Total RNA was extracted from normal, FED, and PBK HCEC-DM complexes (
Table 1 , samples 8–13, 17, 18) as recommended by the manufacturer (TRIzol; Invitrogen). RNA quantity and quality were assessed by spectrophotometric analysis. For all samples, cDNA was prepared by reverse transcription from equal amounts of RNA in a volume of 40 μL using a commercially available kit (Promega).
Table 2provides information regarding the sequences of the upstream and downstream primers used for RT-PCR and specific PCR conditions for CLU and β2-MG (β2-microglobulin).
27 30 The PCR was performed in a 50-μL reaction mixture containing equal amounts of normal, FED, or PBK cDNA and 0.2 μM of each of the upstream and downstream primers, plus reagents from a commercially available kit (Invitrogen). Specificity and yield of the PCR products were enhanced by using the hot-start approach.
31 The linear range of amplification reaction for CLU and β2-MG was tested by using serial cDNA dilutions and by varying the number of cycles. For CLU, the PCR reaction was run for 25, 28, 30, and 35 cycles. At 35 cycles, the cDNA level was still within the exponential range. Thirty cycles was found to be optimal for β2-MG. A 10-minute extension was added at the end of all PCRs. PCR products and 100-bp DNA ladder molecular weight markers were electrophoresed in 1.5% agarose gels containing 0.5 μg/mL ethidium bromide and then photographed. β2-MG was used for normalization of cDNA load based on published papers
30 32 and on personal communication (2007) with Alexander V. Ljubimov (Ophthalmology Research Laboratories, Cedars-Sinai Medical Center, Los Angeles, CA). Negative control experiments consisted of the PCR reaction mixture, including primers, but without cDNA. To ensure that the total RNA samples were not contaminated with genomic DNA, a negative control was used where cDNA of each sample was replaced by the same amount of total RNA in the PCR reaction mixture, along with 0.2 μM each of β2-MG upstream and downstream primers. Images of PCR gels were obtained with an image-analysis system (Gel Doc 2000; Bio-Rad). Semiquantitative analysis of the images was made using NIH Image-J version 1.37v (http://rsb.info.nih.gov/ij/download.html). The experiments were repeated at least two times. The results were averaged and the standard deviation calculated. Statistical analysis was performed with Student’s unpaired
t-test (Excel 2002 for Windows XP; Microsoft).
P < 0.05 was considered to be significant. The specificity of the amplified CLU cDNA PCR product was confirmed by sequencing at the DNA Sequencing Center for Vision Research (DSCVR) at Massachusetts Eye and Ear Infirmary.