DNA Walker-Programmed Nanoparticle Superlattice

doi:10.6023/A20090426

Abstract

As a kind of sophisticated dynamic DNA nanomachine, DNA walker has shown powerful application ability in many aspects due to its excellent structural designability and programmability. Taking advantage of stochastic DNA tracks on surface and adaptable DNA outputs of the well-known catalytic hairpin assembly (CHA) circuits, the DNA walkers that move along DNA-coated three-dimensional particle surfaces have attracted much interests. On the other hand, in the field of DNA-mediated nanoparticle assembly, self-assembly of nanoparticles is a thermodynamically driven nonequilibrium process, which is easily trapped at intermediate local free-energy minima, resulting in a disordered structure. Therefore, effective strategies to evade each local free-energy minimum are highly desired. In addition to the traditional annealing strategy, the time-dependent strategy relied on toehold-mediated strand-displacement DNA circuit recently reported by our group has been proven an alternative solution, where interactions between nanoparticles can be tuned in a time-dependent manner for programming dynamic pathway to achieve a free-energy minimum. Through integrating a CHA-based bipedal DNA walker with a DNA-functionalized gold nanoparticle (i.e., spherical nucleic acid; SNA) assembly, a time-dependent strategy for assembly of SNAs programmed by DNA walker at constant temperature was developed in this work. In our strategy, the active sticky ends used for assembly of SNAs can be gradually generated on nanoparticle surface after the walking of the bipedal DNA walker driven by the CHA reaction to induce the synchronization of assembly and bonding between SNAs, thereby obtaining ordered nanoparticle superlattice structure. Take a one-component SNA assembly system for example, the dynamic walking process of the bipedal DNA walker on the surface of SNA was proved to be stable with good walking ability and persistence at first. Then, the SNA assembly kinetics results showed that the bipedal walker concentrations and DNA linker ratios could greatly influence the aggregation of SNA conjugates. Finally, the performance of the integrated SNA assembly system driven by the bipedal DNA walker was investigated under varied concentrations of bipedal walker. In the presence of lower concentrations of the walker strand, the assembly process of SNAs could have a long residence time to switch between the binding and unbinding of the generated sticky ends and achieved a series of near-equilibrium states. Thus, as the interaction between particles grows, the dynamic pathway of nanoparticles assembly can be programmed to achieve a free-energy minimum to form ordered face-centered cubic (FCC) superlattice structure. Based on similar design principle, an asymmetric two-component SNA assembly system programmed by the bipedal DNA walker was constructed to obtain CsCl superlattice structure. Our DNA walker-programmed SNA assembly strategy will have great potential in the creation of functional nanoscale superlattice materials and in the construction of SNA structures with complex phase behaviors.

Key words: dynamic DNA nanomachine, bipedal DNA walker, gold nanoparticle, spherical nucleic acid assembly, superlattice structure

Cite this article

Yijun Guo, Bing Wei, Xiang Zhou, Dongbao Yao, Haojun Liang. DNA Walker-Programmed Nanoparticle Superlattice[J]. Acta Chimica Sinica, 2021, 79(2): 192-199.

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Fig. & Tab. 7

Figure 1. Schematic illustration of the ordered assembly of SNA programmed by catalytic hairpin assembly-based bipedal DNA walker at constant temperature.

Figure 2. Detailed scheme and performance of the walking process of the bipedal DNA walker on SNA surface. (a) The detailed process for the walking reaction of the DNA walker driven by CHA reaction on SNA surface. The double-stranded fluorescent Reporter is used for signaling. (b) Real-time fluorescence kinetic curves show the reaction efficiency of the system in the presence of varied concentrations of W1. In this experiment, [SNA]=2 nmol/L, [H1]=200 nmol/L, [H2]=400 nmol/L, and [Reporter]=50 nmol/L. The reaction temperature is 25 ℃.

Figure 3. Investigation of the persistence of W1 on the H1/SNA surface. (a) Detailed scheme of persistence test of W1 on surface of H1/SNA using FQ-H1 strategy. (b) Fluorescence leakage curves of the system under different reaction conditions. In this experiment, [SNA]=2 nmol/L, [H1]=200 nmol/L, [H2]=400 nmol/L, and [FQ-H1]=200 nmol/L. The reaction temperature is 25 ℃.

Figure 4. Study of the persistence ability of the bipedal walker on H1/SNA surface with different toehold lengths. (a) Real-time fluorescence kinetics curves of the Reporter system with different toehold lengths of the walker. [SNA]=2 nmol/L, [H1]=200 nmol/L, [H2]=400 nmol/L, and [Reporter]=50 nmol/L. (b) Fluorescence leakage curves of the primed-walker with different toehold lengths. In this experiment, [SNA]=2 nmol/L, [H1]=200 nmol/L, [H2]=400 nmol/L, and [FQ-H1]=200 nmol/L. The reaction temperature is 25 ℃.

Figure 5. (a) The one-component SNA assembly system programmed by the DNA walker. (b) The influence of molar ratios of SNA and H1 on the effect of SNA assembly. Here, [SNA]=3.6 nmol/L, [W3]=20 nmol/L, and [H2]=[Complex-A]=2×[H1]. The reaction temperature is 25 ℃.

Figure 6. (a) SAXS measurements for SNA aggregates assembled using the thermal annealing strategy. The gray curves represent the theoretical SAXS patterns for perfect FCC superlattice. (b) SAXS results for SNA aggregates formed using the DNA walker programmed SNA assembly strategy in the presence of various concentrations of W3. Here, [SNA]=3.6 nmol/L, [H1]=80×[SNA], [H2]=[Complex-A]=2×[H1]. The reaction temperature is 25 ℃.

Figure 7. (a) Scheme for the assembly of the asymmetric two-component SNA system driven by the DNA walker. (b) SAXS patterns of the SNA structures formed under different ratios of two SNAs and various concentrations of W3. The gray curves represent the theoretical SAXS patterns for perfect CsCl superlattice. Here, [SNA-1]=3.6 nmol/L, [H1]=80×[SNA-1], [H2]=[Complex-1]=2×[H1], [SNA-2]=1.8 nmol/L (left), 3.6 nmol/L (center), 7.2 nmol/L (right). The reaction temperature is 25 ℃.

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