DNA纳米自组装的研究进展及应用
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摘要
DNA纳米技术是一种自下而上的分子自组装模式,由分子构造为起点基于核酸分子的物理和化学性质自发地形成稳定结构,遵循严格的核酸碱基配对原则,使得DNA被用作构建结构的材料基元而不是在活细胞中那样作为遗传信息的载体.通过合理地设计碱基链来达成精密控制的纳米级复杂结构的目的,研究人员在这个领域已经建立起诸多二维、三维的复杂纳米结构以及各种具有不同功能的分子机器,比如DNA计算机.本文总结了近年来DNA纳米自组装方面取得的最新进展,同时介绍DNA纳米自组装的几种不同组装方法,并对其相关应用进行了展望.
DNA nanotechnology is an example of bottom-up molecular self-assembly,in which molecular components spontaneously organize into stable structures;the particular form of these structures is induced by the physical and chemical properties of the components selected by the designers.In this field,nucleic acids are used as non-biological engineering materials for nanotechnology rather than as the carriers of genetic information in living cells.This use is enabled by the strict base pairing rules of nucleic acids,which cause only portions of strands with complementary base sequences to bind together to form strong,rigid double helix structures.This allows for the rational design of base sequences that will selectively assemble to form complex target structures with precisely controlled nanoscale features.This article mainly reviews the developments of DNA self-assembly achieved recently and also introduces the design methods of it,which would be helpful and enlightened for our future research.
DNA nanotechnology is an example of bottom-up molecular self-assembly,in which molecular components spontaneously organize into stable structures;the particular form of these structures is induced by the physical and chemical properties of the components selected by the designers.In this field,nucleic acids are used as non-biological engineering materials for nanotechnology rather than as the carriers of genetic information in living cells.This use is enabled by the strict base pairing rules of nucleic acids,which cause only portions of strands with complementary base sequences to bind together to form strong,rigid double helix structures.This allows for the rational design of base sequences that will selectively assemble to form complex target structures with precisely controlled nanoscale features.This article mainly reviews the developments of DNA self-assembly achieved recently and also introduces the design methods of it,which would be helpful and enlightened for our future research.
引文
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29 Mao C D,Sun W Q,Shen Z Y,et al.A nanomechanical device based on the B-Z transition of DNA.Nature,1999,397:144–146
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36 Sherman W B,Seeman N C.A precisely controlled DNA biped walking device.Nano Lett,2004,4:1203–1207
37 Tian Y,He Y,Chen Y,et al.Molecular devices—A DNAzyme that walks processively and autonomously along a one-dimensional track.Angew Chem Int Ed,2005,44:4355–4358
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39 Lund K,Manzo A J,Dabby N,et al.Molecular robots guided by prescriptive landscapes.Nature,2010,465:206–210
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42 Seelig G,Soloveichik D,Zhang D Y,et al.Enzyme-free nucleic acid logic circuits.Science,2006,314:1585–1588
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44 Yin P,Choi H M T,Calvert C R,et al.Programming biomolecular self-assembly pathways.Nature,2008,451:318–322
45 Wang Z G,Elbaz J,Remacle F,et al.All-DNA finite-state automata with finite memory.Proc Natl Acad Sci USA,2010,107:21996–22001
