title: Oligodeoxyribonucleotide probe accessibility on a three-dimensional DNA microarray surface and the effect of hybridization time on the accuracy of expression ratios.
abstract: BACKGROUND
  DNA microarrays are now routinely used to monitor the transcript levels of thousands of genes simultaneously. However, the array fabrication method, hybridization conditions, and oligodeoxyribonucleotide probe length can impact the performance of a DNA microarray platform.
  
  
  RESULTS
  We demonstrate solution-phase hybridization behavior of probe:target interactions by showing a strong correlation between the effect of mismatches in probes attached to a three dimensional matrix of a microarray and solution-based, thermodynamic duplex melting studies. The effects of mismatches in the probes attached to the microarray also demonstrate that most, if not all, of the oligodeoxyribonucleotide is available for hybridization. Kinetic parameters were also investigated. As anticipated, hybridization signals increased in a transcript concentration-dependent manner, and mismatch specificity increased with hybridization time. Unexpectedly, hybridization time increased the accuracy of fold changes by relieving the compression observed in expression ratios, and this effect may be more dramatic for larger fold changes.
  
  
  CONCLUSIONS
  Taken together, these studies demonstrate that a three-dimensional surface may enable use of shorter oligodeoxyribonucleotide probes and that hybridization time may be critical in improving the accuracy of microarray data.
authors.affiliation: Motorola Life Sciences, Northbrook, IL 60062, USA. daviddorris@yahoo.com
authors.forename: David R
authors.initials: DR
authors.lastname: Dorris
authors.forename: Allen
authors.initials: A
authors.lastname: Nguyen
authors.forename: Linn
authors.initials: L
authors.lastname: Gieser
authors.forename: Randall
authors.initials: R
authors.lastname: Lockner
authors.forename: Anna
authors.initials: A
authors.lastname: Lublinsky
authors.forename: Marcus
authors.initials: M
authors.lastname: Patterson
authors.forename: Edward
authors.initials: E
authors.lastname: Touma
authors.forename: Timothy J
authors.initials: TJ
authors.lastname: Sendera
authors.forename: Robert
authors.initials: R
authors.lastname: Elghanian
authors.forename: Abhijit
authors.initials: A
authors.lastname: Mazumder
mesh_terms: D018076:DNA, Complementary / Q000032:analysis; D020869:Gene Expression Profiling / Q000379:methods*; D006824:Hybridization, Genetic; D009693:Nucleic Acid Hybridization / Q000379:methods*; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D015345:Oligonucleotide Probes / Q000737:chemistry*; D012680:Sensitivity and Specificity; D013997:Time Factors
chemical_list: D018076:DNA, Complementary; D015345:Oligonucleotide Probes