Comb-Type Polycations Effectively Stabilize DNA Triplex

Abstract

DNA triplex formation has been studied as a potential strategy for regulation of gene expression. The triplex is, however, unstable under physiological conditions, so that an effective stabilizer for the triplex formation is needed. Here is shown a novel strategy to stabilize the triplex based on the molecular design of a comb-type polycation. Linear polycations, such as poly(L-lysine) and poly(L-arginine), thermally stabilize DNA duplexes (and triplexes). The complexes between DNA and the polycation are irreversible and are liable to precipitate out of aqueous media. The irreversibility and phase separating properties of the complex impede association of single-stranded (ss) DNAs in the complex to form duplexes and triplexes. A comb-type polycation consisting of a poly(L-lysine) backbone and grafted chains of hydrophilic polymers was prepared. The comb-type copolymers increased solubility of their complex with DNA and suppressed conformational changes of DNA. Thermal melting curve analyses revealed that the comb-type copolymer markedly stabilized DNA triplexes and did not disturb ssDNAs in forming duplexes and triplexes. Reversible and one-step melting/reassociation transitions of poly(dA).2poly(dT) triplex were shown in the pressure of the copolymers. The stabilizing effect of the copolymer was larger than that of spermine, a polyamine considered effective in stabilizing triplexes. These results indicated that molecular design of polycations with a comb-type structure is a novel strategy to create efficient triplex stabilizers. Such comb-type copolymer consisting of various types of polycation backbones and hydrophilic graft chains may have many applications in which specific and precise interactions of polynucleotides are involved.