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Volumn 5, Issue , 2014, Pages

Programmable energy landscapes for kinetic control of DNA strand displacement

Author keywords

[No Author keywords available]

Indexed keywords

BIOENERGETICS; DNA; MOLECULAR ANALYSIS; NUMERICAL MODEL; REACTION KINETICS; REACTION RATE;

EID: 84923321731     PISSN: None     EISSN: 20411723     Source Type: Journal    
DOI: 10.1038/ncomms6324     Document Type: Article
Times cited : (187)

References (45)
  • 1
    • 0025804117 scopus 로고
    • The synthesis from DNA of a molecule with the connectivity of a cube
    • Chen, J. & Seeman, N. C. The synthesis from DNA of a molecule with the connectivity of a cube. Nature 350, 631-633 (1991).
    • (1991) Nature , vol.350 , pp. 631-633
    • Chen, J.1    Seeman, N.C.2
  • 2
    • 0032490948 scopus 로고    scopus 로고
    • Design and self-assembly of two-dimensional DNA crystals
    • Winfree, E., Liu, F., Wenzler, L. A. & Seeman, N. C. Design and self-assembly of two-dimensional DNA crystals. Nature 394, 539-544 (1998).
    • (1998) Nature , vol.394 , pp. 539-544
    • Winfree, E.1    Liu, F.2    Wenzler, L.A.3    Seeman, N.C.4
  • 3
    • 28844463033 scopus 로고    scopus 로고
    • Rapid chiral assembly of rigid DNA building blocks for molecular nanofabrication
    • Goodman, R. P. et al. Rapid chiral assembly of rigid DNA building blocks for molecular nanofabrication. Science 310, 1661-1665 (2005).
    • (2005) Science , vol.310 , pp. 1661-1665
    • Goodman, R.P.1
  • 4
    • 33645028600 scopus 로고    scopus 로고
    • Folding DNA to create nanoscale shapes and patterns
    • Rothemund, P. W. K. Folding DNA to create nanoscale shapes and patterns. Nature 440, 297-302 (2006).
    • (2006) Nature , vol.440 , pp. 297-302
    • Rothemund, P.W.K.1
  • 5
    • 84863186339 scopus 로고    scopus 로고
    • Complex shapes self-assembled from single-stranded DNA tiles
    • Wei, B., Dai, M. & Yin, P. Complex shapes self-assembled from single-stranded DNA tiles. Nature 485, 623-626 (2012).
    • (2012) Nature , vol.485 , pp. 623-626
    • Wei, B.1    Dai, M.2    Yin, P.3
  • 6
    • 66249137759 scopus 로고    scopus 로고
    • Self-assembly of DNA into nanoscale three-dimensional shapes
    • Douglas, S. M. et al. Self-assembly of DNA into nanoscale three-dimensional shapes. Nature 459, 414-418 (2009).
    • (2009) Nature , vol.459 , pp. 414-418
    • Douglas, S.M.1
  • 7
    • 84869126805 scopus 로고    scopus 로고
    • Synthetic lipid membrane channels formed by designed DNA nanostructures
    • Langecker, M. et al. Synthetic lipid membrane channels formed by designed DNA nanostructures. Science 338, 932-936 (2012).
    • (2012) Science , vol.338 , pp. 932-936
    • Langecker, M.1
  • 8
    • 84858197920 scopus 로고    scopus 로고
    • DNA-based self-assembly of chiral plasmonic nanostructures with tailored optical response
    • Kuzyk, A. et al. DNA-based self-assembly of chiral plasmonic nanostructures with tailored optical response. Nature 438, 311-314 (2012).
    • (2012) Nature , vol.438 , pp. 311-314
    • Kuzyk, A.1
  • 9
    • 70449122700 scopus 로고    scopus 로고
    • DNA origami as a nanoscopic ruler for super-resolution microscopy
    • Steinhauer, C. et al. DNA origami as a nanoscopic ruler for super-resolution microscopy. Angew. Chem. Int. Ed. 48, 8870-8873 (2009).
    • (2009) Angew. Chem. Int. Ed. , vol.48 , pp. 8870-8873
    • Steinhauer, C.1
  • 10
    • 84858151469 scopus 로고    scopus 로고
    • A DNA-based molecular motor that can navigate a network of tracks
