Large-scale generation of synthetic DNA libraries: Sequence-specific priming of reverse transcription

Custom-designed DNA and RNA oligonucleotide collections are used as building blocks in synthetic biology, complementary probes for targeted sequencing, and nucleic acid aptamers. They encode information for technologies like RNA interference, protein engineering and DNA-encoded chemical libraries. These applications require an economical source of diverse libraries.;High-throughput microarray technology produces hundreds of thousands of diverse sequences on a single planar substrate at low cost (<;As an application of the amplification technology we developed an integrated method for cDNA library construction with sequence-specific primers incorporating a unique tag and universal primer sequence. The method suffers from the formation of three types of false positives that need to be sufficiently removed to reduce contribution of false-positives signals. A 3 step process is implemented to reduce the false positives contributors and still detect differential expression of yeast genes in galactose and glucose conditions. The sequence-specific primers libraries can be used for applications not limited to detection of low abundance and rare RNA and identification of aberrant splicing variants and gene-fusions.