Replication

Replication of genetic material provides a key step in the molecular information processing of artificial cells, but existing mechanisms for template replication without protein enzymes were either relatively slow or suffered from a high background of non-templated synthesis. Redefining a basis for template chemistry that is fast, has a low background and can be integrated with cell compartmentalization chemistry and metabolism is a major issue in artificial cell design (as addressed in the Chemical Subsystems section). In the course of the project, a novel chemical cross-catalytic replication mechanism based on thioDNA was developed. During most of the project however, work on integrating the replication component of the artificial cell needed to be performed with systems that only partially fulfilled the necessary criteria. For this reason, a range of test systems, including enzymatic and non-enzymatic systems was employed in microfluidic experiments.  An isothermal enzymatic system (strand displacement amplification) and the starting chemical replicator system of Kiedrowski's lab were  first employed to establish an ongoing process of template replication, using a special fan reactor with its self-stabilizing potential. The latter reaction is relatively slow, and the distinction between the template process and the background of non-specific ligation, while significant, limits the investigation of purely templated processes. For this reason, an accelerated single-step ligation-based replication reaction, exploiting protein enzymes was designed and developed. This and an even simpler conformational replication process, developed in Yurke's lab, were used to evelop reliable replication control in the microfluidic system. Then, the novel rapid replication scheme, based on thioDNAs, developed during the PACE project in Kiedrowski's lab, was transported and optimized in the microfluidic setup. Finally, the key process of artificially spatially confined replication in the microfluidic system was investigated.

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