    • Wickham, S. F. J. et al. A DNA-based molecular motor that can navigate a network of tracks. Nat. Nanotechnol. 7, 169-173 (2012).
    • (2012) Nat. Nanotechnol. , vol.7 , pp. 169-173
    • Wickham, S.F.J.1
  • 11
    • 84870598483 scopus 로고    scopus 로고
    • Small molecule signals that route a molecular cargo
    • Muscat, R. A., Bath, J. & Turberfield, A. J. Small molecule signals that route a molecular cargo. Small 8, 3593-3597 (2012).
    • (2012) Small , vol.8 , pp. 3593-3597
    • Muscat, R.A.1    Bath, J.2    Turberfield, A.J.3
  • 12
    • 77952404245 scopus 로고    scopus 로고
    • A proximity-based programmable DNA nanoscale assembly line
    • Gu, H., Chao, J., Xiao, S.-J. & Seeman, N. C. A proximity-based programmable DNA nanoscale assembly line. Nature 465, 202-205 (2010).
    • (2010) Nature , vol.465 , pp. 202-205
    • Gu, H.1    Chao, J.2    Xiao, S.-J.3    Seeman, N.C.4
  • 13
    • 77952392836 scopus 로고    scopus 로고
    • Molecular robots guided by prescriptive landscapes
    • Lund, K. et al. Molecular robots guided by prescriptive landscapes. Nature 465, 206-210 (2010).
    • (2010) Nature , vol.465 , pp. 206-210
    • Lund, K.1
  • 15
    • 79960650829 scopus 로고    scopus 로고
    • Neural network computation with DNA strand displacement cascades
    • Qian, L., Winfree, E. & Bruck, J. Neural network computation with DNA strand displacement cascades. Nature 475, 368-372 (2011).
    • (2011) Nature , vol.475 , pp. 368-372
    • Qian, L.1    Winfree, E.2    Bruck, J.3
  • 16
    • 84872416211 scopus 로고    scopus 로고
    • Combinatorial displacement of DNA strands: Application to matrix multiplication and weighted sums
    • Genot, A. J., Bath, J. & Turberfield, A. J. Combinatorial displacement of DNA strands: application to matrix multiplication and weighted sums. Angew. Chem. Int. Ed. 52, 1189-1192 (2013).
    • (2013) Angew. Chem. Int. Ed. , vol.52 , pp. 1189-1192
    • Genot, A.J.1    Bath, J.2    Turberfield, A.J.3
  • 18
    • 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. 131, 17303-17314 (2009).
    • (2009) J. Am. Chem. Soc. , vol.131 , pp. 17303-17314
    • Zhang, D.Y.1    Winfree, E.2
  • 19
    • 84887968813 scopus 로고    scopus 로고
    • On the biophysics and kinetics of toehold-mediated DNA strand displacement
    • Srinivas, N. et al. On the biophysics and kinetics of toehold-mediated DNA strand displacement. Nucleic Acids Res. 41, 10641-10658 (2013).
    • (2013) Nucleic Acids Res. , vol.41 , pp. 10641-10658
    • Srinivas, N.1
  • 20
    • 79951841779 scopus 로고    scopus 로고
    • Remote toehold: A mechanism for flexible control of DNA hybridization kinetics
    • Genot, A. J., Zhang, D. Y., Bath, J. & Turberfield, A. J. Remote toehold: a mechanism for flexible control of DNA hybridization kinetics. J. Am. Chem. Soc. 133, 2177-2182 (2011).
    • (2011) J. Am. Chem. Soc. , vol.133 , pp. 2177-2182
    • Genot, A.J.1    Zhang, D.Y.2    Bath, J.3    Turberfield, A.J.4
  • 21
    • 84863116178 scopus 로고    scopus 로고
    • Optimizing the specificity of nucleic acid hybridization
    • Zhang, D. Y., Chen, S. X. & Peng, Y. Optimizing the specificity of nucleic acid hybridization. Nat. Chem. 4, 208-214 (2012).
    • (2012) Nat. Chem. , vol.4 , pp. 208-214
    • Zhang, D.Y.1    Chen, S.X.2    Peng, Y.3
  • 22
    • 84883190867 scopus 로고    scopus 로고
    • Conditionally fluorescent molecular probes for detecting single base changes in double-stranded DNA
    • Chen, S. X., Zhang, D. Y. & Seelig, G. Conditionally fluorescent molecular probes for detecting single base changes in double-stranded DNA. Nat. Chem. 5, 782-789 (2013).
