Design and analysis of mismatch probes for long oligonucleotide microarrays

Journal Article · Fri Aug 15 04:00:00 EDT 2008 · BMC Genomics

DOI:https://doi.org/10.1186/1471-2164-9-491· OSTI ID:957036

Deng, Ye; He, Zhili; Van Nostrand, Joy D; Zhou, Jizhong

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.

• Research Organization: Ernest Orlando Lawrence Berkeley National Laboratory, Berkeley, CA (US)
• Sponsoring Organization: Physical Biosciences Division
• DOE Contract Number: AC02-05CH11231
• OSTI ID: 957036
• Report Number(s): LBNL-1834E
• Journal Information: BMC Genomics, Journal Name: BMC Genomics Vol. 9; ISSN 1471-2164
• Country of Publication: United States
• Language: English

Related Subjects

54 ENVIRONMENTAL SCIENCES
59 BASIC BIOLOGICAL SCIENCES
60 APPLIED LIFE SCIENCES
DESIGN
DIMERS
FORECASTING
GENES
HYBRIDIZATION
MICROARRAY TECHNOLOGY
MICROORGANISMS
NUCLEOTIDES
Nonspecific hybridization
hybridizations
oligonucleotide probes
microarray
OLIGONUCLEOTIDES
PROBES
SIMULATION
TARGETS
THERMODYNAMICS