DNA及基于DNA链替换反应的分子计算

肖石燕; 梁好均

doi:10.7498/aps.65.178106

摘要

DNA是生物遗传信息的载体，同时也是一种理想的生物相容材料. 单链黏性末端（toehold）协助的链替换反应是DNA常温纳米技术的基础. 利用DNA的碱基互补特性和碱基序列的可编程性，人们可以基于DNA链替换反应构建分子机器并对其运转进行精确调控，实现各种复杂分子计算. 本文回顾了近年来DNA结构和力学性质方面的研究进展，探讨DNA链替换反应的微观理解，介绍DNA分子计算领域的最新成果，以及它在DNA恒温自组装等方面的应用.

关键词:

Abstract

biocompatibility. Considering the critical role of DNA less than 150 base pairs (bp) in cellular processes such as regulated gene expression, quantifying the intrinsic bend ability of DNA on a sub-persistence length scale is essential to understanding its molecular functions and the DNA-protein interaction. From the classical point of view, double-stranded DNA is assumed to be stiff and can be treated by semi-flexible chain, but recent studies have yielded contradictory results. A lot of studies tried to prove that the worm-like chain model can be used to fully describe DNA chain. However, recent theoretical and experimental studies indicated that DNA exhibits high flexibility on a short length scale, which cannot be described by the worm-like chain model. Further studies are needed to address the extreme flexibility of DNA on a short length scale. On the basis of the predictability of the double helical structure and the Watson-Crick binding thermodynamics for DNA, a class of DNA reactions can be defined, called toehold-mediated strand-displacement reaction, in which one complementary single-stranded DNA sequence first binds to the dangling toehold domain of the substrate in a pre-hybridized double-stranded DNA, then triggers the strand-displacement reaction, and finally results in the dissociation of the third strand previously bound to the substrate with partial complementarity. In dynamic DNA nanotechnology, isothermal toehold-mediated DNA strand-displacement reaction has been used to design complex nanostructure and nanodevice for molecular computation. The kinetics of the strand-displacement can be modulated using the toehold length. In order to weaken the coupling between the kinetics of strand-displacement and the thermodynamics of the reaction, the concept of toehold exchange was introduced by Winfree et al. to improve the control of strand-displacement kinetics. More importantly, the biomolecular reaction (BM) rate constant of toehold exchange can be analytically derived using the three-step model. Through utilizing strand-displacement reactions and taking advantage of its programmable sequences and precise recognition properties, DNA can be used to build complex circuits which can proceed robustly at constant temperature, achieving specific functions. DNA strand-displacement reaction can be employed to fabricate logic gates, and large and complex circuits for DNA computing, to mimic the naturally occurring occurrence of biological systems. Based on that, DNA circuit can then be used to direct the assembly of nanodevice following the designed pathway, and modulate the chemical reaction networks on the surface of living cell or in cellular systems for biosensing, even program the cellular machinery in the future for genetic diagnostic or gene therapy. In the present paper, we reviewed the proceedings in the fields of DNA structure and conformational changes, and DNA flexibility, discussed the mechanism of DNA strand-displacement reaction at the molecular level, and introduced the recent studies in DNA computation as well as the dynamic DNA nanotechnology, such as self-assembly.

Keywords:

作者及机构信息

肖石燕¹,
梁好均^1,2

1.
中国科学院软物质化学重点实验室, 能源材料化学协同创新中心, 中国科学技术大学高分子科学与工程系, 合肥 230026;

2.
合肥微尺度物质科学国家实验室, 合肥 230026

通信作者: 梁好均, hjliang@ustc.edu.cn

基金项目: 国家自然科学基金（批准号：91427304，21434007，21574122，51573175，21404098）和国家重点基础研究发展计划（批准号：2012CB821500）资助资助课题.

Authors and contacts

1.
CAS Key Laboratory of Soft Matter Chemistry, Collaborative Innovation Center of Chemistry for Energy Materials, Department of Polymer Science and Engineering, University of Science and Technology of China, Hefei 230026, China;

2.
Hefei National Laboratory for Physical Sciences at the Microscale, University of Science and Technology of China, Hefei 230026, China

Corresponding author: Liang Hao-Jun, hjliang@ustc.edu.cn

Funds: Project supported bythe National Natural Science Foundation of China (Grant Nos. 91427304, 21434007, 21574122, 51573175, 21404098) and the National Basic Research Program of China (Grant No. 2012CB821500).

