Total RNA was isolated from keratinized conjunctiva by the use of RNA extraction reagent in accordance with the manufacturer’s protocol (TRIzol; Gibco). To investigate relative levels of clusterin mRNA expression in diseased conjunctiva, semiquantitative RT-PCR was performed.
28 The human
G3PDH gene was used as the internal control. Primer sequences used were ACCACAGTCCATGCCATCAC (sense) and TCCACCACCCTGTTGCTGTA (antisense). cDNA was generated by mixing the extracted RNA after ethanol precipitation (1 μg/μL per sample) with a random hexamer primer (Takara Biomedicals, Tokyo, Japan) and incubated at 65°C for 5 minutes, chilled on ice. The mixture was then reverse transcribed in 25 mM MgCl
2, 100 mM Tris-HCl (pH 8.3), 500 mM KCl, 40 U/μL RNase inhibitor (Takara Biomedicals), 10 mM dNTP mixture, and 5 U/μL reverse transcriptase (AMV XL; Takara Biomedicals), for a final volume of 20 μL. The mixture was incubated at 30°C for 10 minutes and 42°C for 30 minutes, heated to 99°C for 5 minutes, and then stored at −20°C until use. For every sample, a 10-μL aliquot (half the total volume) of the same RT product was used for PCR amplification. Oligonucleotide primers to the nontandem repeat regions of clusterin were designed from GenBank sequences CTTGATGCCCTTCTCTCCGTA (sense) and AACGTCCGAGTCAGAAGTGTG (antisense), located at, respectively, nucleotides 684 to 704 and 1194 to 1214 of the clusterin cDNA (GenBank is provided in the public domain by the National Center for Biotechnology Information, Bethesda, MD, and is available at http://www.ncbi.nlm.nih.gov/Genbank). PCR amplifications were performed as previously described,
12 with conditions optimized for the clusterin gene using the RT product from total conjunctival RNA. The linear range of the amplification reaction for clusterin and
G3PDH was determined by checking amplification after each cycle from cycles 16 to 26 for clusterin and from cycles 21 to 31 for
G3PDH. This established that 22 cycles was in the midlinear phase for clusterin, whereas 25 cycles was in the midlinear phase for
G3PDH. All PCR amplifications started with denaturation at 95°C for 3 minutes and ended with a final elongation at 72°C for 10 minutes. The parameters for PCR amplification were as follows: clusterin and
G3PDH, 22 and 25 cycles of denaturation, respectively, at 95°C for 1 minute, annealing at 55°C for 1 minute, and extension at 72°C for 1 minute. A 5-μL aliquot of the reaction mixture was then electrophoresed on a 2% agarose gel (Seakem; FMC Bio Products, Rockland, ME) containing ethidium bromide, to evaluate amplification and fragment size. The amount of amplified product was quantified for each sample using a computing densitometer (The 420OE scanner; PDI, Inc., Huntington Station, NY) and software (Quantity One; PDI, Inc.). To account for any differences in starting amounts of RNA, the final amount of PCR product was expressed as the ratio of the amplified clusterin gene to the
G3PDH gene.