Two new dibenzocyclooctyne–thymidine monomers were incorporated into oligonucleotides and crosslinked to azide-labelled complementary strands across the DNA grooves. Equivalent reactions were successful using a (bicyclo[6.1.0]nonyne) alkyne. Oligonucleotides containing internal cyclooctyne and amino groups were simultaneously reacted with azides and NHS esters of different fluorescent dyes to produce functional genetic probes.