Synthesis and properties of cross-linkable DNA duplex using 4-amino-2-oxo-6-vinyl-1,3,5-triazine

We synthesized the DNA oligonucleotide containing a new cross-linkable 4-amino-2-oxo-6-vinyltriazine (AOVT) nucleobase analogue (Et-AOVT) and evaluated these properties. Our results of the cross-link assay and thermal denaturing assay of duplexes containing AOVT demonstrated that the additional aza of AOVT has an impact on the duplex stability and crosslink properties. Our data suggests that the additional 5-aza of AOVT is involved in the hydrogen bonding with the complementary guanine, and this hydrogen bonding system successfully flipped the reactive vinyl group out to the major groove of the duplex demonstrating a new paradigm of a “cross-linkable duplex”.