Jasinski, D., Haque, F., Binzel, D. W. & Guo, P. Development of the rising discipline of RNA nanotechnology. ACS Nano 11, 1142–1164 (2017).
Ohno, H., Akamine, S. & Saito, H. RNA nanostructures and scaffolds for biotechnology functions. Curr. Opin. Biotechnol. 58, 53–61 (2019).
Kim, J. & Franco, E. RNA nanotechnology in artificial biology. Curr. Opin. Biotechnol. 63, 135–141 (2020).
Geary, C., Rothemund, P. W. & Andersen, E. S. A single-stranded structure for cotranscriptional folding of RNA nanostructures. Science 345, 799–804 (2014).
Høiberg, H. C., Sparvath, S. M., Andersen, V. L., Kjems, J. & Andersen, E. S. An RNA origami octahedron with intrinsic siRNAs for potent gene knockdown. Biotechnol. J. 14, 1700634 (2018).
Krissanaprasit, A. et al. Genetically encoded, useful single-strand RNA origami: anticoagulant. Adv. Mater. 31, e1808262 (2019).
Li, M. et al. In vivo manufacturing of RNA nanostructures through programmed folding of single-stranded RNAs. Nat. Commun. 9, 2196 (2018).
Jepsen, M. D. E. et al. Growth of a genetically encodable FRET system utilizing fluorescent RNA aptamers. Nat. Commun. 9, 18 (2018).
Liu, D. et al. Branched kissing loops for the development of numerous RNA homooligomeric nanostructures. Nat. Chem. 12, 249–259 (2020).
Nguyen, M. T. A., Pothoulakis, G. & Andersen, E. S. Artificial translational regulation by protein-binding RNA origami scaffolds. ACS Synth. Biol. 11, 1710–1718 (2022).
Pothoulakis, G., Nguyen, M. T. A. & Andersen, E. S. Using RNA origami scaffolds in Saccharomyces cerevisiae for dCas9-mediated transcriptional management. Nucleic Acids Res. 50, 7176–7187 (2022).
Geary, C., Grossi, G., McRae, E. Ok. S., Rothemund, P. W. Ok. & Andersen, E. S. RNA origami design instruments allow cotranscriptional folding of kilobase-sized nanoscaffolds. Nat. Chem. 13, 549–558 (2021).
Severcan, I. et al. A polyhedron made from tRNAs. Nat. Chem. 2, 772–772 (2010).
Afonin, Ok. A. et al. In vitro meeting of cubic RNA-based scaffolds designed in silico. Nat. Nanotechnol. 5, 676–682 (2010).
Ko, S. H. et al. Synergistic self-assembly of RNA and DNA molecules. Nat. Chem. 2, 1050–1055 (2010).
Hao, C. et al. Building of RNA nanocages by re-engineering the packaging RNA of Phi29 bacteriophage. Nat. Commun. 5, 3890 (2014).
Afonin, Ok. A. et al. Multifunctional RNA nanoparticles. Nano Lett. 14, 5662–5671 (2014).
Yu, J., Liu, Z., Jiang, W., Wang, G. & Mao, C. De novo design of an RNA tile that self-assembles right into a homo-octameric nanoprism. Nat. Commun. 6, 5724 (2015).
Geary, C., Chworos, A., Verzemnieks, E., Voss, N. R. & Jaeger, L. Composing RNA nanostructures from a syntax of RNA structural modules. Nano Lett. 17, 7095–7101 (2017).
Zakrevsky, P. et al. Truncated tetrahedral RNA nanostructures exhibit enhanced options for supply of RNAi substrates. Nanoscale 12, 2555–2568 (2020).
Xu, C. et al. 3D RNA nanocage for encapsulation and shielding of hydrophobic biomolecules to enhance the in vivo biodistribution. Nano Res. 13, 3241–3247 (2020).
Kappel, Ok. et al. De novo computational RNA modeling into cryo-EM maps of enormous ribonucleoprotein complexes. Nat. Strategies 15, 947–954 (2018).
Zhang, Ok. et al. Cryo-EM construction of a 40 kDa SAM-IV riboswitch RNA at 3.7 Å decision. Nat. Commun. 10, 5511 (2019).
