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DNA double helix, a tiny electromotor


  • Pelesko, J. A. & Bernstein, D. H. Modeling MEMS and NEMS (CRC, 2002).

  • Tsoukalas, Okay., Vosoughi Lahijani, B. & Stobbe, S. Affect of transduction scaling legal guidelines on nanoelectromechanical techniques. Phys. Rev. Lett. 124, 223902 (2020).

    Article 
    CAS 

    Google Scholar
     

  • Bustamante, C., Keller, D. & Oster, G. The physics of molecular motors. Acc. Chem. Res. 34, 412–420 (2001).

    Article 
    CAS 

    Google Scholar
     

  • Julicher, F., Ajdari, A. & Prost, J. Modeling molecular motors. Rev. Mod. Phys. 69, 1269–1281 (1997).

    Article 
    CAS 

    Google Scholar
     

  • Boyer, P. D. The ATP synthase—a splendid molecular machine. Annu. Rev. Biochem. 66, 717–749 (1997).

    Article 
    CAS 

    Google Scholar
     

  • Deme, J. C. et al. Constructions of the stator complicated that drives rotation of the bacterial flagellum. Nat. Microbiol. 5, 1553–1564 (2020).

    Article 
    CAS 

    Google Scholar
     

  • Junge, W., Lill, H. & Engelbrecht, S. ATP synthase: an electrochemical transducer with rotatory mechanics. Developments Biochem. Sci. 22, 420–423 (1997).

    Article 
    CAS 

    Google Scholar
     

  • Hernández, J. V., Kay, E. R. & Leigh, D. A. A reversible artificial rotary molecular motor. Science 306, 1532–1537 (2004).

    Article 

    Google Scholar
     

  • Roke, D., Wezenberg, S. J. & Feringa, B. L. Molecular rotary motors: Unidirectional movement round double bonds. Proc. Natl Acad. Sci. USA 115, 9423–9431 (2018).

    Article 
    CAS 

    Google Scholar
     

  • Seeman, N. C. & Sleiman, H. F. DNA nanotechnology. Nat. Rev. Mater. 3, 17068 (2017).

    Article 

    Google Scholar
     

  • Rothemund, P. W. Okay. Folding DNA to create nanoscale shapes and patterns. Nature 440, 297–302 (2006).

    Article 
    CAS 

    Google Scholar
     

  • Gu, H., Chao, J., Xiao, S.-J. J. & Seeman, N. C. A proximity-based programmable DNA nanoscale meeting line. Nature 465, 202–205 (2010).

    Article 
    CAS 

    Google Scholar
     

  • Modi, S. et al. A DNA nanomachine that maps spatial and temporal pH modifications inside dwelling cells. Nat. Nanotechnol. 4, 325–330 (2009).

    Article 
    CAS 

    Google Scholar
     

  • Marras, A. E., Zhou, L., Su, H.-J. & Castro, C. E. Programmable movement of DNA origami mechanisms. Proc. Natl Acad. Sci. USA 112, 713–718 (2015).

    Article 
    CAS 

    Google Scholar
     

  • Kosuri, P., Altheimer, B. D., Dai, M., Yin, P. & Zhuang, X. Rotation monitoring of genome-processing enzymes utilizing DNA origami rotors. Nature 572, 136–140 (2019).

    Article 
    CAS 

    Google Scholar
     

  • Yurke, B., Turberfield, A. J., Mills, A. P., Simmel, F. C. & Neumann, J. L. A DNA-fuelled molecular machine made from DNA. Nature 406, 605–608 (2000).

    Article 
    CAS 

    Google Scholar
     

  • Shin, J.-S. & Pierce, N. A. An artificial DNA walker for molecular transport. J. Am. Chem. Soc. 126, 10834–10835 (2004).

    Article 
    CAS 

    Google Scholar
     

  • Inexperienced, S., Bathtub, J. & Turberfield, A. Coordinated chemomechanical cycles: a mechanism for autonomous molecular movement. Phys. Rev. Lett. 101, 238101 (2008).

    Article 
    CAS 

    Google Scholar
     

  • Omabegho, T., Sha, R. & Seeman, N. C. A bipedal DNA Brownian motor with coordinated legs. Science 324, 67–71 (2009).

    Article 
    CAS 

    Google Scholar
     

  • Lund, Okay. et al. Molecular robots guided by prescriptive landscapes. Nature 465, 206–210 (2010).

    Article 
    CAS 

    Google Scholar
     

  • Khara, D. C. et al. DNA bipedal motor strolling dynamics: an experimental and theoretical examine of the dependency on step dimension. Nucl. Acids Res. 46, 1553–1561 (2017).

