title: Application of equilibrium models of solution hybridization to microarray design and analysis.
abstract: BACKGROUND
  The probe percent bound value, calculated using multi-state equilibrium models of solution hybridization, is shown to be useful in understanding the hybridization behavior of microarray probes having 50 nucleotides, with and without mismatches. These longer oligonucleotides are in widespread use on microarrays, but there are few controlled studies of their interactions with mismatched targets compared to 25-mer based platforms.
  
  
  RESULTS
  50-mer oligonucleotides with centrally placed single, double and triple mismatches were spotted on an array. Over a range of target concentrations it was possible to discriminate binding to perfect matches and mismatches, and the type of mismatch could be predicted accurately in the concentration midrange (100 pM to 200 pM) using solution hybridization modeling methods. These results have implications for microarray design, optimization and analysis methods.
  
  
  CONCLUSIONS
  Our results highlight the importance of incorporating biophysical factors in both the design and the analysis of microarrays. Use of the probe "percent bound" value predicted by equilibrium models of hybridization is confirmed to be important for predicting and interpreting the behavior of long oligonucleotide arrays, as has been shown for short oligonucleotide arrays.
authors.affiliation: Department of Bioinformatics and Genomics, The University of North Carolina at Charlotte, Charlotte, North Carolina, USA.
authors.forename: Raad Z
authors.initials: RZ
authors.lastname: Gharaibeh
authors.forename: Joshua M
authors.initials: JM
authors.lastname: Newton
authors.forename: Jennifer W
authors.initials: JW
authors.lastname: Weller
authors.forename: Cynthia J
authors.initials: CJ
authors.lastname: Gibas
mesh_terms: D015342:DNA Probes; D009693:Nucleic Acid Hybridization; D020411:Oligonucleotide Array Sequence Analysis
chemical_list: D015342:DNA Probes