Kappel, Ok. et al. Accelerated cryo-EM-guided dedication of three-dimensional RNA-only constructions. Nat. Strategies 17, 699–707 (2020).
Zhang, Ok. et al. Cryo-EM and antisense concentrating on of the 28-kDa frameshift stimulation component from the SARS-CoV-2 RNA genome. Nat. Struct. Mol. Biol. 28, 747–754 (2021).
Su, Z. et al. Cryo-EM constructions of full-length Tetrahymena ribozyme at 3.1 Å decision. Nature 596, 603–607 (2021).
Liu, D., Thelot, F. A., Piccirilli, J. A., Liao, M. & Yin, P. Sub-3-Å cryo-EM construction of RNA enabled by engineered homomeric self-assembly. Nat. Strategies 19, 576–585 (2022).
Bonilla, S. L., Vicens, Q. & Kieft, J. S. Cryo-EM reveals an entangled kinetic lure within the folding of a catalytic RNA. Sci. Adv. 8, eabq4144 (2022).
Li, S. et al. Topological crossing within the misfolded Tetrahymena ribozyme resolved by cryo-EM. Proc. Natl Acad. Sci. USA 119, e2209146119 (2022).
Andersen, E. S. et al. Self-assembly of a nanoscale DNA field with a controllable lid. Nature 459, 73–76 (2009).
Bai, X. C., Martin, T. G., Scheres, S. H. & Dietz, H. Cryo-EM construction of a 3D DNA-origami object. Proc. Natl Acad. Sci. USA 109, 20012–20017 (2012).
Martin, T. G. et al. Design of a molecular help for cryo-EM construction dedication. Proc. Natl Acad. Sci. USA 113, E7456–E7463 (2016).
Laing, C. & Schlick, T. Evaluation of four-way junctions in RNA constructions. J. Mol. Biol. 390, 547–559 (2009).
Ennifar, E. et al. The crystal construction of the dimerization initiation website of genomic HIV-1 RNA reveals an prolonged duplex with two adenine bulges. Construction 7, 1439–1449 (1999).
Ennifar, E., Walter, P., Ehresmann, B., Ehresmann, C. & Dumas, P. Crystal constructions of coaxially stacked kissing complexes of the HIV-1 RNA dimerization initiation website. Nat. Struct. Biol. 8, 1064–1064 (2001).
Ennifar, E. & Dumas, P. Polymorphism of bulged-out residues in HIV-1 RNA DIS kissing advanced and construction comparability with answer research. J. Mol. Biol. 356, 771–782 (2006).
Kieken, F., Paquet, F., Brule, F., Paoletti, J. & Lancelot, G. A brand new NMR answer construction of the SL1 HIV-1Lai loop-loop dimer. Nucleic Acids Res. 34, 343–352 (2006).
Baba, S. et al. Resolution RNA constructions of the HIV-1 dimerization initiation website within the kissing-loop and extended-duplex dimers. J. Biochem. 138, 583–592 (2005).
Takahashi, Ok. et al. NMR evaluation of intra- and inter-molecular stems within the dimerization initiation website of the HIV-1 genome. J. Biochem. 127, 681–686 (2000).
Liu, D., Shao, Y., Piccirilli, J. A. & Weizmann, Y. Buildings of artificially designed discrete RNA nanoarchitectures at near-atomic decision. Sci. Adv. 7, eabf4459 (2021).
Richardson, J. S. et al. RNA spine: consensus all-angle conformers and modular string nomenclature (an RNA Ontology Consortium contribution). RNA 14, 465–481 (2008).
Rupert, P. B., Massey, A. P., Sigurdsson, S. T. & Ferre-D’Amare, A. R. Transition state stabilization by a catalytic RNA. Science 298, 1421–1424 (2002).
Isambert, H. The jerky and knotty dynamics of RNA. Strategies 49, 189–196 (2009).
Clatterbuck Soper, S. F., Dator, R. P., Limbach, P. A. & Woodson, S. A. In vivo X-ray footprinting of pre-30S ribosomes reveals chaperone-dependent transforming of late meeting intermediates. Mol. Cell 52, 506–516 (2013).
Punjani, A., Rubinstein, J. L., Fleet, D. J. & Brubaker, M. A. cryoSPARC: algorithms for speedy unsupervised cryo-EM construction dedication. Nat. Strategies 14, 290–296 (2017).