46 Wang Z G,Elbaz J,Willner I.A dynamically programmed DNA transporter.Angew Chem Int Ed,2012,51:4322–4326
47 Wickham S F J,Bath J,Katsuda Y,et al.A DNA-based molecular motor that can navigate a network of tracks.Nat Nanotechnol,2012,7:169 –173
48 Gu H,Chao J,Xiao S J,et al.A proximity-based programmable DNA nanoscale assembly line.Nature,2010,465:202–205
49 Li H,Carter J D,Labean T H.Nanofabrication by DNA self-assembly.Mater Today,2009,12:24–32
50 Lund K,Liu Y,Lindsay S,et al.Self-assembling a molecular pegboard.J Am Chem Soc,2005,127:17606–17607
51 Ke Y,Lindsay S,Chang Y,et al.Self-assembled water-soluble nucleic acid probe tiles for label-free RNA hybridization assays.Science,2008,319:180–183
52 Ke Y,Nangreave J,Yan H,et al.Developing DNA tiles for oligonucleotide hybridization assay with higher accuracy and efficiency.Chem Commun,2008,43:5622–5624
53 Park S H,Yin P,Liu Y,et al.Programmable DNA self-assemblies for nanoscale organization of ligands and proteins.Nano Lett,2005,5:729 –733
54 Liu Y,Lin C X,Li H Y,et al.Protein nanoarrays—Aptamer-directed self-assembly of protein arrays on a DNA nanostructure.Angew Chem Int Ed,2005,44:4333–4338
55 Chhabra R,Sharma J,Ke Y,et al.Spatially addressable multiprotein nanoarrays templated by aptamer-tagged DNA nanoarchitectures.J Am Chem Soc,2007,129:10304–10305
56 Rinker S,Ke Y,Liu Y,et al.Self-assembled DNA nanostructures for distance-dependent multivalent ligand-protein binding.Nat Nanotechnol,2008,3:418–422
57 Fu J,Liu M,Liu Y,et al.Interenzyme substrate diffusion for an enzyme cascade organized on spatially addressable DNA nanostructures.J Am Chem Soc,2012,134:5516–5519
58 Le J D,Pinto Y,Seeman N C,et al.DNA-templated self-assembly of metallic nanocomponent arrays on a surface.Nano Lett,2004,4:2343–2347
59 Pinto Y Y,Le J D,Seeman N C,et al.Sequence-encoded self-assembly of multiple-nanocomponent arrays by 2D DNA scaffolding.Nano Lett,2005,5:2399–2402
60 Zhang J P,Liu Y,Ke Y G,et al.Periodic square-like gold nanoparticle arrays templated by self-assembled 2D DNA nanogrids on a surface.Nano Lett,2006,6:248–251
61 Sharma J,Chhabra R,Andersen C S,et al.Toward reliable gold nanoparticle patterning on self-assembled DNA nanoscaffold.J Am Chem Soc,2008,130:7820–7821
62 Tikhomirov G,Hoogland S,Lee P E,et al.DNA-based programming of quantum dot valency,self-assembly and luminescence.Nat Nanotechnol,2011,6:485–490
63 Chen J H,Seeman N C.Synthesis from DNA of a molecule with the connectivity of a cube.Nature,1991,350:631–633
64 Zhang Y W,Seeman N C.Construction of a DNA-truncated octahedron.J Am Chem Soc,1994,116:1661–1669
65 Scheffler M,Dorenbeck A,Jordan S,et al.Self-assembly of trisoligonucleotidyls:The case for nano-acetylene and nano-cyclobutadiene.Angew Chem Int Ed,1999,38:3311–3315
66 Goodman R P,Schaap I A T,Tardin C F,et al.Rapid chiral assembly of rigid DNA building blocks for molecular nanofabrication.Science,2005,310:1661–1665
67 Pei H,Lu N,Wen Y,et al.A DNA Nanostructure-based biomolecular probe carrier platform for electrochemical biosensing.Adv Mater,2010,22:4754–4758
68 Pei H,Wan Y,Li J,et al.Regenerable electrochemical immunological sensing at DNA nanostructure-decorated gold surfaces.Chem Commun,2011,47:6254–6256
69 Ge Z L,Pei H,Wang L H,et al.Electrochemical single nucleotide polymorphisms genotyping on surface immobilized three-dimensional branched DNA nanostructure.Sci China Chem,2011,54:1273–1276
70 Storhoff J J,Mirkin C A.Programmed materials synthesis with DNA.Chem Rev,1999,99:1849–1862
