RNA sample optimization for cryo-EM analysis

Statello, L., Guo, C. J., Chen, L. L. & Huarte, M. Gene regulation by long non-coding RNAs and its biological functions. Nat. Rev. Mol. Cell Biol. 22, 96–118 (2021).

Article  CAS  PubMed  Google Scholar 

Cech, T. R. & Steitz, J. A. The noncoding RNA revolution—trashing old rules to forge new ones. Cell 157, 77–94 (2014).

Article  CAS  PubMed  Google Scholar 

Atkins, J. F., Gesteland, R. F. & Cech, T. RNA Worlds: From Life’s Origins to Diversity in Gene Regulation (Cold Spring Harbor, 2011).

Butcher, S. E. & Pyle, A. M. The molecular interactions that stabilize RNA tertiary structure: RNA motifs, patterns, and networks. Acc. Chem. Res. 44, 1302–1311 (2011).

Article  CAS  PubMed  Google Scholar 

Narlikar, G. J. & Herschlag, D. Mechanistic aspects of enzymatic catalysis: lessons from comparison of RNA and protein enzymes. Annu. Rev. Biochem. 66, 19–59 (1997).

Article  CAS  PubMed  Google Scholar 

Doherty, E. A. & Doudna, J. A. Ribozyme structures and mechanisms. Annu. Rev. Biophys. 30, 457–475 (2001).

Article  CAS  Google Scholar 

Cech, T. R. Ribozymes, the first 20 years. Biochem. Soc. Trans. 30, 1162–1166 (2002).

Article  CAS  PubMed  Google Scholar 

Sherwood, A. V. & Henkin, T. M. Riboswitch-mediated gene regulation: novel RNA architectures dictate gene expression responses. Annu. Rev. Microbiol. 70, 361–374 (2016).

Article  CAS  PubMed  Google Scholar 

Roth, A. & Breaker, R. R. The structural and functional diversity of metabolite-binding riboswitches. Annu. Rev. Biochem. 78, 305–334 (2009).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Yang, Y., Harris, K. A., Widner, D. L. & Breaker, R. R. Structure of a bacterial OapB protein with its OLE RNA target gives insights into the architecture of the OLE ribonucleoprotein complex. Proc. Natl Acad. Sci. USA 118, e2020393118 (2021).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Jaafar, Z. A. & Kieft, J. S. Viral RNA structure-based strategies to manipulate translation. Nat. Rev. Microbiol. 17, 110–123 (2019).

Article  CAS  PubMed  Google Scholar 

Mattick, J. S. et al. Long non-coding RNAs: definitions, functions, challenges and recommendations. Nat. Rev. Mol. Cell Biol. 24, 430–447 (2023).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Ding, J. et al. Visualizing RNA conformational and architectural heterogeneity in solution. Nat. Commun. 14, 714 (2023).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Luo, B. et al. Cryo-EM reveals dynamics of Tetrahymena group I intron self-splicing. Nat. Catal. 6, 298–309 (2023).

Article  CAS  Google Scholar 

Bonilla, S. L., Sherlock, M. E., MacFadden, A. & Kieft, J. S. A viral RNA hijacks host machinery using dynamic conformational changes of a tRNA-like structure. Science 374, 955–960 (2021).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Ganser, L. R., Kelly, M. L., Herschlag, D. & Al-Hashimi, H. M. The roles of structural dynamics in the cellular functions of RNAs. Nat. Rev. Mol. Cell Biol. 20, 474–489 (2019).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Dethoff, E. A., Chugh, J., Mustoe, A. M. & Al-Hashimi, H. M. Functional complexity and regulation through RNA dynamics. Nature 482, 322–330 (2012).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Spitale, R. C. & Incarnato, D. Probing the dynamic RNA structurome and its functions. Nat. Rev. Genet. 24, 178–196 (2023).

Article  CAS  PubMed  Google Scholar 

Zhang, J. & Ferré-D’Amaré, A. R. New molecular engineering approaches for crystallographic studies of large RNAs. Curr. Opin. Struct. Biol. 26, 9–15 (2014).

Article  PubMed  Google Scholar 

Spitale, R. C. & Wedekind, J. E. Exploring ribozyme conformational changes with X-ray crystallography. Methods 49, 87–100 (2009).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Zhang, H. & Keane, S. C. Advances that facilitate the study of large RNA structure and dynamics by nuclear magnetic resonance spectroscopy. Wiley Interdiscip. Rev. RNA 10, e1541 (2019).

Article  PubMed  PubMed Central  Google Scholar 

Barnwal, R. P., Yang, F. & Varani, G. Applications of NMR to structure determination of RNAs large and small. Arch. Biochem. Biophys. 628, 42–56 (2017).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Ma, H., Jia, X., Zhang, K. & Su, Z. Cryo-EM advances in RNA structure determination. Signal Transduct. Target Ther. 7, 58 (2022).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Zhang, K. et al. Cryo-EM and antisense targeting of the 28-kDa frameshift stimulation element from the SARS-CoV-2 RNA genome. Nat. Struct. Mol. Biol. 28, 747–754 (2021).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Kappel, K. et al. Accelerated cryo-EM-guided determination of three-dimensional RNA-only structures. Nat. Methods 17, 699–707 (2020).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Wang, X., Terashi, G. & Kihara, D. CryoREAD: de novo structure modeling for nucleic acids in cryo-EM maps using deep learning. Nat. Methods 20, 1739–1747 (2023).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Ma, H. et al. Auto-DRRAFTER: automated RNA modeling based on cryo-EM density. Methods Mol. Biol. 2568, 193–211 (2023).

Article  PubMed  Google Scholar 

Biesiada, M., Purzycka, K. J., Szachniuk, M., Blazewicz, J. & Adamiak, R. W. in RNA Structure Determination: Methods and Protocols (eds Turner, D. H. & Mathews, D. H.) 199–215 (Humana, 2016).

Boniecki, M. J. et al. SimRNA: a coarse-grained method for RNA folding simulations and 3D structure prediction. Nucleic Acids Res. 44, e63 (2016).

Article  PubMed  Google Scholar 

Li, T. et al. All-atom RNA structure determination from cryo-EM maps. Nat. Biotechnol. https://doi.org/10.1038/s41587-024-02149-8 (2024).

Jamali, K. et al. Automated model building and protein identification in cryo-EM maps. Nature 628, 450–457 (2024).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Liu, D., Thélot, F. A., Piccirilli, J. A., Liao, M. & Yin, P. Sub-3-Å cryo-EM structure of RNA enabled by engineered homomeric self-assembly. Nat. Methods 19, 576–585 (2022).

Article  CAS  PubMed  Google Scholar 

Sampedro Vallina, N., McRae, E. K. S., Hansen, B. K., Boussebayle, A. & Andersen, E. S. RNA origami scaffolds facilitate cryo-EM characterization of a Broccoli–Pepper aptamer FRET pair. Nucleic Acids Res. 51, 4613–4624 (2023).

Article  PubMed  PubMed Central 

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