Kremer, J. R., Mastronarde, D. N. & McIntosh, J. R. Pc visualization of three-dimensional picture information utilizing IMOD. J. Struct. Biol. 116, 71–76 (1996).
Zhai, X. et al. LoTToR: an algorithm for missing-wedge correction of the low-tilt tomographic 3D reconstruction of a single-molecule construction. Sci. Rep. 10, 10489 (2020).
Benson, E. et al. DNA rendering of polyhedral meshes on the nanoscale. Nature 523, 441–444 (2015).
Silvester, E. et al. DNA origami signposts for figuring out proteins on cell membranes by electron cryotomography. Cell 184, 1110–1121.e16 (2021).
Lei, D. et al. Three-dimensional structural dynamics of DNA origami Bennett linkages utilizing individual-particle electron tomography. Nat. Commun. 9, 592 (2018).
Wang, S. T. et al. Designed and biologically lively protein lattices. Nat. Commun. 12, 3702 (2021).
Watters, Ok. E., Strobel, E. J., Yu, A. M., Lis, J. T. & Lucks, J. B. Cotranscriptional folding of a riboswitch at nucleotide decision. Nat. Struct. Mol. Biol. 23, 1124–1131 (2016).
Liu, D., Wang, M., Deng, Z., Walulu, R. & Mao, C. Tensegrity: building of inflexible DNA triangles with versatile four-arm DNA junctions. J. Am. Chem. Soc. 126, 2324–2325 (2004).
Zhou, H. & Zhang, S. Current improvement of fluorescent light-up RNA aptamers. Crit. Rev. Anal. Chem. 52, 1644–1661 (2021).
Shibata, T. et al. Protein-driven RNA nanostructured units that operate in vitro and management mammalian cell destiny. Nat. Commun. 8, 540 (2017).
Liu, H. et al. Kinetics of RNA and RNA:DNA hybrid strand displacement. ACS Synth. Biol. 10, 3066–3073 (2021).
Guo, S. et al. Tuning the dimensions, form and construction of RNA nanoparticles for favorable most cancers concentrating on and immunostimulation. Wiley Interdiscip. Rev. Nanomed. Nanobiotechnol. 12, e1582 (2020).
Chandler, M., Panigaj, M., Rolband, L. A. & Afonin, Ok. A. Challenges to optimizing RNA nanostructures for large-scale manufacturing and managed therapeutic properties. Nanomedicine 15, 1331–1340 (2020).
Lorenz, R. et al. ViennaRNA bundle 2.0. Algorithms Mol. Biol. 6, 26 (2011).
Zadeh, J. N. et al. NUPACK: evaluation and design of nucleic acid methods. J. Comput. Chem. 32, 170–173 (2011).
Punjani, A. & Fleet, D. J. 3D variability evaluation: resolving steady flexibility and discrete heterogeneity from single particle cryo-EM. J. Struct. Biol. 213, 107702 (2021).
Tegunov, D. & Cramer, P. Actual-time cryo-electron microscopy information preprocessing with Warp. Nat. Strategies 16, 1146–1152 (2019).
Punjani, A., Zhang, H. & Fleet, D. J. Non-uniform refinement: adaptive regularization improves single-particle cryo-EM reconstruction. Nat. Strategies 17, 1214–1221 (2020).
Pettersen, E. F. et al. UCSF Chimera—a visualization system for exploratory analysis and evaluation. J. Comput. Chem. 25, 1605–1612 (2004).
Goddard, T. D. et al. UCSF ChimeraX: assembly trendy challenges in visualization and evaluation. Protein Sci. 27, 14–25 (2018).
Pettersen, E. F. et al. UCSF ChimeraX: construction visualization for researchers, educators, and builders. Protein Sci. 30, 70–82 (2021).
Croll, T. I. ISOLDE: a bodily real looking surroundings for mannequin constructing into low-resolution electron-density maps. Acta Cryst. D 74, 519–530 (2018).
Rodrigues, J., Teixeira, J. M. C., Trellet, M. & Bonvin, A. pdb-tools: a Swiss military knife for molecular constructions. F1000Res. 7, 1961 (2018).