71 Gothelf K V,Labean T H.DNA-programmed assembly of nanostructures.Org Biomol Chem,2005,3:4023–4037
72 Silverman A P,Kool E T.Detecting RNA and DNA with templated chemical reactions.Chem Rev,2006,106:3775–3789
73 Li X Y,Liu D R.DNA-templated organic synthesis:Nature’s strategy for controlling chemical reactivity applied to synthetic molecules.Angew Chem Int Ed,2004,43:4848–4870
74 Gartner Z J,Tse B N,Grubina R,et al.DNA-templated organic synthesis and selection of a library of macrocycles.Science,2004,305:1601–1605
75 Kanan M W,Rozenman M M,Sakurai K,et al.Reaction discovery enabled by DNA-templated synthesis and in vitro selection.Nature,2004,431:545–549
76 Chen Y,Mao C.Reprogramming DNA-directed reactions on the basis of a DNA conformational change.J Am Chem Soc,2004,126:13240–13241
2 Fu T J,Seeman N C.DNA double-crossover molecules.Biochemistry,1993,32:3211–3220
3 Labean T H,Yan H,Kopatsch J,et al.Construction,analysis,ligation,and self-assembly of DNA triple crossover complexes.J Am Chem Soc,2000,122:1848–1860
4 Reishus D,Shaw B,Brun Y,et al.Self-assembly of DNA double-double crossover complexes into high-density,doubly connected,planar structures.J Am Chem Soc,2005,127:17590–17591
5 Mathieu F,Liao S P,Kopatscht J,et al.Six-helix bundles designed from DNA.Nano Lett,2005,5:661–665
6 Yan H,Park S H,Finkelstein G,et al.DNA-templated self-assembly of protein arrays and highly conductive nanowires.Science,2003,301 :1882–1884
7 Liu D,Wang M S,Deng Z X,et al.Tensegrity:Construction of rigid DNA triangles with flexible four-arm DNA junctions.J Am Chem Soc,2004,126:2324–2325
8 He Y,Chen Y,Liu H P,et al.Self-assembly of hexagonal DNA two-dimensional(2D)arrays.J Am Chem Soc,2005,127:12202–12203
9 He Y,Tian Y,Ribbe A E,et al.Highly connected two-dimensional crystals of DNA six-point-stars.J Am Chem Soc,2006,128:15978–15979
10 Zhang C,Su M,He Y,et al.Conformational flexibility facilitates self-assembly of complex DNA nanostructures.Proc Natl Acad Sci USA,2008,105:10665–10669
11 Liu H P,He Y,Ribbe A E,et al.Two-dimensional(2D)DNA crystals assembled from two DNA strands.Biomacromolecules,2005,6:2943–2945
12 Liu H P,Chen Y,He Y,et al.Approaching the limit:Can one DNA oligonucleotide assemble into large nanostructures?Angew Chem Int Ed,2006,45:1942–1945
13 Yin P,Hariadi R F,Sahu S,et al.Programming DNA tube circumferences.Science,2008,321:824–826
14 Wei B,Dai M,Yin P.Complex shapes self-assembled from single-stranded DNA tiles.Nature,2012,485:623–626
15 Ke Y,Ong L L,Shih W M,et al.Three-dimensional structures self-assembled from DNA bricks.Science,2012,338:1177–1183
16 Adleman L M.Molecular computation of solutions to combinatorial problems.Science,1994,266:1021–1024
17 Yan H,Labean T H,Feng L P,et al.Directed nucleation assembly of DNA tile complexes for barcode-patterned lattices.Proc Natl Acad Sci USA,2003,100:8103–8108
18 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
19 Rothemund P W K.Folding DNA to create nanoscale shapes and patterns.Nature,2006,440:297–302
20 Qian L,Wang Y,Zhang Z,et al.Analogic China map constructed by DNA.Chin Sci Bull,2006,51:2973–2976
21 Andersen E S,Dong M,Nielsen M M,et al.Self-assembly of a nanoscale DNA box with a controllable lid.Nature,2009,459:73–75
22 Ke Y,Sharma J,Liu M,et al.Scaffolded DNA origami of a DNA tetrahedron molecular container.Nano Lett,2009,9:2445–2447
23 Douglas S M,Chou J J,Shih W M.DNA-nanotube-induced alignment of membrane proteins for NMR structure determination.Proc Natl Acad Sci USA,2007,104:6644–6648
