A unique fluorescent base analogue for the expansion of the genetic alphabet

Fluorescent nucleobase analogues are useful in a wide variety of biology and biotechnology tools as molecular probes and reporters for nucleic acids. Here we present a novel fluorescent purine analogue, 7-(2,2'-bithien-5-yl)-imidazo[4,5-b]pyridine (denoted as Dss). The nucleoside triphosphates of Dss can be site-specifically incorporated into DNA and RNA by polymerases, opposite its pairing partner, pyrrole-2-carbaldehyde (Pa), in DNA templates. Despite its high specificity in replication and transcription, Dss in oligonucleotides functions as a universal base that pairs with all four natural bases with nearly equal thermal stabilities. Thus, Dss would be a powerful tool for fluorescent base replacements at specific positions in functional DNA and RNA molecules.