Stabilization of DNA Multiassembly by Addition of a Phosphate Group at the 5′-Sticky End

Abstract

The effect of 5 0 -phosphorylation at nicks on DNA stabilization was measured through the formation of DNA multiassemblies consisting of 40-mer half-sliding complementary oligonucleotides, which had overlapping complementary 20-mer base sequences. 5 0 -Phosphorylated oligonucleotides formed longer DNA multiassemblies than 5 0 -hydroxylated ones. This result indicated that the 5 0 -phosphorylated sticky ends contribute to the stabilization of the DNA association due to the hydrogen bonds between 3 0 -hydroxy groups and 5 0 -phosphate groups at the nick positions.DNA nanotechnology has attracted a great deal of attention as DNA has a well-defined geometry and highly predictable, diverse, and programmable hybridization.1,2 Through these DNA properties, various DNA multiassemblies; for example, nanoscaled tiles, cubes, and machines, have been fabricated. [3][4][5] In addition, the arrangement of functional materials based on DNA multiassembly via DNA hybridization has been accomplished. 6,7 Since most DNA multiassemblies are prepared through association with sticky-ended DNA, DNA assemblies are known to contain a large number of single-stranded breaks (nicks). The stability of these nicks influence the total stability of the DNA multiassemblies. The effect of 5 0 -phosphorylation on the stability of the nicks has been investigated from the view point of DNA repair process.8 XRD results have shown that the 5 0 -hydroxy group stabilize nicks by forming of a hydrogen bond with the 3 0 -hydroxy group of neighboring DNA. 9 In the case of 5 0 -phosphorylated DNA, two opposite results have been reported. MD simulation has shown that the presence of 3 0 -hydroxy and 5 0 -phosphate groups at the nick attract each other due to the formation of a hydrogen bond. 10 On the other hand, gel electrophoresis, UV melting measurement, and NMR have shown that the presence of a phosphate group at a nick brought about end-fraying because of electrostatic repulsion between the terminal phosphate and backbone phosphate.11-13 Whether 5 0 -phosphorylation stabilizes the nick structure or not remains unclear. In order to prepare stable DNA multiassemblies, not only complementary base-pairing of the sticky-end but also the stabilization of nicks is required. We found 5 0 -phosphorylation of sticky-ended DNA induces formation of a stable long DNA multi-assembly.Herein, we investigated the influence of 5 0 -phosphorylation on the formation of a one-dimensional DNA multiassembly consisting of four kinds of 40-mer half-sliding complementary oligonucleotides, A, B, pA, and pB, which had overlapping complementary 20-mer base sequences (Figure 1: 5 0 -phosphorylation is abbreviated to ''p.'' The base sequences are 5 0 -TTATGTTGTCTTGCAATACAAATGTTCTTCGAGTACTT-AT-3 0 (A or pA) and 5 0 -TGTATTGCAAGACAACATAAA-TAAGTACTCGAAGAACATT-3 0 (B or pB)). This DNA multiassembly can be regarded as an example of pseudo-addition polymerization. The reaction of the active end of the oligonucleotides monomer in the pseudo-addition polymerization results in the hybridizat...