24 Seeman N C.Nucleic-acid junctions and lattices.J Theoret Biol,1982,99:237–247
25 Labean T H.Nanotechnology another dimension for DNA art.Nature,2009,459:331–332
26 Dietz H,Douglas S M,Shih W M.Folding DNA into twisted and curved nanoscale shapes.Science,2009,325:725–730
27 Ke Y,Douglas S M,Liu M,et al.Multilayer DNA origami packed on a square lattice.J Am Chem Soc,2009,131:15903–15908
28 Han D,Pal S,Nangreave J,et al.DNA origami with complex curvatures in three-dimensional space.Science,2011,332:342–346
29 Mao C D,Sun W Q,Shen Z Y,et al.A nanomechanical device based on the B-Z transition of DNA.Nature,1999,397:144–146
30 Yurke B,Turberfield A J,Mills A P,et al.A DNA-fuelled molecular machine made of DNA.Nature,2000,406:605–608
31 Yan H,Zhang X P,Shen Z Y,et al.A robust DNA mechanical device controlled by hybridization topology.Nature,2002,415:62–65
32 Goodman R P,Heilemann M,Doose S,et al.Reconfigurable,braced,three-dimensional DNA nanostructures.Nat Nanotechnol,2008,3:93–96
33 Park S H,Pistol C,Ahn S J,et al.Finite-size,fully addressable DNA tile lattices formed by hierarchical assembly procedures.Angew Chem Int Ed,2006,45:735–739
34 Douglas S M,Bachelet I,Church G M.A Logic-gated nanorobot for targeted transport of molecular payloads.Science,2012,335:831–834
35 Shin J S,Pierce N A.A synthetic DNA walker for molecular transport.J Am Chem Soc,2004,126:10834–10835
36 Sherman W B,Seeman N C.A precisely controlled DNA biped walking device.Nano Lett,2004,4:1203–1207
37 Tian Y,He Y,Chen Y,et al.Molecular devices—A DNAzyme that walks processively and autonomously along a one-dimensional track.Angew Chem Int Ed,2005,44:4355–4358
38 Bath J,Green S J,Turberfield A J.A free-running DNA motor powered by a nicking enzyme.Angew Chem Int Ed,2005,44:4358–4361
39 Lund K,Manzo A J,Dabby N,et al.Molecular robots guided by prescriptive landscapes.Nature,2010,465:206–210
40 He Y,Liu D R.Autonomous multistep organic synthesis in a single isothermal solution mediated by a DNA walker.Nat Nanotechnol,2010,5:778–782
41 Zhang D Y,Seelig G.Dynamic DNA nanotechnology using strand-displacement reactions.Nat Chem,2011,3:103–113
42 Seelig G,Soloveichik D,Zhang D Y,et al.Enzyme-free nucleic acid logic circuits.Science,2006,314:1585–1588
43 Qian L,Winfree E.Scaling up digital circuit computation with DNA strand displacement cascades.Science,2011,332:1196–1201
44 Yin P,Choi H M T,Calvert C R,et al.Programming biomolecular self-assembly pathways.Nature,2008,451:318–322
45 Wang Z G,Elbaz J,Remacle F,et al.All-DNA finite-state automata with finite memory.Proc Natl Acad Sci USA,2010,107:21996–22001
46 Wang Z G,Elbaz J,Willner I.A dynamically programmed DNA transporter.Angew Chem Int Ed,2012,51:4322–4326
47 Wickham S F J,Bath J,Katsuda Y,et al.A DNA-based molecular motor that can navigate a network of tracks.Nat Nanotechnol,2012,7:169 –173
48 Gu H,Chao J,Xiao S J,et al.A proximity-based programmable DNA nanoscale assembly line.Nature,2010,465:202–205
49 Li H,Carter J D,Labean T H.Nanofabrication by DNA self-assembly.Mater Today,2009,12:24–32
50 Lund K,Liu Y,Lindsay S,et al.Self-assembling a molecular pegboard.J Am Chem Soc,2005,127:17606–17607
51 Ke Y,Lindsay S,Chang Y,et al.Self-assembled water-soluble nucleic acid probe tiles for label-free RNA hybridization assays.Science,2008,319:180–183
52 Ke Y,Nangreave J,Yan H,et al.Developing DNA tiles for oligonucleotide hybridization assay with higher accuracy and efficiency.Chem Commun,2008,43:5622–5624
