DNA-targeting Invader probes: discovery, principles and applications.

Development of chemically modified oligonucleotides, nucleic acid mimics, protein-based constructs, and other ligands - capable of sequence-unrestricted recognition of specific double-stranded (ds) DNA regions - is an area of research that continues to attract considerable attention. Efforts are fueled by the need for diagnostic agents, modulators of gene expression, and novel therapeutic modalities against genetic diseases. While pioneering approaches focused on accessing nucleotide-specific features from the grooves of DNA duplexes, recent developments have entailed strand-invading probes, i.e., probes capable of binding to DNA duplexes by breaking existing Watson-Crick base pairs and forming new, more stable base pairs. For the past twenty years, our laboratory has pursued the development of a type of dsDNA-targeting strand-invading probes, which we have named Invader probes. These double-stranded oligonucleotide probes feature intercalator-functionalized nucleotides that are specifically arranged to promote destabilization of the probe duplex, whereas individual strands exhibit very high affinity towards complementary DNA. This account details the discovery, principles, and applications of Invader probes.