메뉴 건너뛰기




Volumn 47, Issue 6, 2014, Pages 1861-1870

Uncovering the self-assembly of DNA nanostructures by thermodynamics and kinetics

Author keywords

[No Author keywords available]

Indexed keywords

DNA; NANOSTRUCTURES;

EID: 84902585100     PISSN: 00014842     EISSN: 15204898     Source Type: Journal    
DOI: 10.1021/ar5000665     Document Type: Article
Times cited : (64)

References (52)
  • 3
    • 84857335824 scopus 로고    scopus 로고
    • A logic-gated nanorobot for targeted transport of molecular payloads
    • Douglas, S. M.; Bachelet, I.; Church, G. M. A logic-gated nanorobot for targeted transport of molecular payloads Science 2012, 335, 831-834
    • (2012) Science , vol.335 , pp. 831-834
    • Douglas, S.M.1    Bachelet, I.2    Church, G.M.3
  • 4
    • 84859128218 scopus 로고    scopus 로고
    • Interenzyme substrate diffusion for an enzyme cascade organized on spatially addressable DNA nanostructures
    • Fu, J.; Liu, M.; Liu, Y.; Woodbury, N. W.; Yan, H. Interenzyme substrate diffusion for an enzyme cascade organized on spatially addressable DNA nanostructures J. Am. Chem. Soc. 2012, 134, 5516-5519
    • (2012) J. Am. Chem. Soc. , vol.134 , pp. 5516-5519
    • Fu, J.1    Liu, M.2    Liu, Y.3    Woodbury, N.W.4    Yan, H.5
  • 5
    • 33645028600 scopus 로고    scopus 로고
    • Folding DNA to create nanoscale shapes and patterns
    • Rothemund, P. W. Folding DNA to create nanoscale shapes and patterns Nature 2006, 440, 297-302
    • (2006) Nature , vol.440 , pp. 297-302
    • Rothemund, P.W.1
  • 6
    • 84870154659 scopus 로고    scopus 로고
    • Three-dimensional structures self-assembled from DNA bricks
    • Ke, Y.; Ong, L. L.; Shih, W. M.; Yin, P. Three-dimensional structures self-assembled from DNA bricks Science 2012, 338, 1177-1183
    • (2012) Science , vol.338 , pp. 1177-1183
    • Ke, Y.1    Ong, L.L.2    Shih, W.M.3    Yin, P.4
  • 7
    • 0141534348 scopus 로고    scopus 로고
    • DNA-templated self-assembly of protein arrays and highly conductive nanowires
    • Yan, H.; Park, S. H.; Finkelstein, G.; Reif, J. H.; LaBean, T. H. DNA-templated self-assembly of protein arrays and highly conductive nanowires Science 2003, 301, 1882-1884
    • (2003) Science , vol.301 , pp. 1882-1884
    • Yan, H.1    Park, S.H.2    Finkelstein, G.3    Reif, J.H.4    Labean, T.H.5
  • 8
    • 79954620578 scopus 로고    scopus 로고
    • DNA origami with complex curvatures in three-dimensional space
    • Han, D.; Pal, S.; Nangreave, J.; Deng, Z.; Liu, Y.; Yan, H. DNA origami with complex curvatures in three-dimensional space Science 2011, 332, 342-346
    • (2011) Science , vol.332 , pp. 342-346
    • Han, D.1    Pal, S.2    Nangreave, J.3    Deng, Z.4    Liu, Y.5    Yan, H.6
  • 10
    • 33645462765 scopus 로고    scopus 로고
    • A study of DNA tube formation mechanisms using 4-, 8-, and 12-helix DNA nanostructures
    • Ke, Y.; Liu, Y.; Zhang, J.; Yan, H. A study of DNA tube formation mechanisms using 4-, 8-, and 12-helix DNA nanostructures J. Am. Chem. Soc. 2006, 128, 4414-4421
    • (2006) J. Am. Chem. Soc. , vol.128 , pp. 4414-4421
    • Ke, Y.1    Liu, Y.2    Zhang, J.3    Yan, H.4
  • 11
    • 84879624827 scopus 로고    scopus 로고
    • Integrating DNA strand-displacement circuitry with DNA tile self-assembly
    • Zhang, D. Y.; Hariadi, R. F.; Choi, H. M.; Winfree, E. Integrating DNA strand-displacement circuitry with DNA tile self-assembly Nat. Commun. 2013, 4, 1965-1974
    • (2013) Nat. Commun. , vol.4 , pp. 1965-1974
    • Zhang, D.Y.1    Hariadi, R.F.2    Choi, H.M.3    Winfree, E.4
  • 12
