Molecular Design for Specific Recognition and Reaction in Genome-Targeting Chemistry

Molecules that can target DNA or RNA with high efficiency and specificity are of great interest because of potential applications to modulation of gene expression at a specific site. Our approach in genome-targeting chemistry has been focused on development of reactive molecules with high base- as well as sequence selectivity. This paper summarizes our contributions in this field. At first, a general concept of reactive molecules in genome-targeting chemistry is introduced. In the following section, molecular design to achieve specific and efficient reactions in the living system is described. Two new reactive molecules, 2-amino-6-vinylpurine derivative as an efficient cross-linking agent, and the Snitroso- 6-thioguanosine as a selective S to N nitoroso group transfer agent are summarized. These two molecules demonstrate successful examples of reactive agents that are activated only in the complementary hybrids. In the third section, new nucleoside analogs to expand recognition codes of triplex formation are discussed. We have recently developed non-natural nucleoside analogs (W-shaped nucleoside analog: WNA) having a heterocyclic ring as a recognition unit and an aromatic ring as a stacking part on the bicyclo[3.3.0]octane skeleton. It has been shown that the two analogs, WNA-βT with a thymine and WNA-βC with a cytosine, exhibit stable formation of non-natural triplexes containing a TA and a CG interrupting site with high stability, respectively. These new genome-targeting molecules will be applied to artificial modulation of gene expression in vitro as well as in vivo.