title: Mismatch oligonucleotides in human and yeast: guidelines for probe design on tiling microarrays.
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).
  
  
  CONCLUSIONS
  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.
authors.affiliation: Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA. michael.seringhaus@yale.edu
authors.forename: Michael
authors.initials: M
authors.lastname: Seringhaus
authors.forename: Joel
authors.initials: J
authors.lastname: Rozowsky
authors.forename: Thomas
authors.initials: T
authors.lastname: Royce
authors.forename: Ugrappa
authors.initials: U
authors.lastname: Nagalakshmi
authors.forename: Justin
authors.initials: J
authors.lastname: Jee
authors.forename: Michael
authors.initials: M
authors.lastname: Snyder
authors.forename: Mark
authors.initials: M
authors.lastname: Gerstein
mesh_terms: D001482:Base Composition; D020137:Base Pair Mismatch; D006801:Humans; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D015345:Oligonucleotide Probes; D009841:Oligonucleotides; D012331:RNA, Fungal / Q000235:genetics; D012441:Saccharomyces cerevisiae / Q000235:genetics*
chemical_list: D015345:Oligonucleotide Probes; D009841:Oligonucleotides; D012331:RNA, Fungal