    • 77957915679 scopus 로고    scopus 로고
    • Folding and cutting DNA into reconfigurable topological nanostructures
    • Han, D.; Pal, S.; Liu, Y.; Yan, H. Folding and cutting DNA into reconfigurable topological nanostructures Nat. Nanotechnol. 2010, 5, 712-717
    • (2010) Nat. Nanotechnol. , vol.5 , pp. 712-717
    • Han, D.1    Pal, S.2    Liu, Y.3    Yan, H.4
  • 13
    • 14044251445 scopus 로고    scopus 로고
    • Algorithmic self-assembly of DNA Sierpinski triangles
    • Rothemund, P. W.; Papadakis, N.; Winfree, E. Algorithmic self-assembly of DNA Sierpinski triangles PLoS Biol. 2004, 2, 2041-2053
    • (2004) PLoS Biol. , vol.2 , pp. 2041-2053
    • Rothemund, P.W.1    Papadakis, N.2    Winfree, E.3
  • 14
    • 68949090196 scopus 로고    scopus 로고
    • Studies of thermal stability of multivalent DNA hybridization in a nanostructured system
    • Nangreave, J.; Yan, H.; Liu, Y. Studies of thermal stability of multivalent DNA hybridization in a nanostructured system Biophys. J. 2009, 97, 563-571
    • (2009) Biophys. J. , vol.97 , pp. 563-571
    • Nangreave, J.1    Yan, H.2    Liu, Y.3
  • 15
    • 79953041320 scopus 로고    scopus 로고
    • DNA nanostructures as models for evaluating the role of enthalpy and entropy in polyvalent binding
    • Nangreave, J.; Yan, H.; Liu, Y. DNA nanostructures as models for evaluating the role of enthalpy and entropy in polyvalent binding J. Am. Chem. Soc. 2011, 133, 4490-4497
    • (2011) J. Am. Chem. Soc. , vol.133 , pp. 4490-4497
    • Nangreave, J.1    Yan, H.2    Liu, Y.3
  • 17
    • 0031462334 scopus 로고    scopus 로고
    • Measuring the thermodynamics of RNA secondary structure formation
    • SantaLucia, J., Jr.; Turner, D. H. Measuring the thermodynamics of RNA secondary structure formation Biopolymers 1997, 44, 309-319
    • (1997) Biopolymers , vol.44 , pp. 309-319
    • Santalucia Jr., J.1    Turner, D.H.2
  • 18
    • 84871091378 scopus 로고    scopus 로고
    • Rapid folding of DNA into nanoscale shapes at constant temperature
    • Sobczak, J. P.; Martin, T. G.; Gerling, T.; Dietz, H. Rapid folding of DNA into nanoscale shapes at constant temperature Science 2012, 338, 1458-1461
    • (2012) Science , vol.338 , pp. 1458-1461
    • Sobczak, J.P.1    Martin, T.G.2    Gerling, T.3    Dietz, H.4
  • 19
    • 84867758075 scopus 로고    scopus 로고
    • Two design strategies for enhancement of multilayer-DNA-origami folding: Underwinding for specific intercalator rescue and staple-break positioning
    • Ke, Y.; Bellot, G.; Voigt, N. V.; Fradkov, E.; Shih, W. M. Two design strategies for enhancement of multilayer-DNA-origami folding: Underwinding for specific intercalator rescue and staple-break positioning Chem. Sci. 2012, 3, 2587-2597
    • (2012) Chem. Sci. , vol.3 , pp. 2587-2597
    • Ke, Y.1    Bellot, G.2    Voigt, N.V.3    Fradkov, E.4    Shih, W.M.5
  • 20
    • 34250658870 scopus 로고    scopus 로고
    • High-resolution DNA melting analysis for simple and efficient molecular diagnostics
    • Reed, G. H.; Kent, J. O.; Wittwer, C. T. High-resolution DNA melting analysis for simple and efficient molecular diagnostics Pharmacogenomics 2007, 8, 597-608
    • (2007) Pharmacogenomics , vol.8 , pp. 597-608
    • Reed, G.H.1    Kent, J.O.2    Wittwer, C.T.3
  • 21
    • 41949131772 scopus 로고    scopus 로고
    • High-throughput, real-time monitoring of the self-assembly of DNA nanostructures by FRET spectroscopy
    • Sacca, B.; Meyer, R.; Feldkamp, U.; Schroeder, H.; Niemeyer, C. M. High-throughput, real-time monitoring of the self-assembly of DNA nanostructures by FRET spectroscopy Angew. Chem., Int. Ed. 2008, 47, 2135-2137