参考文献

[1]	Bustamante C, Bryant Z, Smith S B 2003 Nature 421 423
[2]	Seeman N C 1982 J. Theor. Biol. 99 237
[3]	Alivisatos A P, Johnsson K P, Peng X, Wilson T E, Loweth C J, Bruchez M P, Schultz P G 1996 Nature 382 609
[4]	Mirkin C A, Letsinger R L, Mucic R C, Storhoff J J 1996 Nature 382 607
[5]	Macfarlane R J, Lee B, Jones M R, Harris N, Schatz G C, Mirkin C A 2011 Science 334 204
[6]	Maffeo C, Yoo J, Comer J, Wells D B, Luan B, Aksimentiev A 2014 J. Phys.: Condens. Matter 26 413101
[7]	Olson W K, Zhurkin V B 2011 Curr. Opin. Struct. Biol. 21 348
[8]	Orozco M, Noy A, Prez A 2008 Curr. Opin. Struct. Biol. 18 185
[9]	Kim S, Brostromer E, Xing D, Jin J, Chong S, Ge H, Wang S, Gu C, Yang L, Gao Y Q, Su X D, Sun Y, Xie X S 2013 Science 339 816
[10]	Yin Y, Yang L, Zheng G, Gu C, Yi C, He C, Gao Y Q, Zhao X S 2014 Proc. Natl. Acad. Sci. U. S. A. 111 8043
[11]	Sobel E S, Harpst J A 1991 Biopolymers 31 1559
[12]	Borochov N, Eisenberg H, Kam Z 1981 Biopolymers 20 231
[13]	Kam Z, Borochov N, Eisenberg H 1981 Biopolymers 20 2671
[14]	Harrington R E 1978 Biopolymers 17 919
[15]	Cairney K L, Harrington R E 1982 Biopolymers 21 923
[16]	Baumann C G, Smith S B, Bloomfield V A, Bustamante C 1997 Proc. Natl. Acad. Sci. U. S. A. 94 6185
[17]	Rizzo V, Schellman J 1981 Biopolymers 20 2143
[18]	Maret G, Weill G 1983 Biopolymers 22 2727
[19]	Baumann C G, Smith S B, Bloomfield V A, Bustamante C 1997 Proc. Natl. Acad. Sci. U. S. A. 94 6185
[20]	Fixman M 2010 J. Phys. Chem. B 114 3185
[21]	Odijk T 1977 J. Polym. Sci. Polym. Phys. Ed. 15 477
[22]	Manning G S 2006 Biophys. J. 91 3607
[23]	Kosikov K M, Gorin A A, Lu X, Olson W K, Manning G S 2002 J. Am. Chem. Soc. 124 4838
[24]	Tan Z J, Chen S J 2008 Biophys. J. 94 3137
[25]	Xiao S, Zhu H, Wang L, Liang H 2014 Soft Matt. 10 1045
[26]	Wang F H, Wu Y Y, Tan Z J 2013 Biopolymers 99 370
[27]	Wu Y, Bao L, Zhang X, Tan Z, Wu Y, Bao L, Zhang X, Tan Z 2015 J. Chem. Phys. 142 125103
[28]	Bao L, Zhang X, Jin L, Tan Z 2010 Proc. Natl. Acad. Sci. U. S. A. 107 20340
[29]	Savelyev A, Materese C K, Papoian G A 2011 J. Am. Chem. Soc. 133 19290
[30]	Ortiz V, de Pablo J J 2011 Phys. Rev. Lett. 106 238107
[31]	Kratky O, Porod G 1949 Recl. des Trav. Chim. des Pays-Bas 68 1106
[32]	Peters J P, Maher L J 2010 Q. Rev. Biophys. 43 23
[33]	Yuan C, Chen H, Lou X W, Archer L A 2008 Phys. Rev. Lett. 100 018102
[34]	Cloutier T E, Widom J 2005 Proc. Natl. Acad. Sci. U. S. A. 102 3645
[35]	Cloutier T E, Widom J 2004 Mol. Cell 14 355
[36]	Crick F H C, Klug A 1975 Nature 255 530
[37]	Richmond T J, Luger K, Mder A W, Richmond R K, Sargent D F 1997 Nature 389 251
[38]	Hogan M E, Rooney T F, Austin R H 1987 Nature 328 554
[39]	Richmond T J, Davey C A 2003 Nature 423 145
[40]	Wiggins P, Phillips R, Nelson P 2005 Phys. Rev. E 71 021909
[41]	Yan J, Marko J 2004 Phys. Rev. Lett. 93 108108
[42]	Theodorakopoulos N, Peyrard M 2012 Phys. Rev. Lett. 108 078104
[43]	Wiggins P A, van der Heijden T, Moreno-Herrero F, Spakowitz A, Phillips R, Widom J, Dekker C, Nelson P C 2006 Nat. Nanotechnol. 1 137
[44]	Xu X, Thio B J R, Cao J 2014 J. Phys. Chem. Lett. 5 2868
[45]	Vafabakhsh R, Ha T 2012 Science 337 1097
