A protocol to construct RNA-protein devices for photochemical translational regulation of synthetic mRNAs in mammalian cells

Ando, T., Tsukiji, S., Tanaka, T., and Nagamune, T.

(2007). Construction of a small-moleculeintegrated semisynthetic split intein for in vivo

protein ligation. Chem. Commun. 4995–4997.

https://doi.org/10.1039/b712843f.

Baiersdo¨rfer, M., Boros, G., Muramatsu, H., Mahiny,

A., Vlatkovic, I., Sahin, U., and Kariko´, K. (2019). A

facile method for the removal of dsRNA

contaminant from in vitro-transcribed mRNA. Mol.

Ther. Nucleic Acids 15, 26–35. https://doi.org/10.

1016/j.omtn.2019.02.018.

Ballister, E.R., Aonbangkhen, C., Mayo, A.M.,

Lampson, M.A., and Chenoweth, D.M. (2014).

Localized light-induced protein dimerization in

living cells using a photocaged dimerizer. Nat.

Commun. 5, 5475. https://doi.org/10.1038/

ncomms6475.

Cai, B., Kim, D., Akhand, S., Sun, Y., Cassell, R.J.,

Alpsoy, A., Dykhuizen, E.C., Van Rijn, R.M.,

Wendt, M.K., and Krusemark, C.J. (2019).

Selection of DNA-encoded libraries to protein

targets within and on living cells. J. Am. Chem.

22

STAR Protocols 3, 101451, June 17, 2022

Soc. 141, 17057–17061. https://doi.org/10.1021/

jacs.9b08085.

Kawaguchi, R., and Kiryu, H. (2016). Parallel

computation of genome-scale RNA secondary

structure to detect structural constraints on human

genome. BMC Bioinf. 17, 203. https://doi.org/10.

1186/s12859-016-1067-9.

Lambert, T.J. (2019). FPbase: a community-editable

fluorescent protein database. Nat. Methods 16,

277–278. https://doi.org/10.1038/s41592-019-0352-8.

Sato, K., Akiyama, M., and Sakakibara, Y. (2021).

RNA secondary structure prediction using deep

learning with thermodynamic integration. Nat.

Commun. 12, 941. https://doi.org/10.1038/s41467021-21194-4.

Singh, V., Wang, S., and Kool, E.T. (2013).

Genetically encoded multispectral labeling of

proteins with polyfluorophores on a DNA

backbone. J. Am. Chem. Soc. 135, 6184–6191.

https://doi.org/10.1021/ja4004393.

Nakanishi, H., and Saito, H. (2020). Caliciviral

protein-based artificial translational activator for

mammalian gene circuits with RNA-only delivery.

Nat. Commun. 11, 1297. https://doi.org/10.1038/

s41467-020-15061-x.

Untergasser, A., Nijveen, H., Rao, X., Bisseling, T.,

Geurts, R., and Leunissen, J.A.M. (2007).

Primer3Plus, an enhanced web interface to

Primer3. Nucleic Acids Res. 35, W71–W74. https://

doi.org/10.1093/nar/gkm306.

Nakanishi, H., Yoshii, T., Kawasaki, S., Hayashi, K.,

Tsutsui, K., Oki, C., Tsukiji, S., and Saito, H. (2021).

Light-controllable RNA-protein devices for

translational regulation of synthetic mRNAs in

mammalian cells. Cell Chem. Biol. 28, 662–674.e5.

https://doi.org/10.1016/j.chembiol.2021.01.002.

Zhang, Y., So, M.-K., Loening, A.M., Yao, H.,

Gambhir, S.S., and Rao, J. (2006). HaloTag proteinmediated site-specific conjugation of

bioluminescent proteins to quantum dots. Angew.

Chem. Int. Ed. 45, 4936–4940. https://doi.org/10.

1002/anie.200601197.

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