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Design and analysis of mismatch probes for long oligonucleotide microarrays

BACKGROUND: Nonspecific hybridization is currently a major concern with microarray technology. One of most effective approaches to estimating nonspecific hybridizations in oligonucleotide microarrays is the utilization of mismatch probes; however, this approach has not been used for longer oligonucl...

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Autores principales: Deng, Ye, He, Zhili, Van Nostrand, Joy D, Zhou, Jizhong
Formato: Texto
Lenguaje:English
Publicado: BioMed Central 2008
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2576263/
https://www.ncbi.nlm.nih.gov/pubmed/18928550
http://dx.doi.org/10.1186/1471-2164-9-491
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author Deng, Ye
He, Zhili
Van Nostrand, Joy D
Zhou, Jizhong
author_facet Deng, Ye
He, Zhili
Van Nostrand, Joy D
Zhou, Jizhong
author_sort Deng, Ye
collection PubMed
description BACKGROUND: Nonspecific hybridization is currently a major concern with microarray technology. One of most effective approaches to estimating nonspecific hybridizations in oligonucleotide microarrays is the utilization of mismatch probes; however, this approach has not been used for longer oligonucleotide probes. RESULTS: Here, an oligonucleotide microarray was constructed to evaluate and optimize parameters for 50-mer mismatch probe design. A perfect match (PM) and 28 mismatch (MM) probes were designed for each of ten target genes selected from three microorganisms. The microarrays were hybridized with synthesized complementary oligonucleotide targets at different temperatures (e.g., 42, 45 and 50°C). In general, the probes with evenly distributed mismatches were more distinguishable than those with randomly distributed mismatches. MM probes with 3, 4 and 5 mismatched nucleotides were differentiated for 50-mer oligonucleotide probes hybridized at 50, 45 and 42°C, respectively. Based on the experimental data generated from this study, a modified positional dependent nearest neighbor (MPDNN) model was constructed to adjust the thermodynamic parameters of matched and mismatched dimer nucleotides in the microarray environment. The MM probes with four flexible positional mismatches were designed using the newly established MPDNN model and the experimental results demonstrated that the redesigned MM probes could yield more consistent hybridizations. CONCLUSION: This study provides guidance on the design of MM probes for long oligonucleotides (e.g., 50 mers). The novel MPDNN model has improved the consistency for long MM probes, and this modeling method can potentially be used for the prediction of oligonucleotide microarray hybridizations.
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spelling pubmed-25762632008-10-31 Design and analysis of mismatch probes for long oligonucleotide microarrays Deng, Ye He, Zhili Van Nostrand, Joy D Zhou, Jizhong BMC Genomics Research Article BACKGROUND: Nonspecific hybridization is currently a major concern with microarray technology. One of most effective approaches to estimating nonspecific hybridizations in oligonucleotide microarrays is the utilization of mismatch probes; however, this approach has not been used for longer oligonucleotide probes. RESULTS: Here, an oligonucleotide microarray was constructed to evaluate and optimize parameters for 50-mer mismatch probe design. A perfect match (PM) and 28 mismatch (MM) probes were designed for each of ten target genes selected from three microorganisms. The microarrays were hybridized with synthesized complementary oligonucleotide targets at different temperatures (e.g., 42, 45 and 50°C). In general, the probes with evenly distributed mismatches were more distinguishable than those with randomly distributed mismatches. MM probes with 3, 4 and 5 mismatched nucleotides were differentiated for 50-mer oligonucleotide probes hybridized at 50, 45 and 42°C, respectively. Based on the experimental data generated from this study, a modified positional dependent nearest neighbor (MPDNN) model was constructed to adjust the thermodynamic parameters of matched and mismatched dimer nucleotides in the microarray environment. The MM probes with four flexible positional mismatches were designed using the newly established MPDNN model and the experimental results demonstrated that the redesigned MM probes could yield more consistent hybridizations. CONCLUSION: This study provides guidance on the design of MM probes for long oligonucleotides (e.g., 50 mers). The novel MPDNN model has improved the consistency for long MM probes, and this modeling method can potentially be used for the prediction of oligonucleotide microarray hybridizations. BioMed Central 2008-10-17 /pmc/articles/PMC2576263/ /pubmed/18928550 http://dx.doi.org/10.1186/1471-2164-9-491 Text en Copyright © 2008 Deng et al; licensee BioMed Central Ltd. http://creativecommons.org/licenses/by/2.0 This is an Open Access article distributed under the terms of the Creative Commons Attribution License ( (http://creativecommons.org/licenses/by/2.0) ), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Research Article
Deng, Ye
He, Zhili
Van Nostrand, Joy D
Zhou, Jizhong
Design and analysis of mismatch probes for long oligonucleotide microarrays
title Design and analysis of mismatch probes for long oligonucleotide microarrays
title_full Design and analysis of mismatch probes for long oligonucleotide microarrays
title_fullStr Design and analysis of mismatch probes for long oligonucleotide microarrays
title_full_unstemmed Design and analysis of mismatch probes for long oligonucleotide microarrays
title_short Design and analysis of mismatch probes for long oligonucleotide microarrays
title_sort design and analysis of mismatch probes for long oligonucleotide microarrays
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2576263/
https://www.ncbi.nlm.nih.gov/pubmed/18928550
http://dx.doi.org/10.1186/1471-2164-9-491
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