[46]	Du Q, Smith C, Shiffeldrim N, Vologodskaia M, Vologodskii A 2005 Proc. Natl. Acad. Sci. U. S. A. 102 5397
[47]	Mastroianni A J, Sivak D A, Geissler P L, Alivisatos A P 2009 Biophys. J. 97 1408
[48]	Mazur A K 2007 Phys. Rev. Lett. 98 1
[49]	Mazur A K, Maaloum M 2014 Phys. Rev. Lett. 112 068104
[50]	Neidle S 2008 Principles of Nucleic Acid Structure (Boston: Academic Press)
[51]	Yan H 2003 Science 301 1882
[52]	Malo J, Mitchell J C, Vnien-Bryan C, Harris J R, Wille H, Sherratt D J, Turberfield A J 2005 Angew. Chem. Int. Ed. 44 3057
[53]	Rothemund P W K 2006 Nature 440 297
[54]	Zheng J, Birktoft J J, Chen Y, Wang T, Sha R, Constantinou P E, Ginell S L, Mao C, Seeman N C 2009 Nature 461 74
[55]	Klafter J, Sokolov I M 2005 Phys. World 18 29
[56]	Andersen E S, Dong M, Nielsen M M, Jahn K, Subramani R, Mamdouh W, Golas M M, Sander B, Stark H, Oliveira C L P, Pedersen J S, Birkedal V, Besenbacher F, Gothelf K V, Kjems J 2009 Nature 459 73
[57]	Han D, Pal S, Nangreave J, Deng Z, Liu Y, Yan H 2011 Science 332 342
[58]	Zhang D Y, Seelig G 2011 Nat. Chem. 3 103
[59]	Zhang D Y, Hariadi R F, Choi H M T, Winfree E 2013 Nat. Commun. 4 1965
[60]	Turberfield A J, Yurke B, Mills A P, Simmel F C, Neumann J L 2000 Nature 406 605
[61]	Zhang D Y, Winfree E 2009 J. Am. Chem. Soc. 131 17303
[62]	Srinivas N, Ouldridge T E, Sulc P, Schaeffer J M, Yurke B, Louis A A, Doye J P K, Winfree E 2013 Nucleic Acids Res. 41 10641
[63]	Soloveichik D, Seelig G, Winfree E 2010 Proc. Natl. Acad. Sci. U. S. A. 107 5393
[64]	Genot A J, Zhang D Y, Bath J, Turberfield A J 2011 J. Am. Chem. Soc. 133 2177
[65]	Machinek R R F, Ouldridge T E, Haley N E C, Bath J, Turberfield A J 2014 Nat. Commun. 5 5324
[66]	Smith B D, Liu J 2010 J. Am. Chem. Soc. 132 6300
[67]	Dave N, Liu J 2010 J. Phys. Chem. B 114 15694
[68]	Kang D, Duan R, Tan Y, Hong F, Wang B, Chen Z, Xu S, Lou X, Wei W, Yurke B, Xia F 2014 Nanoscale 6 14153
[69]	Ravan H, Kashanian S, Sanadgol N, Badoei-Dalfard A, Karami Z 2014 Anal. Biochem. 444 41
[70]	Yurke B, Mills Jr A P 2003 Genet. Program. Evolvable Mach. 4 111
[71]	Zadeh J N, Steenberg C D, Bois J S, Wolfe B R, Pierce M B, Khan A R, Dirks R M, Pierce N A 2011 J. Comput. Chem. 32 170
[72]	SantaLucia J, Hicks D 2004 Annu. Rev. Biophys. Biomol. Struct. 33 415
[73]	Bommarito S, Peyret N, SantaLucia Jr J S 2000 Nucleic Acids Res. 28 1929
[74]	Pyshnyi D, Ivanova E 2002 Russ. Chem. Bull. 51 1145
[75]	Protozanova E, Yakovchuk P, Frank-Kamenetskii M D 2004 J. Mol. Biol. 342 775
[76]	Potoyan D A, Savelyev A, Papoian G A 2013 WIREs Comput. Mol Sci 3 69
[77]	Sambriski E J, Schwartz D C, de Pablo J J 2009 Biophys. J. 96 1675
[78]	Knotts T A, Rathore N, Schwartz D C, de Pablo J J 2007 J. Chem. Phys. 126 084901
[79]	Sambriski E J, Schwartz D C, de Pablo J J 2009 Proc. Natl. Acad. Sci. U. S. A. 106 18125
[80]	Li H, Wang Z, Li N, He X, Liang H 2014 J. Chem. Phys. 141 044911
[81]	Ouldridge T E, Louis A A, Doye J P K 2011 J. Chem. Phys. 134 085101
[82]	Ouldridge T E, Louis A A, Doye J P K 2010 Phys. Rev. Lett. 104 178101
[83]	Ouldridge T E, Sulc P, Romano F, Doye J P K, Louis A A 2013 Nucleic Acids Res. 41 8886
