The relative abundance of the TAp63 and ΔNp63 transcripts in the epithelia of the rabbit limbus, peripheral cornea, and central cornea was analyzed by real-time quantitative RT-PCR (real-time Q-RT-PCR). New Zealand White rabbit was anesthetized, and the ocular surface was excised aseptically and placed on a 60-mm culture dish containing phosphate-buffered saline (PBS). The superfluous connective tissue was removed under a dissecting microscope. The limbal zone was defined as the ring with one-mm width from both sides of the cornea-conjunctival junction. The central corneal zone was defined as the circular area with a 2-mm radius from the center of the cornea. The peripheral corneal zone was defined as the ring between the central cornea and limbal zone.
13 14 This visual definition of the limbal and peripheral zones was determined by the histologic differences in the underlying stroma matrix. Total RNA was extracted (TRIzol; Invitrogen-Gibco) reagent according to the manufacturer’s specifications. RNA sample was dissolved in RNase-free water and the A260/A280 ratio was measured. One microgram of the RNA was used for real-time Q-RT-PCR. The rabbit p63 isoform-specific primers used were ΔNp63 forward, 5′-AAC AGC ATG GAC CAG CAG ATC-3′; ΔNp63 reverse, 5′-TCT GTG CGT GGT CTG TGT TGT-3′; TAp63 forward, 5′-GAG TCC TGC ATG CGG ATA CA-3′; and TAp63 reverse, 5′-AAA ATG GCG CAA CAA ACA AGA-3′. The thermal cycle parameters of real-time Q-RT-PCR were as follow: 2 minutes at 50°C, 10 minutes at 95°C, 40 PCR cycles of 15 seconds at 95°C, and 1 minute at 60°C. The real-time Q-RT-PCR reaction mixture was prepared in a 50 μL solution, containing 2× master mix (SYBR Green PCR Master Mix) and the desired primers (0.5 nM). The PCR-amplified product was quantitated by a sequence detector (Prism 7000; Applied Biosystems, Inc. [ABI], Foster City, CA). The intensity of the green fluorescent dye emissions increased in direct proportion to the increase of the PCR amplified product. The amplification plot was examined early in the reaction, at a point that represents the logarithmic phase of the product accumulation. The point representing the detection threshold of the increase of the fluorescent signal associated with the exponential growth of the PCR product for the detector is defined as the cycle threshold (
C T).
C T is predictive of the quantity of input target—that is, when the conditions of the PCR are the same, the larger the starting concentration of a transcript, the lower the
C T. A normalization experiment was performed simultaneously for each sample (Eukaryotic 18S rRNA Endogenous Control Kit; cat. no. 4333760T; ABI). The data obtained from real-time Q-RT-PCR were calibrated with those of 18S rRNA in the respective tissue and recalibrated with the data obtained from central cornea to obtain the relative expression levels. To validate the specificity of the Q-RT-PCR reaction, the heat-dissociation kinetics for TAp63 and ΔNp63 were performed. Briefly, after Q-RT-PCR, samples and the respective nontemplate control (NTC) were subjected to a heat-dissociation protocol between 60°C and 95°C. The TAp63 and ΔNp63 Q-RT-PCR samples dissociated, respectively, at 76.8°C and 82.4°C. In contrast, the NTC samples showed no dissociation
(Fig. 2) . The single dissociation peak exhibited by the TAp63 and ΔNp63 Q-RT-PCR samples strongly suggested that the amplification is template specific. Polyacrylamide gel (20%) electrophoretic analysis of the reaction mixture also showed the presence of a single product with the expected size range (58 bp for TAp63, and 74 bp for ΔNp63, data not shown).