Cancer cell target discovery: comparing laboratory evolution of expanded DNA six-nucleotide alphabets with standard four-nucleotide alphabets.

Abstract

Anthropogenic evolvable genetic information systems (AEGIS) are DNA-like molecules that can be copied, support laboratory in vitro evolution (LIVE), and evolve to give AegisBodies, analogs of antibodies. However, unlike DNA aptamers built from four different nucleotides, AegisBodies are currently built from six different nucleotides. Thus, six-letter AEGIS-LIVE delivers AegisBodies with greater stability in biological mixtures, more folds, and enhanced binding and catalytic power. Unlike DNA however, AEGIS has not benefited from 4 billion years of biological evolution to create AEGIS-specialized enzymes, but only a decade or so of human design. To learn whether AEGIS can nevertheless perform as well as natural DNA as a platform to create functional molecules, we compared two six-letter AegisBodies (LZH5b and LZH8) with a single standard four-letter aptamer, both evolved to bind specific cancer cells with ∼10 cycles of LIVE. Both evolved ∼50 nM affinities. Both discovered proteins on their cancer cell surfaces thought to function only inside of cells. Both can be internalized. Internalizing of LZH5b attached to an AEGIS nanotrain brings attached drugs into the cell. These data show that AEGIS-LIVE can do what four-letter LIVE can do at its limits of performance after 4 billion years of evolution of DNA-specialized enzymes, and better by a few metrics. As synthetic biologists continue to improve enzymology and analytical chemistry to support AEGIS-LIVE, this technology shoud prove increasingly useful as a tool, especially in cancer research.