DNA逻辑自组装体构建的研究进展
Research progress in the construction of DNA logic self-assembly
-
摘要: 对DNA自组装原理、DNA编码序列设计、DNA自组装基元和自组装体的构建等方面的研究现状进行了述评，提出构建复杂的DNA自组装体仍是该领域的研究难题，未来的研究将主要集中于三方面：1）基于DNA的热力学属性和物理化学属性，建立DNA自组装基元类型库和DNA自组装结构体；2）整合和挖掘高通量的DNA自组装实证数据，以数据为驱动，搭建适合描述DNA自组装体的系统模型；3）进行DNA自组装载药体系的可控性、适应性和应用性分析.Abstract: The principles of the DNA self-assembly,the design of the DNA coding sequence,DNA essential assemble units, and the construction of the DNA self-assembly system have been reviewed.The construction of the DNA self-assembly system is a difficult problem in this field.Three aspects will be focused in future research:first,based on thermodynamic and physico-chemical properties of DNA,DNA essential assemble units and DNA self-assembly system will be constructed;second,high-throughput empirical data of DNA self-assembly will be integrated and mined,the model of the DNA self-assembly system will be designed according to data-driven;at last,the controllability,adaptability and applicability of drug delivery system DNA self-assembly will be analyzed.
-
Key words:
- DNA logic self-assembly /
- DNA encoding /
- DNA tile /
- fundamental assemble unit
-
-
[1]
SEEMAN N C.Biochemistry and structural DNA nanotechnology:an evolving symbiotic relationship[J].Biochemistry,2003,42(24):7259.
-
[2]
CHEN H L,SCHULMAN R,GOEL A,et al.Reducing facet nucleation during algorithmic self-assembly[J].Nano Letters,2007,7(9):2913.
-
[3]
GARZON M H,DEATON R J.Codeword design and information encoding in DNA ensembles[J].Natural Computing,2004,3(3):253.
-
[4]
SHIN S Y,LEE I H,KIM D M,et al.Multiobjective evolutionary optimization of DNA sequences for reliable DNA computing[J].IEEE Trans Evolut Comput,2005,9(2):143.
-
[5]
FELDKAMP U,RAUHE H,BANZHAF W.Software tools for DNA sequence design[J].Genet Program Evol M,2003,4(2):153.
-
[6]
ZHANG K,XU J,GENG X,et al.Improved taboo search algorithm for designing DNA sequence[J].Prog Nat Sci,2008,18(5):623.
-
[7]
ZHANG Q,WANG B.An improved genetic algorithm for design of DNA sequence sets[J].J Comput Theor Nanosci,2010,7(6):1159.
-
[8]
XIAO J H,ZHANG X Y,XU J.A membrane evolutionary algorithm for DNA sequence design in DNA computing[J].Chin Sci Bull,2012,57(6):698.
-
[9]
王延峰,崔光照.DNA编码序列的设计与优化[M].北京:电子工业出版社,2013.
-
[10]
FU T J,TSE-DINH Y C,SEEMAN N C.Holliday junction crossover topology[J].J Mol Biol,1994,236(11):91.
-
[11]
KALLENBACH N R,MA R I,SEEMAN N C.An immobile nucleic-acid junction constructed from oligonucleotides[J].Nature,1983,305:829.
-
[12]
MA R I,KALLENBACH N R,SHEARDY R D,et al.Three-arm nucleic acid junctions are flexible[J].Nucleic Acids Res,1996,14(24):9745.
-
[13]
SEEMAN N C.De novo design of sequences for nucleic-acid structural-engineering[J].J Biomol Struct Dyn,1990,8(3):573.
-
[14]
SEEMAN N C.The perils of polynucleotides:the experimental gap between the design and assembly of unusual DNA structures[C]//Proceedings of the Second Annual Meeting on DNA-based Computers, Providence:American Mathematical Society,1996.
-
[15]
DU S M,SEEMAN N C.The construction of a trefoil knot from a DNA branched junction motif[J].Biopolymers,1994,34(11):31.
-
[16]
ZHANG Y,SEEMAN N C.The construction of a DNA truncated octahedron[J].J Am Chem Soc,1994,116(5):1661.
-
[17]
LIU F,SHA R,SEEMAN N C.Modifying the surface features of two dimensional DNA crystals[J].J Am Chem Soc,1999,121(5):917.
-
[18]
FU T J,SEEMAN N C.DNA double-crossover molecules[J].Biochemistry,1993,32:3211.
-
[19]
LABEAN T H,YAN H,KOPATSCH J,et al.Construction, analysis,ligation,and self-assembly of DNA triple crossover complexes[J].J Am Chem Soc,2000,122:1848.
-
[20]
REISHUS D,SHAW B,BRUN Y,et al.Self-assembly of DNA double-double crossover complexes into high-density,doubly connected,planar structures[J].J Am Chem Soc,2005,127:17590.
-
[21]
MATHIEU F,LIAO S P,KOPATSCHT J,et al.Six-helix bundles designed from DNA[J].Nano Lett,2005(5):661.
-
[22]
ROTHEMUND P W K.Folding DNA to create nanoscale shapes and patterns[J].Nature,2006,440:297.
-
[23]
DOUGLAS S M,CHOU J J,SHIH W M.DNA-nanotube-induced alignment of membrane proteins for NMR structure determination[J].Proc Natl Acad Sci USA,2007,104:6644.
-
[24]
ANDERSEN E S,DONG M,NIELSEN M M,et al.Self-assembly of a nanoscale DNA box with a controllable lid[J].Nature,2009,459:73.
-
[25]
HAN D,PAL S,NANGREAVE J,et al.DNA origami with complex curvatures in three-dimensional space[J].Science,2011,332:342.
-
[26]
WEI B,DAI M,YIN P.Complex shapes self-assembled from single-stranded DNA tiles[J].Nature,2012,485:623.
-
[27]
KE Y,ONG L L,SHIH W M,et al.Three-dimensional structures self-assembled from DNA bricks[J].Science,2012,338:1177.
-
[28]
SHI X,LU W,WANG Z,et al.Programmable DNA tile self-assembly using a hierarchical subtile strategy[J].Nanotechnology,2014(25):075602.
-
[29]
TIAN C,LI X,LIU Z,et al.Directed self-assembly of DNA tiles into complex nanocages[J].Angewandte Chemie,2014,126(31):8179.
-
[30]
LIU Z,TIAN C,YU J,et al.Self-assembly of responsive multilayered DNA nanocages[J].J Am Chem Soc,2015,137(5):1730.
-
[1]
-
点击查看大图
计量
- PDF下载量: 39
- 文章访问数: 765
- 引证文献数: 0
下载:
