RNA-mediated DNA modifications and RNA-templated DNA repair

Oligonucleotides represent the most versatile and high-throughput tool for introducing specific modifications in the genome of living cells. These short nucleic acid molecules can be designed and synthesized in large amounts, dispensing with laborious cloning, in vitro mutagenesis and extensive sequencing procedures. Oligonucleotides, which are utilized for in vivo mutagenesis in organisms ranging from bacteria to mammalian cells, are composed of DNA residues only, or DNA with a complementary RNA tract (chimeras) folded into a double hairpin structure. It is generally believed that the DNA stretch functions to correct the genomic alteration, while the RNA part, when present, serves to stabilize the duplex. RNA bases, as well as RNA molecules, can also have a direct and active role in genome modification and remodeling. The development of strategies that can exploit such unique RNA functions may have important implications in gene targeting and gene therapy, especially considering that RNA molecules mimicking RNA oligonucleotides could be generated directly in the nucleus of targeted cells via transcription from viral vectors.