[84]	Mosayebi M, Romano F, Ouldridge T E, Louis A A, Doye J P K 2014 J. Phys. Chem. B 118 14326
[85]	Matek C, Ouldridge T E, Levy A, Doye J P K, Louis A A 2012 J. Phys. Chem. B 116 11616
[86]	Ouldridge T E 2014 Mol. Phys. 113 1
[87]	Adleman L 1994 Science 266 1021
[88]	Benenson Y, Paz-Elizur T, Adar R, Keinan E, Livneh Z, Shapiro E 2001 Nature 414 430
[89]	Benenson Y, Adar R, Paz-Elizur T, Livneh Z, Shapiro E 2003 Proc. Natl. Acad. Sci. U. S. A. 100 2191
[90]	Sakamoto K 2000 Science 288 1223
[91]	Benenson Y, Gil B, Ben-Dor U, Adar R, Shapiro E 2004 Nature 429 423
[92]	Yin P, Choi H M T, Calvert C R, Pierce N A 2008 Nature 451 318
[93]	Zhang D Y, Turberfield A J, Yurke B, Winfree E 2007 Science 318 1121
[94]	Seelig G, Soloveichik D, Zhang D Y, Winfree E 2006 Science 314 1585
[95]	Qian L, Winfree E 2011 Science 332 1196
[96]	Qian L, Winfree E, Bruck J 2011 Nature 475 368
[97]	Kim J, Winfree E 2014 Mol. Syst. Biol. 7 465
[98]	Han D, Wu C, You M, Zhang T, Wan S, Chen T, Qiu L, Zheng Z, Liang H, Tan W 2015 Nat. Chem. 7 835
[99]	Chen Y, Dalchau N, Srinivas N, Phillips A, Cardelli L, Soloveichik D, Seelig G 2013 Nat. Nanotechnol. 8 755
[100]	Lakin M R, Youssef S, Cardelli L, Phillips A 2012 J. R. Soc. Interface 9 470
[101]	Phillips A, Cardelli L 2009 J. R. Soc. Interface 6 S419
[102]	Chen X, Briggs N, McLain J R, Ellington A D 2013 Proc. Natl. Acad. Sci. U. S. A. 110 5386
[103]	Jiang Y S, Bhadra S, Li B, Ellington A D 2014 Angew. Chem. Int. Ed. 53 1845
[104]	Carlson R 2009 Nat. Biotechnol. 27 1091
[105]	Simmel F C, Yurke B 2001 Phys. Rev. E 63 041913
[106]	Simmel F C, Yurke B 2002 Appl. Phys. Lett. 80 883
[107]	Tian Y, Mao C 2004 J. Am. Chem. Soc. 126 11410
[108]	Yan H, Zhang X, Shen Z, Seeman N C 2002 Nature 415 62
[109]	Chakraborty B, Sha R, Seeman N C 2008 Proc. Natl. Acad. Sci. U. S. A. 105 17245
[110]	Zhong H, Seeman N C 2006 Nano Lett. 6 2899
[111]	Ding B, Seeman N C 2006 Science 314 1583
[112]	Feng L, Park S H, Reif J H, Yan H 2003 Angew. Chem. 115 4478
[113]	Lubrich D, Lin J, Yan J 2008 Angew. Chem. Int. Ed. 47 7026
[114]	Goodman R P, Heilemann M, Doose S, Erben C M, Kapanidis A N, Turberfield A J 2008 Nat. Nanotechnol. 3 93
[115]	Dirks R M, Pierce N A 2004 Proc. Natl. Acad. Sci. U.S.A. 101 15275
[116]	Xing Y, Cheng E, Yang Y, Chen P, Zhang T, Sun Y, Yang Z, Liu D 2011 Adv. Mater. 23 1117
[117]	Xing Y, Yang Z, Liu D 2011 Angew. Chem. Int. Ed. 50 11934
[118]	Idili A, Porchetta A, Amodio A, Valle-Blisle A, Ricci F 2015 Nano Lett. 15 5539
[119]	Idili A, Valle-Blisle A, Ricci F 2014 J. Am. Chem. Soc. 136 5836
[120]	Yao D, Li H, Guo Y, Zhou X, Xiao S, Liang H 2016 Chem. Commun. 52 7556
[121]	Liu D, Cheng E, Yang Z 2011 NPG Asia Mater. 3 109
[122]	Dong Y, Yang Z, Liu D 2014 Acc. Chem. Res. 47 1853
[123]	Sherman W B, Seeman N C 2004 Nano Lett. 4 1203
[124]	Shin J S, Pierce N A 2004 J. Am. Chem. Soc. 126 10834
[125]	Gu H, Chao J, Xiao S J, Seeman N C 2010 Nature 465 202
[126]	You M, Chen Y, Zhang X, Liu H, Wang R, Wang K, Williams K R, Tan W 2012 Angew. Chem. Int. Ed. 51 2457
[127]	Yang Y, Goetzfried M A, Hidaka K, You M, Tan W, Sugiyama H, Endo M 2015 Nano Lett. 15 6672
