Experimental efficiency of programmed mutagenesis
- 20 Downloads
Mismatched DNA annealing followed by strand replication can cause the programmed evolution of DNA sequences. We have reported that this process is theoretically equivalent in computational power to a desktop computer by demonstrating a constructive way to encode arbitrary computations as DNA molecules within the framework of programmed mutagenesis, a system that consists solely of cycles of DNA annealing, polymerization, and ligation.1,2) Thus, programmed mutagenesis is theoretically universal and we report here the experimental efficiency of its primitive operations. The measured efficiency of an in vitro programmed mutagenesis system suggests that segregating the products of DNA replication into separate compartments would be an efficient way to implement molecular computation. For computer science, using single DNA molecules to represent the state of a computation holds the promise of a new paradigm of composable molecular computing. For biology, the demonstration that DNA sequences could guide their own evolution under computational rules may have implications as we begin to unravel the mysteries of genome encoding and natural evolution.
KeywordsProgrammed Mutagenesis Universal System Biological Computing String Rewrite Systems Turing Machines
Unable to display preview. Download preview PDF.
- 6).Komiya, K., Sakamoto, K., Gouzu, H., Yokoyama, S., Arita, M., Nishilkawa, A., and Hagiya, M., “Successive State Transitions with I/O Interface by Molecules,”in Proc. of Sixth International Meeting on DNA Based Computers, Preliminary, pp. 21–30, 2000.Google Scholar
- 10).Beaver, D., “Molecular Computing,”1st DIMACS Workshop on DNA-based computers, Princeton, DIMACS Series, 27, pp. 29–36, 1996.Google Scholar
- 13).Winfree, E., “On the Computational Power of DNA Annealing and Ligation,”DNA Based Computers II: DIMACS Workshop, June 10–12, 1996, American Mathematical Society, pp. 191–213, 1998.Google Scholar
- 17).Current Protocols in Molecular Biology (Ausubel, I. and Frederick, M., eds), 8.5, John Wiley & Sons, Inc, 1997.Google Scholar