메뉴 건너뛰기




Volumn 4, Issue 3, 2010, Pages 1367-1376

Structure of nanoscale truncated octahedral DNA cages: Variation of single-stranded linker regions and influence on assembly yields

Author keywords

Assembly efficiency; DNA nanostructure; Flexibility; Single stranded linker variation; Small angle X ray scattering

Indexed keywords

ASSEMBLY YIELDS; CAGE SIZES; CAGE STRUCTURES; DEGREE OF FLEXIBILITY; DNA NANOSTRUCTURES; DOUBLE HELIX; ENERGY MINIMIZATION; HIGH EFFICIENCY; LINKER REGION; NANO SCALE; NANOCAGES; SINGLE-STRANDED LINKER VARIATION; SMALL ANGLE X-RAY SCATTERING; STRUCTURAL CHARACTERISTICS; SYMMETRY PLANES; TWIST ANGLES;

EID: 77950128663     PISSN: 19360851     EISSN: 1936086X     Source Type: Journal    
DOI: 10.1021/nn901510v     Document Type: Article
Times cited : (54)

References (38)
  • 1
    • 36949030704 scopus 로고    scopus 로고
    • An overview of structural DNA nanotechnology
    • Seeman, N. C. An Overview of Structural DNA Nanotechnology. Mol Biotechnol. 2007, 37, 246-257.
    • (2007) Mol Biotechnol. , vol.37 , pp. 246-257
    • Seeman, N.C.1
  • 2
    • 0025804117 scopus 로고
    • Synthesis from DNA of a molecule with the connectivity of a cube
    • Chen, J. H.; Seeman, N. C. Synthesis from DNA of a Molecule with the Connectivity of a Cube. Nature 1991, 350, 631-633.
    • (1991) Nature , vol.350 , pp. 631-633
    • Chen, J.H.1    Seeman, N.C.2
  • 3
    • 0028003579 scopus 로고
    • The construction of a DNA truncated octahedron
    • Zhang, Y.; Seeman, N. C. The Construction of a DNA Truncated Octahedron. J. Am. Chem. Soc. 1994, 116, 1661-1669.
    • (1994) J. Am. Chem. Soc. , vol.116 , pp. 1661-1669
    • Zhang, Y.1    Seeman, N.C.2
  • 4
    • 1342325559 scopus 로고    scopus 로고
    • A 1.7-kilobase single-stranded DNA that folds into a nanoscale octahedron
    • Shih, W. M.; Quispe, J. D.; Joyce, G. F. A 1.7-kilobase Single-Stranded DNA That Folds into a Nanoscale Octahedron. Nature 2004, 427, 618-621.
    • (2004) Nature , vol.427 , pp. 618-621
    • Shih, W.M.1    Quispe, J.D.2    Joyce, G.F.3
  • 5
    • 35948960658 scopus 로고    scopus 로고
    • Modular access to structurally switchable 3D discrete DNA assemblies
    • Aldaye, F. A.; Sleiman, H. F. Modular Access to Structurally Switchable 3D Discrete DNA Assemblies. J. Am. Chem. Soc. 2007, 129, 13376-13377.
    • (2007) J. Am. Chem. Soc. , vol.129 , pp. 13376-13377
    • Aldaye, F.A.1    Sleiman, H.F.2
  • 8
    • 40749140401 scopus 로고    scopus 로고
    • Hierarchical self-assembly of DNA into symmetric supramolecular polyhedra
    • He, Y.; Ye, T.; Su, M.; Zhang, C.; Ribbe, A. E.; Jiang, W.; Mao, C. Hierarchical Self-Assembly of DNA into Symmetric Supramolecular Polyhedra. Nature 2008, 452, 198-201.
    • (2008) Nature , vol.452 , pp. 198-201
    • He, Y.1    Ye, T.2    Su, M.3    Zhang, C.4    Ribbe, A.E.5    Jiang, W.6    Mao, C.7
  • 9
    • 51449119857 scopus 로고    scopus 로고
    • Three-dimensional nanoconstruction with DNA
    • Simmel, F. C. Three-Dimensional Nanoconstruction with DNA. Angew. Chem., Int. Ed. 2008, 47, 5884-5887.
    • (2008) Angew. Chem., Int. Ed. , vol.47 , pp. 5884-5887
    • Simmel, F.C.1
  • 11
    • 77950101384 scopus 로고    scopus 로고
    • Three-dimensional DNA nanostructures constructed by folding of multiple rectangles
    • Endo, M.; Sugiyama, H. Three-Dimensional DNA Nanostructures Constructed by Folding of Multiple Rectangles. Nucleic Acids Symp. Ser. 2009, 53, 81-82.
    • (2009) Nucleic Acids Symp. Ser. , vol.53 , pp. 81-82
    • Endo, M.1    Sugiyama, H.2
  • 12
    • 70349134760 scopus 로고    scopus 로고
    • A replicable tetrahedral nanostructure self-assembled from a single DNA strand
    • Li, Z.; Wei, B.; Nangreave, J.; Lin, C.; Liu, Y.; Mi, Y.; Yan, H. A Replicable Tetrahedral Nanostructure Self-Assembled from a Single DNA Strand. J. Am. Chem. Soc. 2009, 131, 13093-13098.
    • (2009) J. Am. Chem. Soc. , vol.131 , pp. 13093-13098
