Kammerer, C. et al. Biomimetic and technomimetic single molecular machines. Chem. Lett. 48, 299–308 (2019).
Feringa, B. L. The art of building small: from molecular switches to molecular motors. J. Org. Chem. 72, 6635–6652 (2007).
Bath, J. & Turberfield, A. J. DNA nanomachines. Nat. Nanotechnol. 2, 275–284 (2007).
Erbas-Cakmak, S., Leigh, D. A., McTernan, C. T. & Nussbaumer, A. L. Artificial molecular machines. Chem. Rev. 115, 10081–10206 (2015).
Feng, Y. et al. Molecular pumps and motors. J. Am. Chem. Soc. 143, 5569–5591 (2021).
von Delius, M. & Leigh, D. A. Walking molecules. Chem. Soc. Rev. 40, 3656–3676 (2011).
Chakraborty, K., Veetil, A. T., Jaffrey, S. R. & Krishnan, Y. Nucleic acid-based nanodevices in biological imaging. Annu. Rev. Biochem. 85, 349–373 (2016).
Cui, C. et al. A lysosome-targeted DNA nanodevice selectively targets macrophages to attenuate tumours. Nat. Nanotechnol. 16, 1394–1402 (2021).
Stommer, P. et al. A synthetic tubular molecular transport system. Nat. Commun. 12, 4393 (2021).
Li, Y. et al. Leakless end-to-end transport of small molecules through micron-length DNA nanochannels. Sci. Adv. 8, eabq4834 (2022).
Kamiya, Y. & Asanuma, H. Light-driven DNA nanomachine with a photoresponsive molecular engine. Acc. Chem. Res. 47, 1663–1672 (2014).
Marras, A. E., Zhou, L., Su, H. J. & Castro, C. E. Programmable motion of DNA origami mechanisms. Proc. Natl Acad. Sci. USA 112, 713–718 (2015).
Kudernac, T. et al. Electrically driven directional motion of a four-wheeled molecule on a metal surface. Nature 479, 208–211 (2011).
Ragazzon, G., Baroncini, M., Silvi, S., Venturi, M. & Credi, A. Light-powered autonomous and directional molecular motion of a dissipative self-assembling system. Nat. Nanotechnol. 10, 70–75 (2015).
Erbas-Cakmak, S. et al. Rotary and linear molecular motors driven by pulses of a chemical fuel. Science 358, 340–343 (2017).
Amano, S., Fielden, S. D. P. & Leigh, D. A. A catalysis-driven artificial molecular pump. Nature 594, 529–534 (2021).
Pumm, A. K. et al. A DNA origami rotary ratchet motor. Nature 607, 492–498 (2022).
Shi, X. et al. Sustained unidirectional rotation of a self-organized DNA rotor on a nanopore. Nat. Phys. 18, 1105 (2022).
Wilson, M. R. et al. An autonomous chemically fuelled small-molecule motor. Nature 534, 235–240 (2016).
Baroncini, M. et al. Making and operating molecular machines: a multidisciplinary challenge. ChemistryOpen 7, 169–179 (2018).
Valero, J., Pal, N., Dhakal, S., Walter, N. G. & Famulok, M. A bio-hybrid DNA rotor-stator nanoengine that moves along predefined tracks. Nat. Nanotechnol. 13, 496–503 (2018).
Poppleton, E., Mallya, A., Dey, S., Joseph, J. & Sulc, P. Nanobase.org: a repository for DNA and RNA nanostructures. Nucleic Acids Res. 50, D246–D252 (2022).
Zhou, L., Marras, A. E., Su, H. J. & Castro, C. E. DNA origami compliant nanostructures with tunable mechanical properties. ACS Nano 8, 27–34 (2014).
Shi, Z., Castro, C. E. & Arya, G. Conformational dynamics of mechanically compliant DNA nanostructures from coarse-grained molecular dynamics simulations. ACS Nano 11, 4617–4630 (2017).
Los, G. V. et al. HaloTag: a novel protein labeling technology for cell imaging and protein analysis. ACS Chem. Biol. 3, 373–382 (2008).
Valero, J. & Famulok, M. Regeneration of burnt bridges on a DNA catenane walker. Angew. Chem. Int. Ed. Engl. 59, 16366–16370 (2020).
Yu, Z. et al. A self-regulating DNA rotaxane linear actuator driven by chemical energy. J. Am. Chem. Soc. 143, 13292–13298 (2021).
