메뉴 건너뛰기




Volumn 110, Issue 50, 2013, Pages 20099-20104

In situ structure and dynamics of DNA origami determined through molecular dynamics simulations

Author keywords

Nanopore; Nanotechnology; Nucleic acids; Self assembly

Indexed keywords

DNA; NANOPARTICLE;

EID: 84890307278     PISSN: 00278424     EISSN: 10916490     Source Type: Journal    
DOI: 10.1073/pnas.1316521110     Document Type: Article
Times cited : (151)

References (37)
  • 1
    • 77953645331 scopus 로고    scopus 로고
    • Nanomaterials based on DNA
    • Seeman NC (2010) Nanomaterials based on DNA. Annu Rev Biochem 79:65-87.
    • (2010) Annu Rev Biochem , vol.79 , pp. 65-87
    • Seeman, N.C.1
  • 2
    • 83555174809 scopus 로고    scopus 로고
    • Challenges and opportunities for structural DNA nanotechnology
    • Pinheiro AV, Han D, Shih WM, Yan H (2011) Challenges and opportunities for structural DNA nanotechnology. Nat Nanotechnol 6(12):763-772.
    • (2011) Nat Nanotechnol , vol.6 , Issue.12 , pp. 763-772
    • Pinheiro, A.V.1    Han, D.2    Shih, W.M.3    Yan, H.4
  • 3
    • 33645028600 scopus 로고    scopus 로고
    • Folding DNA to create nanoscale shapes and patterns
    • Rothemund PW (2006) Folding DNA to create nanoscale shapes and patterns. Nature 440(7082):297-302.
    • (2006) Nature , vol.440 , Issue.7082 , pp. 297-302
    • Rothemund, P.W.1
  • 4
    • 66249137759 scopus 로고    scopus 로고
    • Self-assembly of DNA into nanoscale three-dimensional shapes
    • Douglas SM, et al. (2009) Self-assembly of DNA into nanoscale three-dimensional shapes. Nature 459(7245):414-418.
    • (2009) Nature , vol.459 , Issue.7245 , pp. 414-418
    • Douglas, S.M.1
  • 5
    • 68449088261 scopus 로고    scopus 로고
    • Folding DNA into twisted and curved nanoscale shapes
    • Dietz H, Douglas SM, Shih WM (2009) Folding DNA into twisted and curved nanoscale shapes. Science 325(5941):725-730.
    • (2009) Science , vol.325 , Issue.5941 , pp. 725-730
    • Dietz, H.1    Douglas, S.M.2    Shih, W.M.3
  • 6
    • 79954620578 scopus 로고    scopus 로고
    • DNA origami with complex curvatures in three-dimensional space
    • Han D, et al. (2011) DNA origami with complex curvatures in three-dimensional space. Science 332(6027):342-346.
    • (2011) Science , vol.332 , Issue.6027 , pp. 342-346
    • Han, D.1
  • 7
    • 34249856814 scopus 로고    scopus 로고
    • DNA-nanotube-induced alignment of membrane proteins for NMR structure determination
    • Douglas SM, Chou JJ, Shih WM (2007) DNA-nanotube-induced alignment of membrane proteins for NMR structure determination. Proc Natl Acad Sci USA 104(16):6644-6648.
    • (2007) Proc Natl Acad Sci USA , vol.104 , Issue.16 , pp. 6644-6648
    • Douglas, S.M.1    Chou, J.J.2    Shih, W.M.3
  • 8
    • 65549170920 scopus 로고    scopus 로고
    • Self-assembly of a nanoscale DNA box with a controllable lid
    • Andersen ES, et al. (2009) Self-assembly of a nanoscale DNA box with a controllable lid. Nature 459(7243):73-76.
    • (2009) Nature , vol.459 , Issue.7243 , pp. 73-76
    • Andersen, E.S.1
  • 9
    • 77955204651 scopus 로고    scopus 로고
    • Self-assembly of three-dimensional prestressed tensegrity structures from DNA
    • Liedl T, Högberg B, Tytell J, Ingber DE, Shih WM (2010) Self-assembly of three-dimensional prestressed tensegrity structures from DNA. Nat Nanotechnol 5(7):520-524.
    • (2010) Nat Nanotechnol , vol.5 , Issue.7 , pp. 520-524
    • Liedl, T.1    Högberg, B.2    Tytell, J.3    Ingber, D.E.4    Shih, W.M.5
  • 10
    • 84866919528 scopus 로고    scopus 로고
    • Submicrometre geometrically encoded fluorescent barcodes self-assembled from DNA
    • Lin C, et al. (2012) Submicrometre geometrically encoded fluorescent barcodes self-assembled from DNA. Nat Chem 4(10):832-839.
    • (2012) Nat Chem , vol.4 , Issue.10 , pp. 832-839
    • Lin, C.1
  • 11
    • 84871091378 scopus 로고    scopus 로고
    • Rapid folding of DNA into nanoscale shapes at constant temperature