    • (2008) Angew. Chem., Int. Ed. , vol.47 , pp. 2135-2137
    • Sacca, B.1    Meyer, R.2    Feldkamp, U.3    Schroeder, H.4    Niemeyer, C.M.5
  • 22
    • 0027469785 scopus 로고
    • Sensitive fluorescence-based thermodynamic and kinetic measurements of DNA hybridization in solution
    • Morrison, L. E.; Stols, L. M. Sensitive fluorescence-based thermodynamic and kinetic measurements of DNA hybridization in solution Biochemistry 1993, 32, 3095-3104
    • (1993) Biochemistry , vol.32 , pp. 3095-3104
    • Morrison, L.E.1    Stols, L.M.2
  • 23
    • 84876737522 scopus 로고    scopus 로고
    • Mapping the thermal behavior of DNA origami nanostructures
    • Wei, X.; Nangreave, J.; Jiang, S.; Yan, H.; Liu, Y. Mapping the thermal behavior of DNA origami nanostructures J. Am. Chem. Soc. 2013, 135, 6165-6176
    • (2013) J. Am. Chem. Soc. , vol.135 , pp. 6165-6176
    • Wei, X.1    Nangreave, J.2    Jiang, S.3    Yan, H.4    Liu, Y.5
  • 24
    • 84862839272 scopus 로고    scopus 로고
    • Steric crowding and the kinetics of DNA hybridization within a DNA nanostructure system
    • Pinheiro, A. V.; Nangreave, J.; Jiang, S.; Yan, H.; Liu, Y. Steric crowding and the kinetics of DNA hybridization within a DNA nanostructure system ACS Nano 2012, 6, 5521-5530
    • (2012) ACS Nano , vol.6 , pp. 5521-5530
    • Pinheiro, A.V.1    Nangreave, J.2    Jiang, S.3    Yan, H.4    Liu, Y.5
  • 25
    • 0023407434 scopus 로고
    • The melting behavior of a DNA junction structure: A calorimetric and spectroscopic study
    • Marky, L. A.; Kallenbach, N. R.; McDonough, K. A.; Seeman, N. C.; Breslauer, K. J. The melting behavior of a DNA junction structure: A calorimetric and spectroscopic study Biopolymers 1987, 26, 1621-1634
    • (1987) Biopolymers , vol.26 , pp. 1621-1634
    • Marky, L.A.1    Kallenbach, N.R.2    McDonough, K.A.3    Seeman, N.C.4    Breslauer, K.J.5
  • 27
    • 0032539693 scopus 로고    scopus 로고
    • A unified view of polymer, dumbbell, and oligonucleotide DNA nearest-neighbor thermodynamics
    • SantaLucia, J., Jr. A unified view of polymer, dumbbell, and oligonucleotide DNA nearest-neighbor thermodynamics Proc. Natl. Acad. Sci. U.S.A. 1998, 95, 1460-1465
    • (1998) Proc. Natl. Acad. Sci. U.S.A. , vol.95 , pp. 1460-1465
    • Santalucia Jr., J.1
  • 28
    • 0347745160 scopus 로고    scopus 로고
    • Thermodynamics of DNA Duplex Formation: A Biophysical Chemistry Laboratory Experiment
    • Howard, K. P. Thermodynamics of DNA Duplex Formation: A Biophysical Chemistry Laboratory Experiment J. Chem. Educ. 2000, 77, 1469-1471
    • (2000) J. Chem. Educ. , vol.77 , pp. 1469-1471
    • Howard, K.P.1
  • 29
    • 0035945251 scopus 로고    scopus 로고
    • Effects of polyamines on the thermal stability and formation kinetics of DNA duplexes with abnormal structure
    • Hou, M. H.; Lin, S. B.; Yuann, J. M.; Lin, W. C.; Wang, A. H.; Kan Ls, L. Effects of polyamines on the thermal stability and formation kinetics of DNA duplexes with abnormal structure Nucleic Acids Res. 2001, 29, 5121-5128
    • (2001) Nucleic Acids Res. , vol.29 , pp. 5121-5128
    • Hou, M.H.1    Lin, S.B.2    Yuann, J.M.3    Lin, W.C.4    Wang, A.H.5    Kan Ls, L.6
  • 31
    • 0027255843 scopus 로고
    • DNA double-crossover molecules
    • Fu, T. J.; Seeman, N. C. DNA double-crossover molecules Biochemistry 1993, 32, 3211-3220
    • (1993) Biochemistry , vol.32 , pp. 3211-3220
    • Fu, T.J.1    Seeman, N.C.2
  • 32
    • 34948832780 scopus 로고    scopus 로고
    • Reducing facet nucleation during algorithmic self-assembly
