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The expanding world of DNA and RNA

T. Chen, N. Hongdilokkul, Z. Liu, D. Thirunavukarasu, F.E. Romesberg, Curr. Op. Chem. Biol. (2016) 34:80–87.
pubpic2016bchenWe review nucleotide modifications, such as those to phosphate and sugar moieties that increase nuclease resistance or the range of activities possible, as well as whole nucleobase replacement that results in selective pairing and the creation of unnatural base pairs. Both in vitro and in vivo examples are discussed, including efforts to create semi-synthetic organisms with altered or expanded genetic alphabets.

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Evolution of thermophilic DNA polymerases for the recognition and amplification of C2′-modified DNA

T. Chen, N. Hongdilokkul, Z. Liu, R. Adhikary, S.S. Tsuen, F.E. Romesberg, Nat. Chem. (2016) 8:556-562.
pubpic2016chenWe report the development of a polymerase evolution system and its use to evolve thermostable polymerases that efficiently interconvert C2′-OMe modified oligonucleotides and their DNA counterparts via “transcription” and “reverse transcription,” or more importantly, PCR amplify partially C2′-OMe or C2′-F modified oligonucleotides.

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FRET characterization of complex conformational changes in a large 16S ribosomal RNA fragment site-specifically labeled using unnatural base pairs

T. Lavergne, R. Lamichhane, D.A. Malyshev, Z. Li, L. Li, E. Sperling, J.R. Williamson, D.P. Millar, F.E. Romesberg, ACS Chem. Biol. (2016) 11:1347-1353.
pubpic2016lavergneWe report the synthesis and evaluation of several unnatural ribotriphosphates bearing linkers that allow the chemoselective attachment of different functionalities. One unnatural base pair is used to dual label a 243-nt fragment of a 16S RNA with Cy3 and Cy5, which are then used to characterize conformational changes in the presence of ribosomal proteins.