Self-assembled nucleic acid nanoparticles capable of controlled disassembly in response to a single nucleotide mismatch.

ABSTRACT

We have demonstrated the self-assembled DNA nanoparticles capable of controlled disassembly in response to a single nucleotide change (SNC) in a target nucleic acid. The DNA nanoparticles (avg diameter=51+/-22 nm) were constructed by joining two types of streptavidin-DNA conjugates with 2 molar equiv of a linker strand that carries complementary sequences to both conjugates. Nanoparticle disassembly triggered by a target strand (i.e., a perfect complement to the linker) selectively over mismatched targets was achieved by kinetically controlled nucleation occurring at a 6-nt overhang in the linker. The disassembly process was shown to be dramatically slowed down when using mismatch targets in which the SNC was positioned at the fourth nucleotide from the 3'-end. To verify whether the controlled disassembly also works for a SNC located in the middle of a target strand, we tested a deleterious Z variant (G1024A) of human alpha(1)-antitrypsin as a mismatch target (60-nt) carrying the point mutation at position 39. The wild-type target completed the disassembly process in less than 10 min, whereas the mismatch Z-type target could not complete the disassembly even in 3 h. The DNA nanoparticles are promising for sequence-dependent controlled release of short nucleic acids, including siRNA and antisense oligonucleotides, and construction of smart nanomaterials capable of sensing and processing single-nucleotide polymorphisms.