Inactivation of both alleles of the RBI gene during normal retinal development initiates the formation of a retinoblastoma (RB) In 70% of tumors, the second mutation involves the somatic loss of the normal allele, often by mitotic recombination and loss of heterozygosity (LOH) in the RBI locus (4, 9).A cDNA corresponding to the RBI locus has been cloned and sequenced (2,11,12). The mRNA is ubiquitously expressed, producing a 928-amino-acid, 105-kilodalton nuclear phosphoprotein, detectable in a variety of tissues (12,24). Homozygous deletion of RBJ has been noted in several RB tumors and in other tumor types (12,13,17,18,23,24
MATERIALS AND METHODSCell culture and nucleic acid isolation. RB tumor cell lines (14, 15) and Epstein-Barr virus (EBV)-transformed lymphocytes (34) were grown as described previously. Fresh surgical RB tumor specimens and cultured cells were lysed in guanidine thiocyanate and layered on a CsCl gradient. The RNA and DNA were isolated as described before (6, 17).PCR oligonucleotides. The oligonucleotides were synthesized with an Applied Biosystems model 380A DNA synthesizer.First-strand cDNA synthesis from total RNA, using specific primers. Oligonucleotides JD1, JD3, and JD5 (0.5 pmol each) were added to 10 to 20 ,ug of total RNA in 10 ,ul of 200 mM NaCl-40 mM PIPES [piperazine-N,N'-bis(2-ethanesulfonic acid)], pH 6.5-1 mM EDTA and heated to 70°C for 2 min, followed by incubation at 42°C for 4 h. cDNA synthesis was initiated by the addition of 40 ,ul of RTase buffer containing 60 mM Tris hydrochloride, pH 8.3, 12.5 mM MgCl2, 50 mM KCl, 2.5 mM NaPPi, 2.5 mM dithiothreitol, a 0.5 mM concentration of each deoxynucleoside triphosphate, 25 U of RNAguard (Pharmacia), 20 U of avian myeloblastosis virus (Boehringer Mannheim Diagnostics), and 22 U of murine (Pharmacia) reverse transcriptases. Reaction mixtures were incubated at 40°C for 2 h and then frozen at -20°C until needed.Amplification of cDNA and genomic DNA, using the PCR. Genomic DNA (1 ,ug) or cDNA (1/10 of first-strand synthesis) was denatured in 0.2 M NaOH for 5 min at room temperature and then neutralized with HCl prior to amplification. PCR was performed as described before (28), using three constant-temperature water baths and a robot arm to move the samples between water baths. For amplifications of s500 base pairs (bp), we used 80-s denaturation at 93°C, 100-s annealing at 56°C, and 60-s extension at 72°C. For longer products, the extension times were increased. The extension times were increased to 5 to 10 min on the last cycle to ensure complete synthesis. Typically, 30 cycles were sufficient for cloning and RNase protection experiments. The PCR reaction mixture was brought to 5 mM EDTA and 300 mM NaOAc and extracted sequentially with equal volumes of phenol and chloroform-isoamyl alcohol 4596