Gao, F. and Simon, A.E.2017. Differential use of 3’CITEs by the subgenomic RNA of Pea enation mosaic virus 2. Virology 510, 194-204.
Du, Z., Alekhina, O.M., Vassilenko, K.S., and Simon, A.E. 2017. Concerted action of two 3’ cap-independent translation enhancers increases the competitive strength of translated viral genomes. Nucleic Acids Res. doi: 10.1093/nar/gkx643
Le, M.-T., Kasprzak, W.K., Kim, T., Gao, F., Young, M.Y.L, Yuan, X., Shapiro, B.A., Seog, J., and Simon, A.E. 2017. Combined single molecule experimental and computational approaches for understanding the unfolding pathway of a viral translation enhancer that participates in a conformational switch. RNA Biology (Solicited Point of View), in press. doi: 10.1080/15476286.2017.1325069
Le, M.-T., Kasprzak, W.K., Kim, T., Gao, F., Young, M.Y.L, Yuan, X., Shapiro, B.A., Seog, J., and Simon, A.E. 2017. Folding behavior of a T-shaped, ribosome-binding translation enhancer implicated in a wide-spread conformational switch. eLife 6:e22883. https://t.co/JwfvZSZOmd
May, J., Johnson, P., Saleen, H., and Simon, A.E. 2017. A sequence-independent, unstructured IRES is responsible for internal expression of the coat protein of Turnip crinkle virus. J Virol 91, e02421 [SPOTLIGHT selection].
Kuhlmann, M.M., Chattopadhyay, M., Stupina, V. A., Gao, F., and Simon, A. E. 2016. An RNA element that facilitates programmed ribosomal readthrough in Turnip crinkle virus adopts multiple conformations. J Virol. 90, 8575-8591.
Gao, F., and Simon, A. E. 2016. Multiple cis-acting elements modulate programmed-1 ribosomal frameshifting in Pea enation mosaic virus. Nucleic Acids Res 44, 878-895.
Dashi, A., Schwander, P., Langlois, R., Fung, R., Li, W., Hosseinizadeh, A.,Liao, H. Y., Pallesen, J., Sharma, G., Stupina, V.A., Simon, A.E., Dinman, J.D., Frank, J., Ourmazd, A. 2014. Trajectories of the ribosome as a Brownian nanomachine. Proc. Natl. Acad. Sci. USA, 49, 17492-17497.
Gao, F., Kasprzak, W., Szabo, C., Shapiro, B.A., and Simon, A.E. 2014. The 3’UTR of Pea enation mosaic virus contains two T-shaped ribosome-binding cap-independent translation enhancers. J. Virol. 89, 11696-11712.
Gao, F., Reddy, S., Kasprzak, W., Shapiro, B.A., Dinman, J.D., and Simon, A.E. 2014. The kl-TSS translational enhancer of PEMV can bind simultaneously to ribosomes and a 5’ proximal hairpin. J. Virol. 88, 11696–11712.
Chattopadhyay, M., Kuhlmann, M., Kumar, K., and Simon, A.E. 2014. Position of the kissing-loop interaction associated with PTE-type 3’CITEs can affect enhancement of cap-independent translation. Virology, 458-459, 43-52.
Stupina, V.A. and Simon, A.E. 2013. Preparation of biologically active Arabidopsis ribosomes and comparison with yeast ribosomes for binding to a tRNA-mimic that enhances translation of plant plus-strand RNA viruses. Front. Plant Sci. 4, 271. doi: 10.3389/fpls.2013.
Gao, F., Kasprzak, W., Stupina, V.A., Shapiro, B.A. and Simon, A.E. 2012. A ribosome-binding, 3’ translational enhancer has a T-shaped structure and engages in a long distance RNA:RNA interaction. J. Virol. 86, 9828-9842.
Yuan, X., Shi, K., and Simon, A.E. 2012. A local interactive network of 3' RNA elements supports translation and replication in Turnip crinkle virus. J. Virol. 86, 4065-4081.
Guo, R., Meskauskas, A., Dinman, J.D., and Simon, A.E. 2011. Evolution of a helper virus-derived ribosome binding translational enhancer in an untranslated satellite RNA of Turnip crinkle virus. Virology 419, 10-16.
Chattopadhyay, M., Shi, K., Yuan, X., and Simon, A.E. 2011. Long-distance kissing loop interactions between a 3’ proximal Y-shaped structure and apical loops of 5’ hairpins enhance translation of Saguaro cactus virus. Virology 417, 113-125.
Stupina, V.A, Yuan, X, Meskauskas, A., Dinman. J.D., and Simon, A.E. 2011. Ribosome binding to a 5’ translational enhancer is altered in the presence of the 3’UTR in cap-independent translation of Turnip crinkle virus. J. Virol. 85, 4638-4653.
Zuo, X, Wang, J., Yu, P., Eyler, D., Xu, H., Starich, M.R., Tiede, D.M., Simon, A.E., Kasprzak, W., Schwieters, C.D., Shapiro, B.A., and Wang, Y.-W. 2010 The cap-independent translational enhancer and ribosome binding structure element in 3' UTR of Turnip crinkle virus RNA folds into a tRNA-like shape in solution. Proc. Natl. Acad. Sci. USA 107, 1385-1390.
Yuan, X., Shi, K., Meskauskas, A. and Simon, A.E. 2009. The 3’ End of Turnip crinkle virus contains a highly interactive structure with a translational enhancer that is disrupted by binding to the RNA-dependent RNA polymerase. RNA 15, 1849-1864.
Guo, R., Lin, W., Zhang, J., Simon, A. E., and Kushner, D. B. 2009. Structural plasticity and rapid evolution in a viral RNA revealed by in vivo genetic selection. J. Virol. 83, 927-939.
McCormack, J. C., Yuan, X., Yingling, Y. G., Zamora, R. E., Shapiro, B. A., and Simon, A. E. 2008. Structural domains within the 3' UTR of Turnip crinkle virus. J. Virol. 82, 8706-8720.
Stupina, V. A., Meskauskas, A., McCormack, J. C., Yingling, Y. G., Kasprzak, W., Shapiro, B. A., Dinman, J. D., and Simon, A. E. 2008. The 3' proximal translational enhancer of Turnip crinkle virus binds to 60S ribosomal subunits. RNA 14, 2379-2393.