[128]	Venkataraman S, Dirks R M, Rothemund P W K, Winfree E, Pierce N A 2007 Nat. Nanotechnol. 2 490
[129]	Lubrich D, Green S J, Turberfield A J 2009 J. Am. Chem. Soc. 131 2422
[130]	Xuan F, Hsing I M 2014 J. Am. Chem. Soc. 136 9810
[131]	Zhang D Y, Winfree E 2008 J. Am. Chem. Soc. 130 13921
[132]	Wang Y, Lin H X, Chen L, Ding S Y, Lei Z C, Liu D Y, Cao X Y, Liang H J, Jiang Y B, Tian Z Q 2014 Chem. Soc. Rev. 43 399
[133]	Song T, Xiao S, Yao D, Huang F, Hu M, Liang H 2014 Adv. Mater. 26 6181
[134]	Song T, Liang H 2012 J. Am. Chem. Soc. 134 10803
[135]	Bi S, Chen M, Jia X, Dong Y, Wang Z 2015 Angew. Chem. Int. Ed. 54 8144
[136]	Huang F, You M, Han D, Xiong X, Liang H, Tan W 2013 J. Am. Chem. Soc. 135 7967
[137]	Huang F, Xu H, Tan W, Liang H 2014 ACS Nano 8 6849
[138]	Huang F, Zhou X, Yao D, Xiao S, Liang H 2015 Small 11 5800
[139]	Yurke B, Mills A P, Lai Cheng S 1999 Biosystems 52 165
[140]	Dittmer W U, Reuter A, Simmel F C 2004 Angew. Chem. Int. Ed. 43 3550
[141]	Ko S H, Liu H, Chen Y, Mao C 2008 Biomacromolecules 9 3039
[142]	Mei Q, Wei X, Su F, Liu Y, Youngbull C, Johnson R, Lindsay S, Yan H, Meldrum D 2011 Nano Lett. 11 1477
[143]	Conway J W, McLaughlin C K, Castor K J, Sleiman H 2013 Chem. Commun. 49 1172
[144]	Hahn J, Wickham S F J, Shih W M, Perrault S D 2014 ACS Nano 8 8765
[145]	Castro C E, Kilchherr F, Kim D N, Shiao E L, Wauer T, Wortmann P, Bathe M, Dietz H 2011 Nat. Methods 8 221
[146]	Douglas S M, Bachelet I, Church G M 2012 Science 335 831
[147]	Rudchenko M, Taylor S, Pallavi P, Dechkovskaia A, Khan S, Butler V P, Rudchenko S, Stojanovic M N 2013 Nat. Nanotechnol. 8 580
[148]	You M, Zhu G, Chen T, Donovan M J, Tan W 2015 J. Am. Chem. Soc. 137 667
[149]	You M, Peng L, Shao N, Zhang L, Qiu L, Cui C, Tan W 2014 J. Am. Chem. Soc. 136 1256
[150]	Gartner Z J, Bertozzi C R 2009 Proc. Natl. Acad. Sci. U. S. A. 106 4606
[151]	Chandra R A, Douglas E S, Mathies R A, Bertozzi C R, Francis M B 2006 Angew. Chem. Int. Ed. 45 896
[152]	Modi S, M. G. S, Goswami D, Gupta G D, Mayor S, Krishnan Y 2009 Nat. Nanotechnol. 4 325
[153]	Modi S, Nizak C, Surana S, Halder S, Krishnan Y 2013 Nat. Nanotechnol. 8 459
[154]	Chen A K, Davydenko O, Behlke M A, Tsourkas A 2010 Nucleic Acids Res. 38 e148
[155]	Qiu L, Wu C, You M, Han D, Chen T, Zhu G, Jiang J, Yu R, Tan W 2013 J. Am. Chem. Soc. 135 12952
[156]	Tyagi S, Kramer F R 1996 Nat. Biotechnol. 14 303
[157]	Wu C, Cansiz S, Zhang L, Teng I T, Qiu L, Li J, Liu Y, Zhou C, Hu R, Zhang T, Cui C, Cui L, Tan W 2015 J. Am. Chem. Soc. 137 4900
[158]	Seferos D S, Giljohann D A, Hill H D, Prigodich A E, Mirkin C A 2007 J. Am. Chem. Soc. 129 15477
[159]	Prigodich A E, Seferos D S, Massich M D, Giljohann D A, Lane B C, Mirkin C A 2009 ACS Nano 3 2147
[160]	Massich M D, Giljohann D A, Schmucker A L, Patel P C, Mirkin C A 2010 ACS Nano 4 5641
[161]	Amir Y, Ben-Ishay E, Levner D, Ittah S, Abu-Horowitz A, Bachelet I 2014 Nat. Nanotechnol. 9 353
[162]	Hemphill J, Deiters A 2013 J. Am. Chem. Soc. 135 10512
[163]	Sponer J, Cang X, Cheatham T E 2012 Methods 57 25
[164]	poner J, Ban P, Jurečka P, Zgarbov M, Khrov P, Havrila M, Krepl M, Stadlbauer P, Otyepka M 2014 J. Phys. Chem. Lett. 5 1771