    • (2013) Nat. Chem. , vol.5 , pp. 782-789
    • Chen, S.X.1    Zhang, D.Y.2    Seelig, G.3
  • 23
    • 0027200006 scopus 로고
    • Formation of a single base mismatch impedes spontaneous DNA branch migration
    • Panyutin, I. G. & Hsieh, P. Formation of a single base mismatch impedes spontaneous DNA branch migration. J. Mol. Biol. 230, 413-424 (1993).
    • (1993) J. Mol. Biol. , vol.230 , pp. 413-424
    • Panyutin, I.G.1    Hsieh, P.2
  • 24
    • 79851471472 scopus 로고    scopus 로고
    • The label-free unambiguous detection and symbolic display of single nucleotide polymorphisms on DNA origami
    • Subramanian, H. K. K., Chakraborty, B., Sha, R. & Seeman, N. C. The label-free unambiguous detection and symbolic display of single nucleotide polymorphisms on DNA origami. Nano Lett. 11, 910-913 (2011).
    • (2011) Nano Lett. , vol.11 , pp. 910-913
    • Subramanian, H.K.K.1    Chakraborty, B.2    Sha, R.3    Seeman, N.C.4
  • 25
    • 77955064536 scopus 로고    scopus 로고
    • Robustness and modularity properties of a noncovalent DNA catalytic reaction
    • Zhang, D. Y. & Winfree, E. Robustness and modularity properties of a noncovalent DNA catalytic reaction. Nucleic Acids Res. 38, 4182-4197 (2010).
    • (2010) Nucleic Acids Res. , vol.38 , pp. 4182-4197
    • Zhang, D.Y.1    Winfree, E.2
  • 26
    • 18744432001 scopus 로고    scopus 로고
    • A new class of homogenous nucleic acid probes based on specific displacement hybridization
    • Li, Q., Luan, G., Guo, Q. & Liang, J. A new class of homogenous nucleic acid probes based on specific displacement hybridization. Nucleic Acids Res. 30, e5 (2002).
    • (2002) Nucleic Acids Res. , vol.30 , pp. e5
    • Li, Q.1    Luan, G.2    Guo, Q.3    Liang, J.4
  • 27
    • 0032546751 scopus 로고    scopus 로고
    • Branch migration through DNA sequence heterology
    • Biswas, I., Yamamoto, A. & Hsieh, P. Branch migration through DNA sequence heterology. J. Mol. Biol. 279, 795-806 (1998).
    • (1998) J. Mol. Biol. , vol.279 , pp. 795-806
    • Biswas, I.1    Yamamoto, A.2    Hsieh, P.3
  • 28
    • 84893595669 scopus 로고    scopus 로고
    • Mismatches improve the performance of strand-displacement nucleic acid circuits
    • Jiang, Y. S., Bhadra, S., Li, B. & Ellington, A. D. Mismatches improve the performance of strand-displacement nucleic acid circuits. Angew. Chem. Int. Ed. 53, 1845-1848 (2014).
    • (2014) Angew. Chem. Int. Ed. , vol.53 , pp. 1845-1848
    • Jiang, Y.S.1    Bhadra, S.2    Li, B.3    Ellington, A.D.4
  • 29
    • 79952091255 scopus 로고    scopus 로고
    • Structural, mechanical, and thermodynamic properties of a coarse-grained DNA model
    • 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).
    • (2011) J. Chem. Phys. , vol.134 , pp. 085101
    • Ouldridge, T.E.1    Louis, A.A.2    Doye, J.P.K.3
  • 30
    • 84867508975 scopus 로고    scopus 로고
    • Sequence-dependent thermodynamics of a coarse-grained DNA model
    • Šulc, P. et al. Sequence-dependent thermodynamics of a coarse-grained DNA model. J. Chem. Phys. 137, 135101 (2012).
    • (2012) J. Chem. Phys. , vol.137 , pp. 135101
    • Šulc, P.1
  • 31
    • 11144297638 scopus 로고    scopus 로고
    • Effects of fluorescent dyes, quenchers, and dangling ends on DNA duplex stability
    • Moreira, B. G., You, Y., Behlke, M. A. & Owczarzy, R. Effects of fluorescent dyes, quenchers, and dangling ends on DNA duplex stability. Biochem. Biophys. Res. Commun. 327, 473-484 (2005).
    • (2005) Biochem. Biophys. Res. Commun. , vol.327 , pp. 473-484