Scheres, S. H. RELION: implementation of a Bayesian approach to cryo-EM structure determination. J. Struct. Biol. 180, 519–530 (2012).
Pereira, M. J. et al. Single VS ribozyme molecules reveal dynamic and hierarchical folding toward catalysis. J. Mol. Biol. 382, 496–509 (2008).
Sabanayagam, C. R., Eid, J. S. & Meller, A. Using fluorescence resonance energy transfer to measure distances along individual DNA molecules: corrections due to nonideal transfer. J. Chem. Phys. 122, 061103 (2005).
Guajardo, R., Lopez, P., Dreyfus, M. & Sousa, R. NTP concentration effects on initial transcription by T7 RNAP indicate that translocation occurs through passive sliding and reveal that divergent promoters have distinct NTP concentration requirements for productive initiation. J. Mol. Biol. 281, 777–792 (1998).
Koh, H. R. et al. Correlating transcription initiation and conformational changes by a single-subunit RNA Polymerase with near base-pair resolution. Mol. Cell 70, 695–706 e695 (2018).
Tang, G. Q., Roy, R., Bandwar, R. P., Ha, T. & Patel, S. S. Real-time observation of the transition from transcription initiation to elongation of the RNA polymerase. Proc. Natl Acad. Sci. USA 106, 22175–22180 (2009).
Kim, J. H. & Larson, R. G. Single-molecule analysis of 1D diffusion and transcription elongation of T7 RNA polymerase along individual stretched DNA molecules. Nucleic Acids Res. 35, 3848–3858 (2007).
Martin, C. T., Muller, D. K. & Coleman, J. E. Processivity in early stages of transcription by T7 RNA polymerase. Biochemistry 27, 3966–3974 (1988).
Lee, S., Nguyen, H. M. & Kang, C. Tiny abortive initiation transcripts exert antitermination activity on an RNA hairpin-dependent intrinsic terminator. Nucleic Acids Res. 38, 6045–6053 (2010).
Henderson, K. L. et al. RNA polymerase: step-by-step kinetics and mechanism of transcription initiation. Biochemistry 58, 2339–2352 (2019).
Revyakin, A., Liu, C., Ebright, R. H. & Strick, T. R. Abortive initiation and productive initiation by RNA polymerase involve DNA scrunching. Science 314, 1139–1143 (2006).
Shen, H. & Kang, C. Two site contact of elongating transcripts to phage T7 RNA polymerase at C-terminal regions. J. Biol. Chem. 276, 4080–4084 (2001).
Ouldridge, T. E., Louis, A. A. & Doye, J. P. K. Structural, mechanical, and thermodynamic properties of a coarse-grained DNA model. J. Chem. Phys. 134, 085101 (2011).
Rovigatti, L., Sulc, P., Reguly, I. Z. & Romano, F. A comparison between parallelization approaches in molecular dynamics simulations on GPUs. J. Comput. Chem. 36, 1–8 (2015).
Snodin, B. E. et al. Introducing improved structural properties and salt dependence into a coarse-grained model of DNA. J. Chem. Phys. 142, 234901 (2015).
Sulc, P. et al. Sequence-dependent thermodynamics of a coarse-grained DNA model. J. Chem. Phys. https://doi.org/10.1063/1.4754132 (2012).
Thomen, P. et al. T7 RNA polymerase studied by force measurements varying cofactor concentration. Biophys. J. 95, 2423–2433 (2008).
Durniak, K. J., Bailey, S. & Steitz, T. A. The structure of a transcribing T7 RNA polymerase in transition from initiation to elongation. Science 322, 553 (2008).
Ramezani, H. & Dietz, H. Building machines with DNA molecules. Nat. Rev. Genet. 21, 5–26 (2020).
Yoon, J., Eyster, T. W., Misra, A. C. & Lahann, J. Cardiomyocyte-driven actuation in biohybrid microcylinders. Adv. Mater. 27, 4509–4515 (2015).
Sagara, Y. et al. Rotaxanes as mechanochromic fluorescent force transducers in polymers. J. Am. Chem. Soc. 140, 1584–1587 (2018).
Chen, S. et al. An artificial molecular shuttle operates in lipid bilayers for ion transport. J. Am. Chem. Soc. 140, 17992–17998 (2018).
DeLuca, M., Shi, Z., Castro, C. E. & Arya, G. Dynamic DNA nanotechnology: toward functional nanoscale devices. Nanoscale Horiz. 5, 182–201 (2020).