    Article 

    Google Scholar
     

  • Bazrafshan, A. et al. Tunable DNA origami motors translocate ballistically over μm distances at nm/s speeds. Angew. Chem. Int. Ed. 59, 9514–9521 (2020).

    Article 
    CAS 

    Google Scholar
     

  • Tomaru, T., Suzuki, Y., Kawamata, I., Shin-ichiro, M. N. & Murata, S. Stepping operation of rotary DNA origami system. Chem. Commun. 53, 7716–7719 (2017).

    Article 
    CAS 

    Google Scholar
     

  • Wang, Z.-G., Elbaz, J. & Willner, I. A dynamically programmed DNA transporter. Angew. Chem. Int. Ed. 51, 4322–4326 (2012).

    Article 
    CAS 

    Google Scholar
     

  • Thubagere, A. J. et al. A cargo-sorting DNA robotic. Science 357, eaan6558 (2017).

    Article 

    Google Scholar
     

  • Kuzyk, A. et al. Reconfigurable 3D plasmonic metamolecules. Nat. Mater. 13, 862–866 (2014).

    Article 
    CAS 

    Google Scholar
     

  • Ketterer, P., Willner, E. M. & Dietz, H. Nanoscale rotary equipment fashioned from tight-fitting 3D DNA elements. Sci. Adv. 2, e1501209 (2016).

    Article 

    Google Scholar
     

  • Ahmadi, Y. et al. The brownian and flow-driven rotational dynamics of a multicomponent DNA origami-based rotor. Small 16, 2001855 (2020).

    Article 
    CAS 

    Google Scholar
     

  • Bertosin, E. et al. A nanoscale reciprocating rotary mechanism with coordinated mobility management. Nat. Commun. 12, 7138 (2021).

    Article 
    CAS 

    Google Scholar
     

  • Kopperger, E. et al. A self-assembled nanoscale robotic arm managed by electrical fields. Science 359, 296–301 (2018).

    Article 
    CAS 

    Google Scholar
     

  • Tripathi, P. et al. Electrical unfolding of cytochrome c throughout translocation via a nanopore constriction. Proc. Natl Acad. Sci. USA 118, e2016262118 (2021).

  • Luan, B. & Aksimentiev, A. Electro-osmotic screening of the DNA cost in a nanopore. Phys. Rev. E 78, 021912 (2008).

    Article 

    Google Scholar
     

  • Holt, J. Okay. et al. Quick mass transport via sub-2-nanometer carbon nanotubes. Science 312, 1034–1037 (2006).

    Article 
    CAS 

    Google Scholar
     

  • Siria, A. et al. Big osmotic vitality conversion measured in a single transmembrane boron nitride nanotube. Nature 494, 455–458 (2013).

    Article 
    CAS 

    Google Scholar
     

  • Secchi, E. et al. Large radius-dependent stream slippage in carbon nanotubes. Nature 537, 210–213 (2016).

    Article 
    CAS 

    Google Scholar
     

  • Marbach, S. & Bocquet, L. Osmosis, from molecular insights to large-scale purposes. Chem. Soc. Rev. 48, 3102–3144 (2019).

    Article 
    CAS 

    Google Scholar
     

  • Chen, Okay. et al. Dynamics of pushed polymer transport via a nanopore. Nat. Phys. 17, 1043–1049 (2021).

    Article 
    CAS 

    Google Scholar
     

  • Plesa, C. et al. Direct commentary of DNA knots utilizing a solid-state nanopore. Nat. Nanotechnol. 11, 1093–1097 (2016).

    Article 
    CAS 

    Google Scholar
     

  • Phillips, J. C. et al. Scalable molecular dynamics on CPU and GPU architectures with NAMD. J. Chem. Phys. 153, 044130 (2020).

    Article 
    CAS 

    Google Scholar
     

  • Denning, E. J., Priyakumar, U. D., Nilsson, L. & MacKerell, A. D. Jr. Affect of 2-hydroxyl sampling on the conformational properties of RNA: replace of the CHARMM all-atom additive power area for RNA. J. Comput. Chem. 32, 1929–1943 (2011).

    Article 
    CAS 

    Google Scholar
     

  • Hart, Okay. et al. Optimization of the CHARMM additive power area for DNA: improved remedy of the BI/BII conformational equilibrium. J. Chem. Idea Comput. 8, 348–362 (2012).