    • Li, Z.1    Wei, B.2    Nangreave, J.3    Lin, C.4    Liu, Y.5    Mi, Y.6    Yan, H.7
  • 14
    • 67650345813 scopus 로고    scopus 로고
    • High-resolution structural analysis of a DNA nanostructure by cryoem
    • Kato, T.; Goodman, R. P.; Erben, C. M.; Turberfield, A. J.; Namba, K. High-Resolution Structural Analysis of a DNA Nanostructure by CryoEM. Nano Lett. 2009, 9, 2747-2750.
    • (2009) Nano Lett. , vol.9 , pp. 2747-2750
    • Kato, T.1    Goodman, R.P.2    Erben, C.M.3    Turberfield, A.J.4    Namba, K.5
  • 15
    • 67651087256 scopus 로고    scopus 로고
    • Modular construction of DNA nanotubes of tunable geometry and single- or double-stranded character
    • Aldaye, F. A.; Lo, P. K.; Karam, P.; McLaughlin, C. K.; Cosa, G.; Sleiman, H. F. Modular Construction of DNA Nanotubes of Tunable Geometry and Single- or Double-Stranded Character. Nat. Nanotechnol. 2009, 4, 349-352.
    • (2009) Nat. Nanotechnol. , vol.4 , pp. 349-352
    • Aldaye, F.A.1    Lo, P.K.2    Karam, P.3    McLaughlin, C.K.4    Cosa, G.5    Sleiman, H.F.6
  • 18
    • 0032555489 scopus 로고    scopus 로고
    • Alcoholysis and strand joining by the flp site-specific recombinase. Mechanistically equivalent reactions mediated by distinct catalytic configurations
    • Knudsen, B. R.; Lee, J.; Lisby, M.; Westergaard, O.; Jayaram, M. Alcoholysis and Strand Joining by the Flp Site-Specific Recombinase. Mechanistically Equivalent Reactions Mediated by Distinct Catalytic Configurations. J. Biol. Chem. 1998, 273, 22028-22036.
    • (1998) J. Biol. Chem. , vol.273 , pp. 22028-22036
    • Knudsen, B.R.1    Lee, J.2    Lisby, M.3    Westergaard, O.4    Jayaram, M.5
  • 20
    • 0000897622 scopus 로고
    • A new method for the evaluation of small-angle scattering data
    • Glatter, O. A New Method for the Evaluation of Small-Angle Scattering Data. J. Appl. Crystallogr. 1977, 10, 415-421.
    • (1977) J. Appl. Crystallogr. , vol.10 , pp. 415-421
    • Glatter, O.1
  • 21
    • 3442880149 scopus 로고    scopus 로고
    • A flux- and background-optimized version of the nanostar small-angle x-ray scattering camera for solution scattering
    • Pedersen, J. S. A Flux- and Background-Optimized Version of the NanoSTAR Small-Angle X-ray Scattering Camera for Solution Scattering. J. Appl. Crystallogr. 2004, 37, 369-380.
    • (2004) J. Appl. Crystallogr. , vol.37 , pp. 369-380
    • Pedersen, J.S.1
  • 22
    • 0028295752 scopus 로고
    • The aggregation behavior of zinc-free insulin studied by small-angle neutron scattering
    • Pedersen, J. S.; Hansen, S.; Bauer, R. The Aggregation Behavior of Zinc-Free Insulin Studied by Small-Angle Neutron Scattering. Eur. Biophys. J. 1994, 22, 379-389.
    • (1994) Eur. Biophys. J. , vol.22 , pp. 379-389
    • Pedersen, J.S.1    Hansen, S.2    Bauer, R.3
  • 24
    • 84908087566 scopus 로고
    • Zerstreuung von röntgenstrahlen
    • Debye, P. Zerstreuung von Röntgenstrahlen. Ann. Phys. Leipzig 1915, 46, 809-823.
    • (1915) Ann. Phys. Leipzig , vol.46 , pp. 809-823
    • Debye, P.1
  • 26
    • 0031191923 scopus 로고    scopus 로고
    • Small-angle scattering from precipitates: Analysis by use of a polydisperse hard-sphere model
    • Pedersen, J. S. Small-Angle Scattering from Precipitates: Analysis by Use of a Polydisperse Hard-Sphere Model. Adv. Colloid Interface Sci. 1997, 70, 171-210.
    • (1997) Adv. Colloid Interface Sci. , vol.70 , pp. 171-210
    • Pedersen, J.S.1
  • 27
    • 0141578859 scopus 로고    scopus 로고
    • Instrumentation for small-angle x-ray and neutron scattering and instrumental smearing effects
    • North-Holland: Amsterdam; Chapter 16
    • Pedersen, J. S. Instrumentation for Small-Angle X-ray and Neutron Scattering and Instrumental Smearing Effects. In Neutrons, X-Rays and Light: Scattering Methods Applied to Soft Condensed Matter; North-Holland: Amsterdam, 2002; Chapter 16, pp 127-144.
    • (2002) Neutrons, X-rays and Light: Scattering Methods Applied to Soft Condensed Matter , pp. 127-144
