BioMed Central Ltd. This is an Open Access article: verbatim copying and redistribution of this article are permitted in all media for any purpose, provided this notice is preserved along with the article's original URL.
spellingShingle Research Article
Dorris, David R
Nguyen, Allen
Gieser, Linn
Lockner, Randall
Lublinsky, Anna
Patterson, Marcus
Touma, Edward
Sendera, Timothy J
Elghanian, Robert
Mazumder, Abhijit
Oligodeoxyribonucleotide probe accessibility on a three-dimensional DNA microarray surface and the effect of hybridization time on the accuracy of expression ratios
title Oligodeoxyribonucleotide probe accessibility on a three-dimensional DNA microarray surface and the effect of hybridization time on the accuracy of expression ratios
title_full Oligodeoxyribonucleotide probe accessibility on a three-dimensional DNA microarray surface and the effect of hybridization time on the accuracy of expression ratios
title_fullStr Oligodeoxyribonucleotide probe accessibility on a three-dimensional DNA microarray surface and the effect of hybridization time on the accuracy of expression ratios
title_full_unstemmed Oligodeoxyribonucleotide probe accessibility on a three-dimensional DNA microarray surface and the effect of hybridization time on the accuracy of expression ratios
title_short Oligodeoxyribonucleotide probe accessibility on a three-dimensional DNA microarray surface and the effect of hybridization time on the accuracy of expression ratios
title_sort oligodeoxyribonucleotide probe accessibility on a three-dimensional dna microarray surface and the effect of hybridization time on the accuracy of expression ratios
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC165584/
https://www.ncbi.nlm.nih.gov/pubmed/12801425
http://dx.doi.org/10.1186/1472-6750-3-6
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