Synthetic Biology Parts, Devices and Applications

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­eferences 215

102 Suess, B. (2003) Conditional gene expression by controlling translation with
tetracycline-binding aptamers. Nucleic Acids Res., 31 , 1853–1858.
103 Suess, B., Fink, B., Berens, C., Stentz, R. et al. (2004) A theophylline responsive
riboswitch based on helix slipping controls gene expression in vivo.
Nucleic Acids Res., 32 , 1610–1614.
104 Desai, S.K. and Gallivan, J.P. (2004) Genetic screens and selections for small
molecules based on a synthetic riboswitch that activates protein translation.
J. Am. Chem. Soc., 126 , 13247–13254.
105 Ogawa, A. and Maeda, M. (2008) An artificial aptazyme-based riboswitch and
its cascading system in E. coli. ChemBioChem, 9 , 206–209.
106 Callura, J.M., Dwyer, D.J., Isaacs, F.J., Cantor, C.R. et al. (2010) Tracking,
tuning, and terminating microbial physiology using synthetic riboregulators.
Proc. Natl. Acad. Sci. U.S.A., 107 , 15898–15903.
107 Callura, J.M., Cantor, C.R., and Collins, J.J. (2012) Genetic switchboard
for synthetic biology applications. Proc. Natl. Acad. Sci. U.S.A., 109 ,
5850–5855.
108 Rodrigo, G., Landrain, T.E., and Jaramillo, A. (2012) De novo automated design
of small RNA circuits for engineering synthetic riboregulation in living cells.
Proc. Natl. Acad. Sci. U.S.A., 109 , 15271–15276.
109 Komatsu, Y., Yamashita, S., Kazama, N., Nobuoka, K. et al. (2000) Construction
of new ribozymes requiring short regulator oligonucleotides as a cofactor.
J. Mol. Biol., 299 , 1231–1243.
110 Burke, D.H., Ozerova, N.D.S., and Nilsen-Hamilton, M. (2002) Allosteric
hammerhead ribozyme TRAPs. Biochemistry, 41 , 6588–6594.
111 Penchovsky, R. and Breaker, R.R. (2005) Computational design and
experimental validation of oligonucleotide-sensing allosteric ribozymes.
Nat. Biotechnol., 23 , 1424–1433.
112 Klauser, B. and Hartig, J.S. (2013) An engineered small RNA-mediated genetic
switch based on a ribozyme expression platform. Nucleic Acids Res., 1–11.
113 Elgart, V., Jia, T., and Kulkarni, R. (2010) Quantifying mRNA synthesis and
decay rates using small RNAs. Biophys. J., 98 , 2780–2784.
114 Zuker, M. (2003) Mfold web server for nucleic acid folding and hybridization
prediction. Nucleic Acids Res., 31 , 3406–3415.
115 Markham, N.R. and Zuker, M. (2008) UNAFold: software for nucleic acid
folding and hybridization. Methods Mol. Biol. (Clifton, N.J.), 453 , 3–31.
116 Zuker, M. and Stiegler, P. (1981) Optimal computer folding of large RNA
sequences using thermodynamics and auxiliary information. Nucleic Acids
Res., 9 , 133–148.
117 Lorenz, R., Bernhart, S.H., Höner Zu Siederdissen, C., Tafer, H. et al. (2011)
ViennaRNA Package 2.0. Algorithms Mol. Biol., 6 , 26.
118 Proctor, J.R. and Meyer, I.M. (2013) COFOLD: an RNA secondary structure
prediction method that takes co-transcriptional folding into account.
Nucleic Acids Res., 41 , e102.
119 Xayaphoummine, A., Bucher, T., and Isambert, H. (2005) Kinefold web server
for RNA/DNA folding path and structure prediction including pseudoknots
and knots. Nucleic Acids Res., 33 , W605–W610.
120 Geis, M., Flamm, C., Wolfinger, M.T., Tanzer, A. et al. (2008) Folding kinetics
of large RNAs. J. Mol. Biol., 379 , 160–173.

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