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

likelihood that no such structural regions form is vanishingly small. Because of the
highly folded structures that result there can also be tertiary structures present,
compounding the likelihood that the availability of intended sites for probe binding
will be sterically hindered, and greatly decreasing the diffusion constant of the
molecule in solution (slowing the rate of duplex formation further) [29]. Shearing of
targets strands is thus recommended, with the goal of ending with target lengths that
are approximately equivalent to probe lengths [5, 10, 35].
3) Temperature. As noted above, the probe length and base composition affect the
melting temperature (Tm) of any duplex, where the melting temperature is defined as
the temperature at which 50% of the duplex structures are dissociated [22, 25, 26,
36]. Experimental conditions are designed as a best fit for the average of the
hundreds of thousands of individual reactions occurring on the array. Solvent
components can be altered to change the dielectric constant of the solution, altering
the energetics of the product’s hydrogen bonds [34, 37].
4) Equilibration Time. As noted above, the competition among highly similar targets
for the same complementary probe sequence requires that adequate hybridization
time be allocated, in order for the reaction to achieve equilibrium. Short hairpin
structures are less energetically favorable than long duplexes, but since unimolecular
reactions occur in a much shorter period of time than bimolecular reactions,
unimolecular reactions can kinetically trap probe or target in non-optimal forms[5,
10] . The various kinetic properties of the tens of thousands of probes realistically
prevent a significant proportion of probe-target interactions from achieving chemical
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