Liebschner, D. et al. Macromolecular construction dedication utilizing X-rays, neutrons and electrons: current developments in Phenix. Acta Cryst. D 75, 861–877 (2019).
Terwilliger, T. C. et al. Mannequin morphing and sequence task after molecular substitute. Acta Cryst. D 69, 2244–2250 (2013).
Afonine, P. V. et al. New instruments for the evaluation and validation of cryo-EM maps and atomic fashions. Acta Cryst. D 74, 814–840 (2018).
Williams, C. J. et al. MolProbity: extra and higher reference information for improved all-atom construction validation. Protein Sci. 27, 293–315 (2018).
Richardson, J. S., Williams, C. J., Videau, L. L., Chen, V. B. & Richardson, D. C. Evaluation of detailed conformations suggests methods for enhancing cryoEM fashions: helix at decrease decision, ensembles, pre-refinement fixups, and validation at multi-residue size scale. J. Struct. Biol. 204, 301–312 (2018).
Lavery, R., Moakher, M., Maddocks, J. H., Petkeviciute, D. & Zakrzewska, Ok. Conformational evaluation of nucleic acids revisited: Curves+. Nucleic Acids Res. 37, 5917–5929 (2009).
Blanchet, C., Pasi, M., Zakrzewska, Ok. & Lavery, R. CURVES+ net server for analyzing and visualizing the helical, spine and groove parameters of nucleic acid constructions. Nucleic Acids Res. 39, W68–W73 (2011).
Lyngso, J. & Pedersen, J. S. A high-flux automated laboratory small-angle X-ray scattering instrument optimized for answer scattering. J. Appl. Crystallogr. 54, 295–305 (2021).
Li, Y., Beck, R., Huang, T., Choi, M. C. & Divinagracia, M. Scatterless hybrid metallic–single-crystal slit for small-angle X-ray scattering and high-resolution X-ray diffraction. J. Appl. Crystallogr. 41, 1134–1139 (2008).
Oliveira, C. L. P., Vorup-Jensen, T., Andersen, C. B. F., Andersen, G. R. & Pedersen, J. S. in Functions of Synchrotron Mild to Scattering and Diffraction in Supplies and Life Sciences (eds Gomez, M.; Nogales, A.; Cruz Garcia-Gutierrez, M. & Ezquerra, T. A.) 231–244 (Springer, 2009).
Steiner, E. M. et al. The construction of the N-terminal module of the cell wall hydrolase RipA and its function in regulating catalytic exercise. Proteins 86, 912–923 (2018).
Carragher, B. et al. Leginon: an automatic system for acquisition of photographs from vitreous ice specimens. J. Struct. Biol. 132, 33–45 (2000).
Tang, G. et al. EMAN2: an extensible picture processing suite for electron microscopy. J. Struct. Biol. 157, 38–46 (2007).
Solar, M. et al. Sensible issues for utilizing K3 cameras in CDS mode for high-resolution and high-throughput single particle cryo-EM. J. Struct. Biol. 213, 107745 (2021).
Mastronarde, D. N. Automated electron microscope tomography utilizing sturdy prediction of specimen actions. J. Struct. Biol. 152, 36–51 (2005).
Zheng, S. Q. et al. MotionCor2: anisotropic correction of beam-induced movement for improved cryo-electron microscopy. Nat. Strategies 14, 331–332 (2017).
Zhang, Ok. Gctf: real-time CTF dedication and correction. J. Struct. Biol. 193, 1–12 (2016).
Fernandez, J. J., Li, S. & Crowther, R. A. CTF dedication and correction in electron cryotomography. Ultramicroscopy 106, 587–596 (2006).
Weigert, M. et al. Content material-aware picture restoration: pushing the boundaries of fluorescence microscopy. Nat. Strategies 15, 1090–1097 (2018).
Zhang, L. & Ren, G. IPET and FETR: experimental strategy for learning molecular construction dynamics by cryo-electron tomography of a single-molecule construction. PLoS ONE 7, e30249 (2012).
Ludtke, S. J., Baldwin, P. R. & Chiu, W. EMAN: semiautomated software program for high-resolution single-particle reconstructions. J. Struct. Biol. 128, 82–97 (1999).