Table 1 Nomenclature

S

cDNA sample anti-sense strand

R

Genomic DNA anti-sense strand

R'

Genomic DNA sense strand

B

Bound (immobilized) anti-sense strand

B'

Bound (immobilized) sense strand

Subscript 0

Initial concentration

SR'

Double strand formed in solution by hybridization of anti-sense cDNA strand and sense genomic DNA strand

RR'

Double strand formed in solution by hybridization of anti-sense and sense genomic DNA strands

SB'

Double strand formed on surface by hybridization of anti-sense cDNA strand and sense bound strands

RB'

Double strand formed on surface by hybridization of anti-sense genomic DNA strand and sense bound strands

R'B

Double strand formed on surface by hybridization of sense genomic DNA strand and anti-sense bound strands

h

Height of spot phase

r

Radius of spot phase

k_b

Rate constant of backward reaction of hybridization

k_f

Rate constant of forward reaction of hybridization between mobile species

k_f-bound

Rate constant of forward reaction of hybridization between mobile and bound species

k_t

Rate constant for transport between the two phases

γ

Ratio obtained from a hybridization assay using genomic DNA as a reference { = [SB']/([RB']+[R'B])}

α

Assay efficiency = (γ₁/γ₂)/(S₁₀/S₂₀), where 1 and 2 denote samples 1 and 2

ε_S

Amount of S reacted with R'

ε_R

Amount of R reacted with R'