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DNA Microarrays: Sample Quality Control, Array Hybridization and Scanning
Published on: March 15, 2011
Application of equilibrium models of solution hybridization to microarray design and analysis
Raad Z Gharaibeh1, Joshua M Newton, Jennifer W Weller
1Department of Bioinformatics and Genomics, The University of North Carolina at Charlotte, Charlotte, North Carolina, USA.
Plos One
|June 16, 2010
Summary
Microarray probe percent bound values, derived from equilibrium models, accurately predict hybridization behavior for 50-nucleotide probes with mismatches. This aids in discriminating perfect matches from mismatches and predicting mismatch types in microarray analysis.
Area of Science:
- Molecular Biology
- Biophysics
Background:
- Microarray technology commonly uses 50-nucleotide probes.
- Limited controlled studies exist on 50-mer interactions with mismatched targets compared to shorter probes.
Purpose of the Study:
- To assess the utility of probe percent bound values in understanding 50-mer hybridization.
- To evaluate the prediction of mismatch types using solution hybridization models.
Main Methods:
- Utilized multi-state equilibrium models to calculate probe percent bound values.
- Designed microarrays with 50-mer oligonucleotides featuring central single, double, and triple mismatches.
- Analyzed hybridization at various target concentrations (100 pM to 200 pM).
Main Results:
- Successfully discriminated binding between perfect matches and mismatches.
- Accurately predicted mismatch types within the 100 pM to 200 pM concentration range.
- Demonstrated the predictive power of solution hybridization modeling for 50-mer probes.
Conclusions:
- Biophysical factors are crucial for microarray design and analysis.
- Probe percent bound values from equilibrium models are vital for interpreting long oligonucleotide array behavior.
- Findings support the application of these models for both short and long oligonucleotide arrays.