施引文献

[1]	Bustamante C, Bryant Z, Smith S B 2003 Nature 421 423
[2]	Seeman N C 1982 J. Theor. Biol. 99 237
[3]	Alivisatos A P, Johnsson K P, Peng X, Wilson T E, Loweth C J, Bruchez M P, Schultz P G 1996 Nature 382 609
[4]	Mirkin C A, Letsinger R L, Mucic R C, Storhoff J J 1996 Nature 382 607
[5]	Macfarlane R J, Lee B, Jones M R, Harris N, Schatz G C, Mirkin C A 2011 Science 334 204
[6]	Maffeo C, Yoo J, Comer J, Wells D B, Luan B, Aksimentiev A 2014 J. Phys.: Condens. Matter 26 413101
[7]	Olson W K, Zhurkin V B 2011 Curr. Opin. Struct. Biol. 21 348
[8]	Orozco M, Noy A, Prez A 2008 Curr. Opin. Struct. Biol. 18 185
[9]	Kim S, Brostromer E, Xing D, Jin J, Chong S, Ge H, Wang S, Gu C, Yang L, Gao Y Q, Su X D, Sun Y, Xie X S 2013 Science 339 816
[10]	Yin Y, Yang L, Zheng G, Gu C, Yi C, He C, Gao Y Q, Zhao X S 2014 Proc. Natl. Acad. Sci. U. S. A. 111 8043
[11]	Sobel E S, Harpst J A 1991 Biopolymers 31 1559
[12]	Borochov N, Eisenberg H, Kam Z 1981 Biopolymers 20 231
[13]	Kam Z, Borochov N, Eisenberg H 1981 Biopolymers 20 2671
[14]	Harrington R E 1978 Biopolymers 17 919
[15]	Cairney K L, Harrington R E 1982 Biopolymers 21 923
[16]	Baumann C G, Smith S B, Bloomfield V A, Bustamante C 1997 Proc. Natl. Acad. Sci. U. S. A. 94 6185
[17]	Rizzo V, Schellman J 1981 Biopolymers 20 2143
[18]	Maret G, Weill G 1983 Biopolymers 22 2727
[19]	Baumann C G, Smith S B, Bloomfield V A, Bustamante C 1997 Proc. Natl. Acad. Sci. U. S. A. 94 6185
[20]	Fixman M 2010 J. Phys. Chem. B 114 3185
[21]	Odijk T 1977 J. Polym. Sci. Polym. Phys. Ed. 15 477
[22]	Manning G S 2006 Biophys. J. 91 3607
[23]	Kosikov K M, Gorin A A, Lu X, Olson W K, Manning G S 2002 J. Am. Chem. Soc. 124 4838
[24]	Tan Z J, Chen S J 2008 Biophys. J. 94 3137
[25]	Xiao S, Zhu H, Wang L, Liang H 2014 Soft Matt. 10 1045
[26]	Wang F H, Wu Y Y, Tan Z J 2013 Biopolymers 99 370
[27]	Wu Y, Bao L, Zhang X, Tan Z, Wu Y, Bao L, Zhang X, Tan Z 2015 J. Chem. Phys. 142 125103
[28]	Bao L, Zhang X, Jin L, Tan Z 2010 Proc. Natl. Acad. Sci. U. S. A. 107 20340
[29]	Savelyev A, Materese C K, Papoian G A 2011 J. Am. Chem. Soc. 133 19290
[30]	Ortiz V, de Pablo J J 2011 Phys. Rev. Lett. 106 238107
[31]	Kratky O, Porod G 1949 Recl. des Trav. Chim. des Pays-Bas 68 1106
[32]	Peters J P, Maher L J 2010 Q. Rev. Biophys. 43 23
[33]	Yuan C, Chen H, Lou X W, Archer L A 2008 Phys. Rev. Lett. 100 018102
[34]	Cloutier T E, Widom J 2005 Proc. Natl. Acad. Sci. U. S. A. 102 3645
[35]	Cloutier T E, Widom J 2004 Mol. Cell 14 355
[36]	Crick F H C, Klug A 1975 Nature 255 530
[37]	Richmond T J, Luger K, Mder A W, Richmond R K, Sargent D F 1997 Nature 389 251
[38]	Hogan M E, Rooney T F, Austin R H 1987 Nature 328 554
[39]	Richmond T J, Davey C A 2003 Nature 423 145
[40]	Wiggins P, Phillips R, Nelson P 2005 Phys. Rev. E 71 021909