    • Pedersen, J.S.1
  • 28
    • 33644606089 scopus 로고
    • Molecular-weight determination by light scattering
    • Debye, P. Molecular-Weight Determination by Light Scattering. J. Phys. Colloid Chem. 1947, 51, 18-32.
    • (1947) J. Phys. Colloid Chem. , vol.51 , pp. 18-32
    • Debye, P.1
  • 29
    • 0001229341 scopus 로고    scopus 로고
    • Calculation of hydrodynamic properties of globular proteins from their atomic-level structure
    • Garcia De La Torre, J.; Huertas, M. L.; Carrasco, B. Calculation of Hydrodynamic Properties of Globular Proteins from Their Atomic-Level Structure. Biophys. J. 2000, 78, 719-730.
    • (2000) Biophys. J. , vol.78 , pp. 719-730
    • Garcia De La Torre, J.1    Huertas, M.L.2    Carrasco, B.3
  • 30
    • 0242396923 scopus 로고    scopus 로고
    • 3DNA: A software package for the analysis, rebuilding and visualization of three-dimensional nucleic acid structures
    • Lu, X.-J.; Olson, W. K. 3DNA: A Software Package for the Analysis, Rebuilding and Visualization of Three-Dimensional Nucleic Acid Structures. Nucleic Acids Res. 2003, 31, 5108-5121.
    • (2003) Nucleic Acids Res. , vol.31 , pp. 5108-5121
    • Lu, X.-J.1    Olson, W.K.2
  • 32
    • 0001008029 scopus 로고
    • An efficient method for finding the minimum of a function of several variables without calculating derivatives
    • Powell, M. J. D. An Efficient Method for Finding the Minimum of a Function of Several Variables without Calculating Derivatives. Comput. J. 1964, 17, 155-162.
    • (1964) Comput. J. , vol.17 , pp. 155-162
    • Powell, M.J.D.1
  • 33
    • 0002636134 scopus 로고
    • Pairwise solute descreening of solute charges from a dielectric medium
    • Hawkins, G. D.; Cramer, C. J.; Truhlar, D. G. Pairwise Solute Descreening of Solute Charges from a Dielectric Medium. Chem. Phys. Lett. 1995, 246, 122-129.
    • (1995) Chem. Phys. Lett. , vol.246 , pp. 122-129
    • Hawkins, G.D.1    Cramer, C.J.2    Truhlar, D.G.3
  • 34
    • 33748390341 scopus 로고    scopus 로고
    • Parametrized models of aqueous free energies of solvation based on pairwise descreening of solute atomic charges from a dielectric medium
    • Hawkins, G. D.; Cramer, C. J.; Truhlar, D. G. Parametrized Models of Aqueous Free Energies of Solvation Based on Pairwise Descreening of Solute Atomic Charges from a Dielectric Medium. J. Phys. Chem. 1996, 100, 19824-19839.
    • (1996) J. Phys. Chem. , vol.100 , pp. 19824-19839
    • Hawkins, G.D.1    Cramer, C.J.2    Truhlar, D.G.3
  • 36
    • 0242663237 scopus 로고    scopus 로고
    • A point-charge force field for molecular mechanics simulations of proteins based on condensed-phase quantum mechanical calculations
    • Duan, Y.; Wu, C.; Chowdhury, S.; Lee, M. C.; Xiong, G.; Zhang, W.; Yang, R.; Cieplak, P.; Luo, R.; Lee, T. A Point-Charge Force Field for Molecular Mechanics Simulations of Proteins Based on Condensed-Phase Quantum Mechanical Calculations. J. Comput. Chem. 2003, 24, 1999-2012.
    • (2003) J. Comput. Chem. , vol.24 , pp. 1999-2012
    • Duan, Y.1    Wu, C.2    Chowdhury, S.3    Lee, M.C.4    Xiong, G.5    Zhang, W.6    Yang, R.7    Cieplak, P.8    Luo, R.9    Lee, T.10
  • 37
    • 0242443693 scopus 로고    scopus 로고
    • Force fields for protein simulations
    • Ponder, J. W.; Case, D. A. Force Fields for Protein Simulations. Adv. Protein Chem. 2003, 66, 27-85.
    • (2003) Adv. Protein Chem. , vol.66 , pp. 27-85
    • Ponder, J.W.1    Case, D.A.2
  • 38
    • 0242290881 scopus 로고    scopus 로고
    • DNA basepair step deformability inferred from molecular dynamics simulations
    • Lankas, F.; Sponer, J.; Langowski, J.; Cheatham, T. E. DNA Basepair Step Deformability Inferred from Molecular Dynamics Simulations. Biophys. J. 2003, 85, 2872-2883.
    • (2003) Biophys. J. , vol.85 , pp. 2872-2883
    • Lankas, F.1    Sponer, J.2    Langowski, J.3    Cheatham, T.E.4


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.