Gerling, T., Wagenbauer, K. F., Neuner, A. M. & Dietz, H. Dynamic DNA devices and assemblies formed by shape-complementary, non-base pairing 3D components. Science 347, 1446–1452 (2015).
Skugor, M. et al. Orthogonally photocontrolled non-autonomous DNA walker. Angew. Chem. Int. Ed. Engl. 58, 6948–6951 (2019).
Wang, S. et al. Light-induced reversible reconfiguration of DNA-based constitutional dynamic networks: application to switchable catalysis. Angew. Chem. Int. Ed. Engl. 57, 8105–8109 (2018).
Asanuma, H., Ito, T., Yoshida, T., Liang, X. & Komiyama, M. Photoregulation of the formation and dissociation of a DNA duplex by using the cis–trans isomerization of azobenzene. Angew. Chem. Int. Ed. Engl. 38, 2393–2395 (1999).
Liu, M., Asanuma, H. & Komiyama, M. Azobenzene-tethered T7 promoter for efficient photoregulation of transcription. J. Am. Chem. Soc. 128, 1009–1015 (2006).
Roy, R., Hohng, S. & Ha, T. A practical guide to single-molecule FRET. Nat. Methods 5, 507–516 (2008).
Chandradoss, S. D. et al. Surface passivation for single-molecule protein studies. J. Vis. Exp. https://doi.org/10.3791/50549 (2014).
Ouldridge, T. E., Sulc, P., Romano, F., Doye, J. P. K. & Louis, A. A. DNA hybridization kinetics: zippering, internal displacement and sequence dependence. Nucleic Acids Res. 41, 8886–8895 (2013).
Snodin, B. E. K. et al. Direct simulation of the self-assembly of a small DNA origami. Acs Nano 10, 1724–1737 (2016).
Douglas, S. M. et al. Rapid prototyping of 3D DNA-origami shapes with caDNAno. Nucleic Acids Res. 37, 5001–5006 (2009).
Suma, A. et al. TacoxDNA: a user-friendly web server for simulations of complex DNA structures, from single strands to origami. J. Comput. Chem. 40, 2586–2595 (2019).
Bohlin, J. et al. Design and simulation of DNA, RNA and hybrid protein–nucleic acid nanostructures with oxView. Nat. Protoc. 17, 1762–1788 (2022).
Poppleton, E. et al. Design, optimization and analysis of large DNA and RNA nanostructures through interactive visualization, editing and molecular simulation. Nucl. Acids Res. https://doi.org/10.1093/nar/gkaa417 (2020)
Doye, J. P. K. et al. The oxDNA coarse-grained model as a tool to simulate DNA origami. Methods Mol. Biol. 2639, 93–112 (2023).
Skinner, G. M., Kalafut, B. S. & Visscher, K. Downstream DNA tension regulates the stability of the T7 RNA polymerase initiation complex. Biophys. J. 100, 1034–1041 (2011).
Kimanius, D., Dong, L., Sharov, G., Nakane, T. & Scheres, S. H. W. New tools for automated cryo-EM single-particle analysis in RELION-4.0. Biochem. J. 478, 4169–4185 (2021).
Kremer, J. R., Mastronarde, D. N. & McIntosh, J. R. Computer visualization of three-dimensional image data using IMOD. J. Struct. Biol. 116, 71–76 (1996).
Mindell, J. A. & Grigorieff, N. Accurate determination of local defocus and specimen tilt in electron microscopy. J. Struct. Biol. 142, 334–347 (2003).
Rohou, A. & Grigorieff, N. CTFFIND4: fast and accurate defocus estimation from electron micrographs. J. Struct. Biol. 192, 216–221 (2015).
Schindelin, J. et al. Fiji: an open-source platform for biological-image analysis. Nat. Methods 9, 676–682 (2012).
Vester, B. & Wengel, J. LNA (locked nucleic acid): high-affinity targeting of complementary RNA and DNA. Biochemistry 43, 13233–13241 (2004).
- SEO Powered Content & PR Distribution. Get Amplified Today.
- PlatoData.Network Vertical Generative Ai. Empower Yourself. Access Here.
- PlatoAiStream. Web3 Intelligence. Knowledge Amplified. Access Here.
- PlatoESG. Carbon, CleanTech, Energy, Environment, Solar, Waste Management. Access Here.
- PlatoHealth. Biotech and Clinical Trials Intelligence. Access Here.
- Source: https://www.nature.com/articles/s41565-023-01516-x