[41]	Yan J, Marko J 2004 Phys. Rev. Lett. 93 108108
[42]	Theodorakopoulos N, Peyrard M 2012 Phys. Rev. Lett. 108 078104
[43]	Wiggins P A, van der Heijden T, Moreno-Herrero F, Spakowitz A, Phillips R, Widom J, Dekker C, Nelson P C 2006 Nat. Nanotechnol. 1 137
[44]	Xu X, Thio B J R, Cao J 2014 J. Phys. Chem. Lett. 5 2868
[45]	Vafabakhsh R, Ha T 2012 Science 337 1097
[46]	Du Q, Smith C, Shiffeldrim N, Vologodskaia M, Vologodskii A 2005 Proc. Natl. Acad. Sci. U. S. A. 102 5397
[47]	Mastroianni A J, Sivak D A, Geissler P L, Alivisatos A P 2009 Biophys. J. 97 1408
[48]	Mazur A K 2007 Phys. Rev. Lett. 98 1
[49]	Mazur A K, Maaloum M 2014 Phys. Rev. Lett. 112 068104
[50]	Neidle S 2008 Principles of Nucleic Acid Structure (Boston: Academic Press)
[51]	Yan H 2003 Science 301 1882
[52]	Malo J, Mitchell J C, Vnien-Bryan C, Harris J R, Wille H, Sherratt D J, Turberfield A J 2005 Angew. Chem. Int. Ed. 44 3057
[53]	Rothemund P W K 2006 Nature 440 297
[54]	Zheng J, Birktoft J J, Chen Y, Wang T, Sha R, Constantinou P E, Ginell S L, Mao C, Seeman N C 2009 Nature 461 74
[55]	Klafter J, Sokolov I M 2005 Phys. World 18 29
[56]	Andersen E S, Dong M, Nielsen M M, Jahn K, Subramani R, Mamdouh W, Golas M M, Sander B, Stark H, Oliveira C L P, Pedersen J S, Birkedal V, Besenbacher F, Gothelf K V, Kjems J 2009 Nature 459 73
[57]	Han D, Pal S, Nangreave J, Deng Z, Liu Y, Yan H 2011 Science 332 342
[58]	Zhang D Y, Seelig G 2011 Nat. Chem. 3 103
[59]	Zhang D Y, Hariadi R F, Choi H M T, Winfree E 2013 Nat. Commun. 4 1965
[60]	Turberfield A J, Yurke B, Mills A P, Simmel F C, Neumann J L 2000 Nature 406 605
[61]	Zhang D Y, Winfree E 2009 J. Am. Chem. Soc. 131 17303
[62]	Srinivas N, Ouldridge T E, Sulc P, Schaeffer J M, Yurke B, Louis A A, Doye J P K, Winfree E 2013 Nucleic Acids Res. 41 10641
[63]	Soloveichik D, Seelig G, Winfree E 2010 Proc. Natl. Acad. Sci. U. S. A. 107 5393
[64]	Genot A J, Zhang D Y, Bath J, Turberfield A J 2011 J. Am. Chem. Soc. 133 2177
[65]	Machinek R R F, Ouldridge T E, Haley N E C, Bath J, Turberfield A J 2014 Nat. Commun. 5 5324
[66]	Smith B D, Liu J 2010 J. Am. Chem. Soc. 132 6300
[67]	Dave N, Liu J 2010 J. Phys. Chem. B 114 15694
[68]	Kang D, Duan R, Tan Y, Hong F, Wang B, Chen Z, Xu S, Lou X, Wei W, Yurke B, Xia F 2014 Nanoscale 6 14153
[69]	Ravan H, Kashanian S, Sanadgol N, Badoei-Dalfard A, Karami Z 2014 Anal. Biochem. 444 41
[70]	Yurke B, Mills Jr A P 2003 Genet. Program. Evolvable Mach. 4 111
[71]	Zadeh J N, Steenberg C D, Bois J S, Wolfe B R, Pierce M B, Khan A R, Dirks R M, Pierce N A 2011 J. Comput. Chem. 32 170
[72]	SantaLucia J, Hicks D 2004 Annu. Rev. Biophys. Biomol. Struct. 33 415
[73]	Bommarito S, Peyret N, SantaLucia Jr J S 2000 Nucleic Acids Res. 28 1929
