Article

Encoding Phenotype in Bacteria with an Alternative Genetic Set

Department of Chemistry, Stanford University, Stanford, California 94305-5080, United States
J. Am. Chem. Soc., 2011, 133 (45), pp 18447–18451
DOI: 10.1021/ja208025e
Publication Date (Web): October 8, 2011
Copyright © 2011 American Chemical Society

 Author Contributions

These authors contributed equally to this work.

Abstract

Abstract Image

An unnatural base-pair architecture with base pairs 2.4 Å larger than the natural DNA-based genetic system (xDNA) is evaluated for its ability to function like DNA, encoding amino acids in the context of living cells. xDNA bases are structurally analogous to natural bases but homologated by the width of a benzene ring, increasing their sizes and resulting in a duplex that is wider than native B-DNA. Plasmids encoding green fluorescent protein were constructed to contain single and multiple xDNA bases (as many as eight) in both strands and were transformed into Escherichia coli. Although they yielded fewer colonies than the natural control plasmid, in all cases in which a modified plasmid (containing one, two, three, or four consecutive size-expanded base pairs) was used, the correct codon bases were substituted, yielding green colonies. All four xDNA bases (xA, xC, xG, and xT) were found to encode the correct partners in the replicated plasmid DNA, both alone and in longer segments of xDNA. Controls with mutant cell lines having repair functions deleted were found to express the gene correctly, ruling out repair of xDNA and confirming polymerase reading of the unnatural bases. Preliminary experiments with polymerase deletion mutants suggested combined roles of replicative and lesion-bypass polymerases in inserting correct bases opposite xDNA bases and in bypassing the xDNA segments. These experiments demonstrate a biologically functioning synthetic genetic set with larger-than-natural architecture.

Experimental details, sequencing data, and characterization of synthetic DNAs/xDNAs. This material is available free of charge via the Internet at http://pubs.acs.org.

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Received 24 August 2011
Published online 8 October 2011
Published in print 16 November 2011
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