A new rapid amplification of cDNA ends method for extremely guanine plus cytosine-rich genes

Abstract

Rapid amplification of cDNA ends (RACE) is widely used to determine the 5′- and 3′-terminal nucleotide sequences of genes. Many different RACE methods have been developed to meet various requirements, but none addresses the difficult problems that arise when trying to isolate the ends of extremely guanine plus cytosine (GC)-rich genes. In this study, we found that we were unable to isolate the correct 5′ or 3′ end of an insect gene, which appeared to include extremely GC-rich sequences, using current RACE methods. Thus, we developed a new RACE method that can be used for this purpose. This new method entails first-strand cDNA synthesis at 70 °C with Thermo-X reverse transcriptase in the presence of homoectoine, followed by a polymerase chain reaction with 98 °C denaturation steps and Phusion DNA polymerase in the presence of 1 M betaine and 5% dimethyl sulfoxide (DMSO). The use of these conditions yielded 5′- and 3′-RACE products that were approximately 80% GC over 213 and 162 bp, respectively, and included shorter internal regions of 82 to 89% GC.