    • Chen, H. L.; Schulman, R.; Goel, A.; Winfree, E. Reducing facet nucleation during algorithmic self-assembly Nano Lett. 2007, 7, 2913-2919
    • (2007) Nano Lett. , vol.7 , pp. 2913-2919
    • Chen, H.L.1    Schulman, R.2    Goel, A.3    Winfree, E.4
  • 33
    • 33745194118 scopus 로고    scopus 로고
    • Two-dimensional LNA/DNA arrays: Estimating the helicity of LNA/DNA hybrid duplex
    • Rinker, S.; Liu, Y.; Yan, H. Two-dimensional LNA/DNA arrays: estimating the helicity of LNA/DNA hybrid duplex Chem. Commun. 2006, 2675-2677
    • (2006) Chem. Commun. , pp. 2675-2677
    • Rinker, S.1    Liu, Y.2    Yan, H.3
  • 34
  • 36
    • 0026443546 scopus 로고
    • DNA junctions, antijunctions, and mesojunctions
    • Du, S. M.; Zhang, S.; Seeman, N. C. DNA junctions, antijunctions, and mesojunctions Biochemistry 1992, 31, 10955-10963
    • (1992) Biochemistry , vol.31 , pp. 10955-10963
    • Du, S.M.1    Zhang, S.2    Seeman, N.C.3
  • 37
    • 72249110882 scopus 로고    scopus 로고
    • Control of DNA strand displacement kinetics using toehold exchange
    • Zhang, D. Y.; Winfree, E. Control of DNA strand displacement kinetics using toehold exchange J. Am. Chem. Soc. 2009, 131, 17303-17314
    • (2009) J. Am. Chem. Soc. , vol.131 , pp. 17303-17314
    • Zhang, D.Y.1    Winfree, E.2
  • 38
    • 33746207804 scopus 로고    scopus 로고
    • Secondary structure effects on DNA hybridization kinetics: A solution versus surface comparison
    • Gao, Y.; Wolf, L. K.; Georgiadis, R. M. Secondary structure effects on DNA hybridization kinetics: a solution versus surface comparison Nucleic Acids Res. 2006, 34, 3370-3377
    • (2006) Nucleic Acids Res. , vol.34 , pp. 3370-3377
    • Gao, Y.1    Wolf, L.K.2    Georgiadis, R.M.3
  • 39
    • 57649136385 scopus 로고    scopus 로고
    • Dodecamer DNA Duplex Formation Is Characterized by Second-Order Kinetics, Positive Activation Energies, and a Dependence on Sequence and Mg2+Ion Concentration
    • Carrillo-Nava, E.; Mejía-Radillo, Y.; Hinz, H.-J. Dodecamer DNA Duplex Formation Is Characterized by Second-Order Kinetics, Positive Activation Energies, and a Dependence on Sequence and Mg2+Ion Concentration; Biochemistry 2008, 47, 13153-13157
    • (2008) Biochemistry , vol.47 , pp. 13153-13157
    • Carrillo-Nava, E.1    Mejía-Radillo, Y.2    Hinz, H.-J.3
  • 40
    • 0016201619 scopus 로고
    • Model calculations on the kinetics of oligonucleotide double helix coil transitions. Evidence for a fast chain sliding reaction
    • Pörschke, D. Model calculations on the kinetics of oligonucleotide double helix coil transitions. Evidence for a fast chain sliding reaction Biophys. Chem. 1974, 2, 83-96
    • (1974) Biophys. Chem. , vol.2 , pp. 83-96
    • Pörschke, D.1
  • 41
    • 0015846852 scopus 로고
    • Thermodynamics and kinetics of the helix-coil transition of oligomers containing GC base pairs
    • Pörschke, D.; Uhlenbeck, O. C.; Martin, F. H. Thermodynamics and kinetics of the helix-coil transition of oligomers containing GC base pairs Biopolymers 1973, 12, 1313-1335
    • (1973) Biopolymers , vol.12 , pp. 1313-1335
    • Pörschke, D.1    Uhlenbeck, O.C.2    Martin, F.H.3
  • 42
    • 0015223584 scopus 로고
    • Relaxation kinetics of dimer formation by self complementary oligonucleotides
    • Craig, M. E.; Crothers, D. M.; Doty, P. Relaxation kinetics of dimer formation by self complementary oligonucleotides J. Mol. Biol. 1971, 62, 383-401
    • (1971) J. Mol. Biol. , vol.62 , pp. 383-401
    • Craig, M.E.1    Crothers, D.M.2    Doty, P.3
  • 43
    • 34250617531 scopus 로고    scopus 로고