    • Sobczak JPJP, Martin TG, Gerling T, Dietz H (2012) Rapid folding of DNA into nanoscale shapes at constant temperature. Science 338(6113):1458-1461.
    • (2012) Science , vol.338 , Issue.6113 , pp. 1458-1461
    • Sobczak, J.P.J.P.1    Martin, T.G.2    Gerling, T.3    Dietz, H.4
  • 12
    • 84869126805 scopus 로고    scopus 로고
    • Synthetic lipid membrane channels formed by designed DNA nanostructures
    • Langecker M, et al. (2012) Synthetic lipid membrane channels formed by designed DNA nanostructures. Science 338(6109):932-936.
    • (2012) Science , vol.338 , Issue.6109 , pp. 932-936
    • Langecker, M.1
  • 13
    • 84867802881 scopus 로고    scopus 로고
    • Fluorescence enhancement at docking sites of DNA-directed self-assembled nanoantennas
    • Acuna GP, et al. (2012) Fluorescence enhancement at docking sites of DNA-directed self-assembled nanoantennas. Science 338(6106):506-510.
    • (2012) Science , vol.338 , Issue.6106 , pp. 506-510
    • Acuna, G.P.1
  • 14
    • 84858197920 scopus 로고    scopus 로고
    • DNA-based self-assembly of chiral plasmonic nanostructures with tailored optical response
    • Kuzyk A, et al. (2012) DNA-based self-assembly of chiral plasmonic nanostructures with tailored optical response. Nature 483(7389):311-314.
    • (2012) Nature , vol.483 , Issue.7389 , pp. 311-314
    • Kuzyk, A.1
  • 15
    • 69849088255 scopus 로고    scopus 로고
    • Rapid prototyping of 3D DNA-origami shapes with caDNAno
    • Douglas SM, et al. (2009) Rapid prototyping of 3D DNA-origami shapes with caDNAno. Nucleic Acids Res 37(15):5001-5006.
    • (2009) Nucleic Acids Res , vol.37 , Issue.15 , pp. 5001-5006
    • Douglas, S.M.1
  • 16
    • 84860171099 scopus 로고    scopus 로고
    • Quantitative prediction of 3D solution shape and flexibility of nucleic acid nanostructures
    • Kim DN, Kilchherr F, Dietz H, Bathe M (2012) Quantitative prediction of 3D solution shape and flexibility of nucleic acid nanostructures. Nucleic Acids Res 40(7):2862-2868.
    • (2012) Nucleic Acids Res , vol.40 , Issue.7 , pp. 2862-2868
    • Kim, D.N.1    Kilchherr, F.2    Dietz, H.3    Bathe, M.4
  • 18
    • 83655192457 scopus 로고    scopus 로고
    • Direct mechanical measurements reveal the material properties of three-dimensional DNA origami
    • Kauert DJ, Kurth T, Liedl T, Seidel R (2011) Direct mechanical measurements reveal the material properties of three-dimensional DNA origami. Nano Lett 11(12):5558-5563.
    • (2011) Nano Lett , vol.11 , Issue.12 , pp. 5558-5563
    • Kauert, D.J.1    Kurth, T.2    Liedl, T.3    Seidel, R.4
  • 20
    • 70350639414 scopus 로고    scopus 로고
    • Multilayer DNA origami packed on a square lattice
    • Ke Y, et al. (2009) Multilayer DNA origami packed on a square lattice. J Am Chem Soc 131(43):15903-15908.
    • (2009) J Am Chem Soc , vol.131 , Issue.43 , pp. 15903-15908
    • Ke, Y.1
  • 21
    • 84879098672 scopus 로고    scopus 로고
    • Self-assembled DNA nanopores that span lipid bilayers
    • Burns JR, Stulz E, Howorka S (2013) Self-assembled DNA nanopores that span lipid bilayers. Nano Lett 13(6):2351-2356.
    • (2013) Nano Lett , vol.13 , Issue.6 , pp. 2351-2356
    • Burns, J.R.1    Stulz, E.2    Howorka, S.3
  • 22
    • 84880824486 scopus 로고    scopus 로고
    • DNA origami nanopores for controlling DNA translocation
    • Hernández-Ainsa S, et al. (2013) DNA origami nanopores for controlling DNA translocation. ACS Nano 7(7):6024-6030.
    • (2013) ACS Nano , vol.7 , Issue.7 , pp. 6024-6030
    • Hernández-Ainsa, S.1
  • 24
    • 35348897239 scopus 로고    scopus 로고
    • Fluorescence-force spectroscopy maps two-dimensional reaction landscape of the holliday junction
    • Hohng S, et al. (2007) Fluorescence-force spectroscopy maps two-dimensional reaction landscape of the holliday junction. Science 318(5848):279-283.
    • (2007) Science , vol.318 , Issue.5848 , pp. 279-283
