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Title: Design and analysis of mismatch probes for long oligonucleotide microarrays

Abstract

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. 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. Conclusions:more » 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.« less

Authors:
; ; ;
Publication Date:
Research Org.:
Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
Sponsoring Org.:
Physical Biosciences Division
OSTI Identifier:
957036
Report Number(s):
LBNL-1834E
Journal ID: 1471-2164; TRN: US201002%%910
DOE Contract Number:  
DE-AC02-05CH11231
Resource Type:
Journal Article
Journal Name:
BMC Genomics
Additional Journal Information:
Journal Volume: 9; Related Information: Journal Publication Date: 10/17/2008
Country of Publication:
United States
Language:
English
Subject:
60 APPLIED LIFE SCIENCES; 59 BASIC BIOLOGICAL SCIENCES; 54 ENVIRONMENTAL SCIENCES; DESIGN; DIMERS; FORECASTING; GENES; HYBRIDIZATION; MICROARRAY TECHNOLOGY; MICROORGANISMS; NUCLEOTIDES; OLIGONUCLEOTIDES; PROBES; SIMULATION; TARGETS; THERMODYNAMICS; Nonspecific hybridization, hybridizations, oligonucleotide probes, microarray

Citation Formats

Deng, Ye, He, Zhili, Van Nostrand, Joy D, and Zhou, Jizhong. Design and analysis of mismatch probes for long oligonucleotide microarrays. United States: N. p., 2008. Web. doi:10.1186/1471-2164-9-491.
Deng, Ye, He, Zhili, Van Nostrand, Joy D, & Zhou, Jizhong. Design and analysis of mismatch probes for long oligonucleotide microarrays. United States. https://doi.org/10.1186/1471-2164-9-491
Deng, Ye, He, Zhili, Van Nostrand, Joy D, and Zhou, Jizhong. Fri . "Design and analysis of mismatch probes for long oligonucleotide microarrays". United States. https://doi.org/10.1186/1471-2164-9-491. https://www.osti.gov/servlets/purl/957036.
@article{osti_957036,
title = {Design and analysis of mismatch probes for long oligonucleotide microarrays},
author = {Deng, Ye and He, Zhili and Van Nostrand, Joy D and Zhou, Jizhong},
abstractNote = {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. 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. Conclusions: 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.},
doi = {10.1186/1471-2164-9-491},
url = {https://www.osti.gov/biblio/957036}, journal = {BMC Genomics},
number = ,
volume = 9,
place = {United States},
year = {2008},
month = {8}
}