    Article 
    CAS 

    Google Scholar
     

  • Yoo, J. & Aksimentiev, A. Improved parametrization of Li, Na, Okay, and Mg ions for all-atom molecular dynamics simulations of nucleic acid techniques. J. Phys. Chem. Lett. 3, 45–50 (2012).

    Article 
    CAS 

    Google Scholar
     

  • Jorgensen, W. L., Chandrasekhar, J., Madura, J. D., Impey, R. W. & Klein, M. L. Comparability of straightforward potential features for simulating liquid water. J. Chem. Phys. 79, 926–935 (1983).

    Article 
    CAS 

    Google Scholar
     

  • Darden, T. A., York, D. & Pedersen, L. Particle mesh ewald: an N log(N) methodology for ewald sums in giant techniques. J. Chem. Phys. 98, 10089–10092 (1993).

    Article 
    CAS 

    Google Scholar
     

  • Case, D. et al. Amber 12 Reference Handbook (Amber, 2012).

  • Humphrey, W., Dalke, A. & Schulten, Okay. VMD: visible molecular dynamics. J. Mol. Graph. 14, 33–38 (1996).

    Article 
    CAS 

    Google Scholar
     

  • Wilson, J. & Aksimentiev, A. Water-compression gating of nanopore transport. Phys. Rev. Lett. 120, 268101 (2018).

    Article 
    CAS 

    Google Scholar
     

  • Zhu, F., Tajkhorshid, E. & Schulten, Okay. Stress-induced water transport in membrane channels studied by molecular dynamics. Biophys. J. 83, 154–160 (2002).

    Article 
    CAS 

    Google Scholar
     

  • Piana, S., Donchev, A. G., Robustelli, P. & Shaw, D. E. Water dispersion interactions strongly affect simulated structural properties of disordered protein states. J. Phys. Chem. B 119, 5113–5123 (2015).

    Article 
    CAS 

    Google Scholar
     

  • Aksimentiev, A., Brunner, R., Cruz-Chu, E. R., Comer, J. & Schulten, Okay. Modeling transport via artificial nanopores. IEEE Nanotechnol. Magazine. 3, 20–28 (2009).

    Article 

    Google Scholar
     

  • Patra, N., Wang, B. & Král, P. Nanodroplet activated and guided folding of graphene nanostructures. Nano Lett. 9, 3766–3771 (2009).

    Article 
    CAS 

    Google Scholar
     

  • Aksimentiev, A. & Schulten, Okay. Imaging α-hemolysin with molecular dynamics: ionic conductance, osmotic permeability and the electrostatic potential map. Biophys. J. 88, 3745–3761 (2005).

    Article 
    CAS 

    Google Scholar
     

  • Aksimentiev, A., Heng, J. B., Timp, G. & Schulten, Okay. Microscopic kinetics of DNA translocation via artificial nanopores. Biophys. J. 87, 2086–2097 (2004).

    Article 
    CAS 

    Google Scholar
     

  • Maffeo, C. & Aksimentiev, A. MrDNA: a multi-resolution mannequin for predicting the construction and dynamics of DNA techniques. Nucleic Acids Res. 48, 5135–5146 (2020).

    Article 
    CAS 

    Google Scholar
     

  • Gerling, T., Kube, M., Kick, B. & Dietz, H. Sequence-programmable covalent bonding of designed DNA assemblies. Sci. Adv. 4, eaau1157 (2018).

    Article 
    CAS 

    Google Scholar
     

  • Comer, J. & Aksimentiev, A. Predicting the DNA sequence dependence of nanopore ion present utilizing atomic-resolution brownian dynamics. J. Phys. Chem. C. 116, 3376–3393 (2012).

    Article 
    CAS 

    Google Scholar
     

  • Roux, B. The calculation of the potential of imply power utilizing pc simulations. Comput. Phys. Commun. 91, 275–282 (1995).

    Article 
    CAS 

    Google Scholar
     

  • Friedman, A. M. & Kennedy, J. W. The self-diffusion coefficients of potassium, cesium, iodide and chloride ions in aqueous options. J. Am. Chem. Soc. 77, 4499–4501 (1955).

    Article 
    CAS 

    Google Scholar
     

  • Liu, Q. & Prosperetti, A. Wall results on a rotating sphere. J. Fluid Mech. 657, 1–21 (2010).

    Article 

    Google Scholar
     

  • Pänke, O., Cherepanov, D. A., Gumbowski, Okay., Engelbrecht, S. & Junge, W. Viscoelastic dyanamics of actin filaments coupled to rotary F-ATPase: angular torque profile of the enzyme. Biophys. J. 81, 1220–1233 (2001).

    Article 

    Google Scholar
     



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