Methodology article

Mismatch oligonucleotides in human and yeast: guidelines for probe design on tiling microarrays

Michael Seringhaus¹ , Joel Rozowsky¹ , Thomas Royce² , Ugrappa Nagalakshmi³ , Justin Jee¹ , Michael Snyder^1,3 and Mark Gerstein^1,2,4

¹  Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA

²  Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06520, USA

³  Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT 06520, USA

⁴  Department of Computer Science, Yale University, New Haven, CT 06520, USA

author email corresponding author email

BMC Genomics 2008, 9:635doi:10.1186/1471-2164-9-635

Published:	31 December 2008

Abstract

Background

Mismatched oligonucleotides are widely used on microarrays to differentiate specific from nonspecific hybridization. While many experiments rely on such oligos, the hybridization behavior of various degrees of mismatch (MM) structure has not been extensively studied. Here, we present the results of two large-scale microarray experiments on S. cerevisiae and H. sapiens genomic DNA, to explore MM oligonucleotide behavior with real sample mixtures under tiling-array conditions.

Results

We examined all possible nucleotide substitutions at the central position of 36-nucleotide probes, and found that nonspecific binding by MM oligos depends upon the individual nucleotide substitutions they incorporate: C→A, C→G and T→A (yielding purine-purine mispairs) are most disruptive, whereas A→X were least disruptive. We also quantify a marked GC skew effect: substitutions raising probe GC content exhibit higher intensity (and vice versa). This skew is small in highly-expressed regions (± 0.5% of total intensity range) and large (± 2% or more) elsewhere. Multiple mismatches per oligo are largely additive in effect: each MM added in a distributed fashion causes an additional 21% intensity drop relative to PM, three-fold more disruptive than adding adjacent mispairs (7% drop per MM).

Conclusion

We investigate several parameters for oligonucleotide design, including the effects of each central nucleotide substitution on array signal intensity and of multiple MM per oligo. To avoid GC skew, individual substitutions should not alter probe GC content. RNA sample mixture complexity may increase the amount of nonspecific hybridization, magnify GC skew and boost the intensity of MM oligos at all levels.