理解DNA杂交动力学对诸多研究具有重要意义,例如核酸检测、基因生物技术和DNA纳米技术等.DNA偶联纳米材料丰富了可编程纳米组装结构的功能性,且可实现生物分析和纳米技术应用的超精细控制.尽管末端标记小分子不会对DNA的杂交能力造成太大影响,但与纳米粒子偶联会显著抑制DNA链杂交动力学.DNA杂交受阻不仅降低了复杂纳米结构的构建效率,还会使传感器和纳米马达等响应缓慢.以DNA单价偶联纳米粒子作为理想体系,本文尝试使用琼脂糖凝胶电泳分析研究DNA杂交驱动二聚组装过程的动力学复杂性,揭示了影响DNA杂交反应的多个共存因素.这些因素包括:靠近纳米粒子表面DNA间隔区的刚性;DNA间隔区和杂交区之间发生碱基堆积;固有的碱基序列依赖的杂交活性;DNA杂交序列空间运动的受限性.本研究为DNA功能化纳米材料提供了一种可靠的杂交动力学评价策略,可望为发展结构复杂且响应快速的功能分析器件和高性能生物标记纳米探针提供重要保障.
Understanding DNA hybridization kinetics is highly important for nucleic acid detections, genomic biotechniques, and DNA nanotechnology. DNA-conjugated nanomaterials offer versatile functionalities for DNA-programmable nanoassembly with superfine controls toward bioanalytical and nanotechnological applications. Although small molecule end-tagging does not incur much attenuation of DNA' s hybridizability, nanoparticle-conjugation greatly suppresses the hybridization kinetics of DNA strands. The impeded hybridization not only decreases the efficiency in building complicated nanostructures, but also causes difficulty in realizing rapidly responsive sensors and nanomotors. With monovalent DNA-nanoparticle conjugates as an ideal system, this work aims to unveil the kinetic complexity of hybridization-driven dimeric assembly assayed by agarose gel electrophoresis. Our results point out a coexistence of different factors that can affect the hybridization kinetics of DNA-conjugated nanoparticles, including:the rigidity of a DNA spacer proximal to the nanoparticle surface; the base-stacking between the spacer and a hybridized domain; the inherent base-sequence-dependent DNA hybridizability; and the spatially confined movement of the hybridization sequences. The dimeric hybridization assay offers a reliable platform for kinetic evaluation of DNA-conjugated nanoparticles to enable structurally complicated and rapidly functioning analytical devices and bio-labelling nanoprobes.