    • Influence of secondary structure on kinetics and reaction mechanism of DNA hybridization
    • Chen, C.; Wang, W.; Wang, Z.; Wei, F.; Zhao, X. S. Influence of secondary structure on kinetics and reaction mechanism of DNA hybridization Nucleic Acids Res. 2007, 35, 2875-2884
    • (2007) Nucleic Acids Res. , vol.35 , pp. 2875-2884
    • Chen, C.1    Wang, W.2    Wang, Z.3    Wei, F.4    Zhao, X.S.5
  • 44
    • 70849103169 scopus 로고    scopus 로고
    • Uncovering pathways in DNA oligonucleotide hybridization via transition state analysis
    • Sambriski, E. J.; Schwartz, D. C.; de Pablo, J. J. Uncovering pathways in DNA oligonucleotide hybridization via transition state analysis Proc. Natl. Acad. Sci. U.S.A. 2009, 106, 18125-18130
    • (2009) Proc. Natl. Acad. Sci. U.S.A. , vol.106 , pp. 18125-18130
    • Sambriski, E.J.1    Schwartz, D.C.2    De Pablo, J.J.3
  • 45
    • 84886016409 scopus 로고    scopus 로고
    • DNA hybridization kinetics: Zippering, internal displacement and sequence dependence
    • Ouldridge, T. E.; Sulc, P.; Romano, F.; Doye, J. P.; Louis, A. A. DNA hybridization kinetics: zippering, internal displacement and sequence dependence Nucleic Acids Res. 2013, 41, 8886-8895
    • (2013) Nucleic Acids Res. , vol.41 , pp. 8886-8895
    • Ouldridge, T.E.1    Sulc, P.2    Romano, F.3    Doye, J.P.4    Louis, A.A.5
  • 47
    • 84884223348 scopus 로고    scopus 로고
    • Isothermal self-assembly of complex DNA structures under diverse and biocompatible conditions
    • Myhrvold, C.; Dai, M.; Silver, P. A.; Yin, P. Isothermal self-assembly of complex DNA structures under diverse and biocompatible conditions Nano Lett. 2013, 13, 4242-4248
    • (2013) Nano Lett. , vol.13 , pp. 4242-4248
    • Myhrvold, C.1    Dai, M.2    Silver, P.A.3    Yin, P.4
  • 48
    • 84882950990 scopus 로고    scopus 로고
    • Self-assembly of DNA origami and single-stranded tile structures at room temperature
    • Zhang, Z.; Song, J.; Besenbacher, F.; Dong, M.; Gothelf, K. V. Self-assembly of DNA origami and single-stranded tile structures at room temperature Angew. Chem., Int. Ed. 2013, 52, 9219-9223
    • (2013) Angew. Chem., Int. Ed. , vol.52 , pp. 9219-9223
    • Zhang, Z.1    Song, J.2    Besenbacher, F.3    Dong, M.4    Gothelf, K.V.5
  • 49
    • 48749083056 scopus 로고    scopus 로고
    • Isothermal Assembly of DNA Origami Structures Using Denaturing Agents
    • Jungmann, R.; Liedl, T.; Sobey, T. L.; Shih, W.; Simmel, F. C. Isothermal Assembly of DNA Origami Structures Using Denaturing Agents J. Am. Chem. Soc. 2008, 130, 10062-10063
    • (2008) J. Am. Chem. Soc. , vol.130 , pp. 10062-10063
    • Jungmann, R.1    Liedl, T.2    Sobey, T.L.3    Shih, W.4    Simmel, F.C.5
  • 50
    • 84862275855 scopus 로고    scopus 로고
    • Reconfigurable DNA origami to generate quasifractal patterns
    • Zhang, F.; Nangreave, J.; Liu, Y.; Yan, H. Reconfigurable DNA origami to generate quasifractal patterns Nano Lett. 2012, 12, 3290-3295
    • (2012) Nano Lett. , vol.12 , pp. 3290-3295
    • Zhang, F.1    Nangreave, J.2    Liu, Y.3    Yan, H.4
  • 52
    • 84890307278 scopus 로고    scopus 로고
    • In situ structure and dynamics of DNA origami determined through molecular dynamics simulations
    • Yoo, J.; Aksimentiev, A. In situ structure and dynamics of DNA origami determined through molecular dynamics simulations Proc. Natl. Acad. Sci. U.S.A. 2013, 110, 20099-20104
    • (2013) Proc. Natl. Acad. Sci. U.S.A. , vol.110 , pp. 20099-20104
    • Yoo, J.1    Aksimentiev, A.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.