1. H. Yu, S. Zhang, M. Dunn, and J. C. Chaput, An efficient and faithful in vitro replication system for threose nucleic acid, J. Am. Chem. Soc. 135, 3583–3591 (2013).
In this work, we established a replication system for TNA based on two commercial enzymes - Therminator DNA polymerase and SuperScript II Reverse Transcriptase. We determined the efficiency and fidelity of such replication system, and studied the influencing factors such as sequence bias. This strategy enables bi-directional flow of genetic information between DNA and TNA systems, and paves way for in vitro selection of functional TNA molecules.
2. H. Yu, S. Zhang, and J. C. Chaput, Darwinian evolution of an alternative genetic system provides support for TNA as an RNA progenitor, Nat. Chem. 4, 183-187 (2012).
In this work we isolated, for the first time, aptamers composed entirely of unnatural nucleic acids. From an evolutionary perspective, this result provides experimental evidence that supports TNA as a possible RNA progenitor during early evolution on Earth.
3. H. Yu, B. Jiang, and J. C. Chaput, Aptamers can discriminate alkaline proteins with high specificity, ChemBioChem, 12, 2659-2666 (2011).
In this work, we used positive selection and negative selection to isolate DNA aptamers that preferentially recognize histone H4 protein. Under our experimental conditions, the best DNA aptamer binds target histone H4 protein at least 100-fold more tightly than it binds the other histone proteins.
4. J. C. Chaput, H. Yu, and S. Zhang, The emerging world of synthetic genetics, Chem. Biol. 19, 1360-1371 (2012).
5. S. Zhang, H. Yu, and J. C. Chaput, Synthesis of threose nucleic acid (TNA) triphosphates and oligonucleotides by polymerase-mediated primer extension, Curr. Protoc. Nucleic Acid Chem. 4, Unit 4.54 (2013).
6. R. Liu, B. Jiang, H. Yu, and J. C. Chaput, Generating DNA synbodies from previously discovered peptides, ChemBioChem, 12, 1813-1817 (2011).