    • Moreira, B.G.1    You, Y.2    Behlke, M.A.3    Owczarzy, R.4
  • 32
    • 0036835759 scopus 로고    scopus 로고
    • Efficiencies of fluorescence resonance energy transfer and contact-mediated quenching in oligonucleotide probes
    • Marras, S. A. E., Kramer, F. R. & Tyagi, S. Efficiencies of fluorescence resonance energy transfer and contact-mediated quenching in oligonucleotide probes. Nucleic Acids Res. 30, e122 (2002).
    • (2002) Nucleic Acids Res. , vol.30 , pp. e122
    • Marras, S.A.E.1    Kramer, F.R.2    Tyagi, S.3
  • 33
    • 78149355812 scopus 로고    scopus 로고
    • NUPACK: Analysis and design of nucleic acid systems
    • Zadeh, J. N. et al. NUPACK: analysis and design of nucleic acid systems. J. Comput. Chem. 32, 170-173 (2011).
    • (2011) J. Comput. Chem. , vol.32 , pp. 170-173
    • Zadeh, J.N.1
  • 34
    • 0033596964 scopus 로고    scopus 로고
    • Nearest-neighbor thermodynamics and NMR of DNA sequences with internal A · A, C · C, G · G, and T · T mismatches
    • Peyret, N., Seneviratne, P. A., Allawi, H. T. & SantaLucia, J. Nearest-neighbor thermodynamics and NMR of DNA sequences with internal A · A, C · C, G · G, and T · T mismatches. Biochemistry 38, 3468-3477 (1999).
    • (1999) Biochemistry , vol.38 , pp. 3468-3477
    • Peyret, N.1    Seneviratne, P.A.2    Allawi, H.T.3    Santalucia, J.4
  • 38
    • 38749146474 scopus 로고    scopus 로고
    • Predicting ultraviolet spectrum of single stranded and double stranded deoxyribonucleic acids
    • Tataurov, A. V., You, Y. & Owczarzy, R. Predicting ultraviolet spectrum of single stranded and double stranded deoxyribonucleic acids. Biophys. Chem. 133, 66-70 (2008).
    • (2008) Biophys. Chem. , vol.133 , pp. 66-70
    • Tataurov, A.V.1    You, Y.2    Owczarzy, R.3
  • 39
    • 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 32, 3095-3104 (1993).
    • (1993) Biochemistry , vol.32 , pp. 3095-3104
    • Morrison, L.E.1    Stols, L.M.2
  • 41
    • 18144425774 scopus 로고    scopus 로고
    • Sampling rare switching events in biochemical networks
    • Allen, R. J., Warren, P. B. & ten Wolde, P. R. Sampling rare switching events in biochemical networks. Phys. Rev. Lett. 94, 018104 (2005).
    • (2005) Phys. Rev. Lett. , vol.94 , pp. 018104
    • Allen, R.J.1    Warren, P.B.2    Ten Wolde, P.R.3
  • 43
    • 84886016409 scopus 로고    scopus 로고
    • DNA hybridization kinetics: Zippering, internal displacement and sequence dependence
    • Ouldridge, T. E., Šulc, 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).
    • (2013) Nucleic Acids Res. , vol.41 , pp. 8886-8895
    • Ouldridge, T.E.1    Šulc, P.2    Romano, F.3    Doye, J.P.K.4    Louis, A.A.5
  • 44
    • 62249221278 scopus 로고    scopus 로고
    • The role of collective motion in examples of coarsening and self-assembly
    • Whitelam, S., Feng, E. H., Hagan, M. F. & Geissler, P. L. The role of collective motion in examples of coarsening and self-assembly. Soft Matter 5, 1251-1262 (2009).
    • (2009) Soft Matter , vol.5 , pp. 1251-1262
    • Whitelam, S.1    Feng, E.H.2    Hagan, M.F.3    Geissler, P.L.4
  • 45
    • 0342929614 scopus 로고
    • Nonphysical sampling distributions in Monte Carlo free-energy estimation: Umbrella sampling
    • Torrie, G. M. & Valleau, J. P. Nonphysical sampling distributions in Monte Carlo free-energy estimation: Umbrella sampling. J. Comput. Phys. 23, 187-199 (1977).
    • (1977) J. Comput. Phys. , vol.23 , pp. 187-199
    • Torrie, G.M.1    Valleau, J.P.2


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