53 Park S H,Yin P,Liu Y,et al.Programmable DNA self-assemblies for nanoscale organization of ligands and proteins.Nano Lett,2005,5:729 –733
54 Liu Y,Lin C X,Li H Y,et al.Protein nanoarrays—Aptamer-directed self-assembly of protein arrays on a DNA nanostructure.Angew Chem Int Ed,2005,44:4333–4338
55 Chhabra R,Sharma J,Ke Y,et al.Spatially addressable multiprotein nanoarrays templated by aptamer-tagged DNA nanoarchitectures.J Am Chem Soc,2007,129:10304–10305
56 Rinker S,Ke Y,Liu Y,et al.Self-assembled DNA nanostructures for distance-dependent multivalent ligand-protein binding.Nat Nanotechnol,2008,3:418–422
57 Fu J,Liu M,Liu Y,et al.Interenzyme substrate diffusion for an enzyme cascade organized on spatially addressable DNA nanostructures.J Am Chem Soc,2012,134:5516–5519
58 Le J D,Pinto Y,Seeman N C,et al.DNA-templated self-assembly of metallic nanocomponent arrays on a surface.Nano Lett,2004,4:2343–2347
59 Pinto Y Y,Le J D,Seeman N C,et al.Sequence-encoded self-assembly of multiple-nanocomponent arrays by 2D DNA scaffolding.Nano Lett,2005,5:2399–2402
60 Zhang J P,Liu Y,Ke Y G,et al.Periodic square-like gold nanoparticle arrays templated by self-assembled 2D DNA nanogrids on a surface.Nano Lett,2006,6:248–251
61 Sharma J,Chhabra R,Andersen C S,et al.Toward reliable gold nanoparticle patterning on self-assembled DNA nanoscaffold.J Am Chem Soc,2008,130:7820–7821
62 Tikhomirov G,Hoogland S,Lee P E,et al.DNA-based programming of quantum dot valency,self-assembly and luminescence.Nat Nanotechnol,2011,6:485–490
63 Chen J H,Seeman N C.Synthesis from DNA of a molecule with the connectivity of a cube.Nature,1991,350:631–633
64 Zhang Y W,Seeman N C.Construction of a DNA-truncated octahedron.J Am Chem Soc,1994,116:1661–1669
65 Scheffler M,Dorenbeck A,Jordan S,et al.Self-assembly of trisoligonucleotidyls:The case for nano-acetylene and nano-cyclobutadiene.Angew Chem Int Ed,1999,38:3311–3315
66 Goodman R P,Schaap I A T,Tardin C F,et al.Rapid chiral assembly of rigid DNA building blocks for molecular nanofabrication.Science,2005,310:1661–1665
67 Pei H,Lu N,Wen Y,et al.A DNA Nanostructure-based biomolecular probe carrier platform for electrochemical biosensing.Adv Mater,2010,22:4754–4758
68 Pei H,Wan Y,Li J,et al.Regenerable electrochemical immunological sensing at DNA nanostructure-decorated gold surfaces.Chem Commun,2011,47:6254–6256
69 Ge Z L,Pei H,Wang L H,et al.Electrochemical single nucleotide polymorphisms genotyping on surface immobilized three-dimensional branched DNA nanostructure.Sci China Chem,2011,54:1273–1276
70 Storhoff J J,Mirkin C A.Programmed materials synthesis with DNA.Chem Rev,1999,99:1849–1862
71 Gothelf K V,Labean T H.DNA-programmed assembly of nanostructures.Org Biomol Chem,2005,3:4023–4037
72 Silverman A P,Kool E T.Detecting RNA and DNA with templated chemical reactions.Chem Rev,2006,106:3775–3789
73 Li X Y,Liu D R.DNA-templated organic synthesis:Nature’s strategy for controlling chemical reactivity applied to synthetic molecules.Angew Chem Int Ed,2004,43:4848–4870
74 Gartner Z J,Tse B N,Grubina R,et al.DNA-templated organic synthesis and selection of a library of macrocycles.Science,2004,305:1601–1605
75 Kanan M W,Rozenman M M,Sakurai K,et al.Reaction discovery enabled by DNA-templated synthesis and in vitro selection.Nature,2004,431:545–549
76 Chen Y,Mao C.Reprogramming DNA-directed reactions on the basis of a DNA conformational change.J Am Chem Soc,2004,126:13240–13241