Guidelines for Designing Mismatch Oligonucleotides on Microarrays
Author Information
Author(s): Michael Seringhaus, Joel Rozowsky, Thomas Royce, Ugrappa Nagalakshmi, Justin Jee, Michael Snyder, Mark Gerstein
Primary Institution: Yale University
Hypothesis
How do different nucleotide substitutions in mismatch oligonucleotides affect hybridization behavior on microarrays?
Conclusion
The study provides guidelines for oligonucleotide design, emphasizing that substitutions should not alter probe GC content to avoid skew in hybridization intensity.
Supporting Evidence
- Mismatch oligonucleotides are used to differentiate specific from nonspecific hybridization.
- C→A, C→G, and T→A substitutions are most disruptive to hybridization.
- Multiple mismatches per oligo cause an additive effect on signal intensity.
Takeaway
This study helps scientists design better DNA probes for experiments by showing how different changes can affect their performance.
Methodology
Two large-scale microarray experiments were conducted using yeast and human genomic DNA to assess the performance of mismatch oligonucleotides.
Potential Biases
Potential for non-specific hybridization affecting results.
Limitations
The conclusions may not apply to different array types, oligonucleotide lengths, or labeling methods.
Participant Demographics
Yeast (S. cerevisiae) and human (H. sapiens) genomic DNA were used.
Statistical Information
P-Value
p<1 × 10-100
Statistical Significance
p<1 × 10-100
Digital Object Identifier (DOI)
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