Sample A: Cover Page of Thesis, Project, or Dissertation Proposal

Factors influencing Signal Interpretation
Hybridization Factors
Microarray experiments result in an image output recording the extent of millions of uncatalyzed
chemical reactions; these reactions are influenced by reactant concentrations, solvent conditions,
time, and temperature [10]. In addition to these basic reaction parameters the reagents themselves
have properties which affect the reaction, as discussed below:
1) Probe Concentration. Probes are affixed to their designated grid positions in high
concentrations, in order to drive the reaction towards product formation [14]. This is
necessary since the sample’s target concentration is unknown and often times low. In
addition to concentration, individual probe attributes such as length and base
composition and order affect the stability of the product [10]. Probe length limits the
concentration of probes which can be affixed since individual probes must not
interact with one another and there must be sufficient space for target diffusion
between the probe molecules [29]. Longer products, those over ~70 nucleotides in
length, approach a common melting temperature and have little sequence
dependence, while shorter duplexes demonstrate more variability in temperatures and
are influenced by base composition and order as well as length [10, 22, 25, 26]. Self
complementary pairings lead to the formation of secondary structure in both the
probes and targets, which compete for maximal product duplex formation [30].
Probe secondary structure formation becomes increasingly likely as the probe length
increases. The stability of a duplex is more sensitive to mismatches when the duplex
is shorter, which can be treated as either a confounding factor or a desirable feature,
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