Complete Open Reading Frame (C-ORF) Technique: Rapid and Efficient Method for Obtaining Complete Protein Coding Sequences

Several approaches, generally referred to as rapid amplification of cDNA ends, are currently used as a means of obtaining full-length cDNA clones by PCR. However, these protocols are not infallible and in specific instances they have proven unsuccessful, emphasizing a need for further refinement. A novel method, the complete open reading frame (C-ORF) technique, is presently described, which has proven successful in cases, where standard rapid amplification of cDNA ends (RACE) has not worked. In C-ORF, the 5′ PCR primer site is provided by a degenerative stem-loop annealing primer, which consists of a stem-loop structure and a 3′ random 12-mer. degenerative stem-loop annealing primer is designed to anneal at random sites of the first strand cDNA, while promoting second strand synthesis from the end of given cDNA. Although this technique manifests weak sequence preference for GC-rich regions, in practice it has been successfully applied to clone both known and unknown genes with varying regions of GC-rich content. C-ORF does not use additional enzymes other than reverse transcriptase and Taq polymerase making it a cost-effective and relatively simple method that should be of general utility for gene cloning in multiple laboratories.