Anchoring a Defined Sequence to the 5′ Ends of mRNAs

Abstract

Among numerous applications, the polymerase chain reaction (PCR) (1,2) provides a convenient means to clone 5′ ends of rare mRNAs and to generate cDNA libraries from tissue available in amounts too low to be processed by conventional methods. Basically, the amplification of cDNAs by the PCR requires the availability of the sequences of two stretches of the molecule to be amplified. A sequence can easily be imposed at the 5′ end of the first-strand cDNAs (corresponding to the 3′ end of the mRNAs) by priming the reverse transcription with a specific primer (for cloning the 5′ end of rare messenger) or with an oligonucleotide tailored with a poly (dT) stretch (for cDNA library construction), taking advantage of the poly (A) sequence that is located at the 3′ end of mRNAs. Several strategies have been devised to tag the 3′ end of the ss-cDNAs (corresponding to the 55′ end of the mRNAs). We (3) and others have described strategies based on the addition of a homopolymeric dG (4,5) or dA (6,7) tail using terminal deoxyribonucleotide transferase (TdT) (“anchor-PCR” [4]). However, this strategy has important limitations. The TdT reaction is difficult to control and has a low efficiency (unpublished observations). But most importantly, the return primers containing a homopolymeric (dC or dT) tail generate nonspecific amplifications, a phenomenon that prevents the isolation of low abundance mRNA species and/or interferes with the relative abundance of primary clones in the library. To circumvent these drawbacks, we have used two approaches. First, we devised a strategy based on a cRNA enrichment procedure, which has been useful to eliminate nonspecific-PCR products and to allow detection and cloning of cDNAs of low abundance (3). More recently, to avoid the nonspecific amplification resulting from the annealing of the homopolymeric tail oligonucleotide, we have developed a novel anchoring strategy that is based on the ligation of an oligonucleotide to the 35′ end of ss-cDNAs. This strategy is referred to as SLIC for single-strand ligation to ss-cDNA (8).