    • Hohng, S.1
  • 26
    • 34548101910 scopus 로고    scopus 로고
    • The elasticity of alpha-helices
    • Choe S, Sun SX (2005) The elasticity of alpha-helices. J Chem Phys 122(24):244912.
    • (2005) J Chem Phys , vol.122 , Issue.24 , pp. 244912
    • Choe, S.1    Sun, S.X.2
  • 27
    • 84883241908 scopus 로고    scopus 로고
    • Nanoscale structure and microscale stiffness of DNA nanotubes
    • Schiffels D, Liedl T, Fygenson DK (2013) Nanoscale structure and microscale stiffness of DNA nanotubes. ACS Nano 7(8):6700-6710.
    • (2013) ACS Nano , vol.7 , Issue.8 , pp. 6700-6710
    • Schiffels, D.1    Liedl, T.2    Fygenson, D.K.3
  • 28
    • 84860863907 scopus 로고    scopus 로고
    • DNA origami gatekeepers for solid-state nanopores
    • Wei R, Martin TG, Rant U, Dietz H (2012) DNA origami gatekeepers for solid-state nanopores. Angew Chem Int Ed Engl 51(20):4864-4867.
    • (2012) Angew Chem Int Ed Engl , vol.51 , Issue.20 , pp. 4864-4867
    • Wei, R.1    Martin, T.G.2    Rant, U.3    Dietz, H.4
  • 29
    • 84855778953 scopus 로고    scopus 로고
    • DNA origami nanopores
    • Bell NAW, et al. (2012) DNA origami nanopores. Nano Lett 12(1):512-517.
    • (2012) Nano Lett , vol.12 , Issue.1 , pp. 512-517
    • Bell, N.A.W.1
  • 30
    • 46249092554 scopus 로고    scopus 로고
    • Gromacs 4: Algorithms for highly efficient, load-balanced, and scalable molecular simulation
    • Hess B, Kutzner C, Van Der Spoel D, Lindahl E (2008) Gromacs 4: Algorithms for highly efficient, load-balanced, and scalable molecular simulation. J Chem Theory Comput 4(3):435-447.
    • (2008) J Chem Theory Comput , vol.4 , Issue.3 , pp. 435-447
    • Hess, B.1    Kutzner, C.2    Van Der Spoel, D.3    Lindahl, E.4
  • 31
    • 27344436659 scopus 로고    scopus 로고
    • Scalable molecular dynamics with NAMD
    • Phillips JC, et al. (2005) Scalable molecular dynamics with NAMD. J Comput Chem 26(16):1781-1802.
    • (2005) J Comput Chem , vol.26 , Issue.16 , pp. 1781-1802
    • Phillips, J.C.1
  • 32
    • 84855661433 scopus 로고    scopus 로고
    • Optimization of the CHARMM additive force field for DNA: Improved treatment of the BI/BII conformational equilibrium
    • Hart K, et al. (2012) Optimization of the CHARMM additive force field for DNA: Improved treatment of the BI/BII conformational equilibrium. J Chem Theory Comput 8(1):348-362.
    • (2012) J Chem Theory Comput , vol.8 , Issue.1 , pp. 348-362
    • Hart, K.1
  • 34
    • 84855431691 scopus 로고    scopus 로고
    • 2+ ions for all-atom molecular dynamics simulations of nucleic acid systems
    • 2+ ions for all-atom molecular dynamics simulations of nucleic acid systems. J Phys Chem Lett 3(1):45-50.
    • (2012) J Phys Chem Lett , vol.3 , Issue.1 , pp. 45-50
    • Yoo, J.1    Aksimentiev, A.2
  • 35
    • 33846823909 scopus 로고
    • Particle mesh ewald: An n log(n) method for ewald sums in large systems
    • Darden T, York D, Pedersen L (1993) Particle mesh ewald: An n log(n) method for ewald sums in large systems. J Chem Phys 98(12):10089-10092.
    • (1993) J Chem Phys , vol.98 , Issue.12 , pp. 10089-10092
    • Darden, T.1    York, D.2    Pedersen, L.3
  • 36
    • 36449003554 scopus 로고
    • Constant pressure molecular dynamics algorithms
    • Martyna GJ, Tobias DJ, Klein ML (1994) Constant pressure molecular dynamics algorithms. J Chem Phys 101(5):4177-4189.
    • (1994) J Chem Phys , vol.101 , Issue.5 , pp. 4177-4189
    • Martyna, G.J.1    Tobias, D.J.2    Klein, M.L.3
  • 37
    • 34250318638 scopus 로고    scopus 로고
    • Refinement of the AMBER force field for nucleic acids: Improving the description of α/γ conformers
    • Pérez A, et al. (2007) Refinement of the AMBER force field for nucleic acids: Improving the description of α/γ conformers. Biophys J 92(11):3817-3829.
    • (2007) Biophys J , vol.92 , Issue.11 , pp. 3817-3829
    • Pérez, A.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.