[74]	Pyshnyi D, Ivanova E 2002 Russ. Chem. Bull. 51 1145
[75]	Protozanova E, Yakovchuk P, Frank-Kamenetskii M D 2004 J. Mol. Biol. 342 775
[76]	Potoyan D A, Savelyev A, Papoian G A 2013 WIREs Comput. Mol Sci 3 69
[77]	Sambriski E J, Schwartz D C, de Pablo J J 2009 Biophys. J. 96 1675
[78]	Knotts T A, Rathore N, Schwartz D C, de Pablo J J 2007 J. Chem. Phys. 126 084901
[79]	Sambriski E J, Schwartz D C, de Pablo J J 2009 Proc. Natl. Acad. Sci. U. S. A. 106 18125
[80]	Li H, Wang Z, Li N, He X, Liang H 2014 J. Chem. Phys. 141 044911
[81]	Ouldridge T E, Louis A A, Doye J P K 2011 J. Chem. Phys. 134 085101
[82]	Ouldridge T E, Louis A A, Doye J P K 2010 Phys. Rev. Lett. 104 178101
[83]	Ouldridge T E, Sulc P, Romano F, Doye J P K, Louis A A 2013 Nucleic Acids Res. 41 8886
[84]	Mosayebi M, Romano F, Ouldridge T E, Louis A A, Doye J P K 2014 J. Phys. Chem. B 118 14326
[85]	Matek C, Ouldridge T E, Levy A, Doye J P K, Louis A A 2012 J. Phys. Chem. B 116 11616
[86]	Ouldridge T E 2014 Mol. Phys. 113 1
[87]	Adleman L 1994 Science 266 1021
[88]	Benenson Y, Paz-Elizur T, Adar R, Keinan E, Livneh Z, Shapiro E 2001 Nature 414 430
[89]	Benenson Y, Adar R, Paz-Elizur T, Livneh Z, Shapiro E 2003 Proc. Natl. Acad. Sci. U. S. A. 100 2191
[90]	Sakamoto K 2000 Science 288 1223
[91]	Benenson Y, Gil B, Ben-Dor U, Adar R, Shapiro E 2004 Nature 429 423
[92]	Yin P, Choi H M T, Calvert C R, Pierce N A 2008 Nature 451 318
[93]	Zhang D Y, Turberfield A J, Yurke B, Winfree E 2007 Science 318 1121
[94]	Seelig G, Soloveichik D, Zhang D Y, Winfree E 2006 Science 314 1585
[95]	Qian L, Winfree E 2011 Science 332 1196
[96]	Qian L, Winfree E, Bruck J 2011 Nature 475 368
[97]	Kim J, Winfree E 2014 Mol. Syst. Biol. 7 465
[98]	Han D, Wu C, You M, Zhang T, Wan S, Chen T, Qiu L, Zheng Z, Liang H, Tan W 2015 Nat. Chem. 7 835
[99]	Chen Y, Dalchau N, Srinivas N, Phillips A, Cardelli L, Soloveichik D, Seelig G 2013 Nat. Nanotechnol. 8 755
[100]	Lakin M R, Youssef S, Cardelli L, Phillips A 2012 J. R. Soc. Interface 9 470
[101]	Phillips A, Cardelli L 2009 J. R. Soc. Interface 6 S419
[102]	Chen X, Briggs N, McLain J R, Ellington A D 2013 Proc. Natl. Acad. Sci. U. S. A. 110 5386
[103]	Jiang Y S, Bhadra S, Li B, Ellington A D 2014 Angew. Chem. Int. Ed. 53 1845
[104]	Carlson R 2009 Nat. Biotechnol. 27 1091
[105]	Simmel F C, Yurke B 2001 Phys. Rev. E 63 041913
[106]	Simmel F C, Yurke B 2002 Appl. Phys. Lett. 80 883
[107]	Tian Y, Mao C 2004 J. Am. Chem. Soc. 126 11410
[108]	Yan H, Zhang X, Shen Z, Seeman N C 2002 Nature 415 62
[109]	Chakraborty B, Sha R, Seeman N C 2008 Proc. Natl. Acad. Sci. U. S. A. 105 17245
[110]	Zhong H, Seeman N C 2006 Nano Lett. 6 2899
[111]	Ding B, Seeman N C 2006 Science 314 1583
[112]	Feng L, Park S H, Reif J H, Yan H 2003 Angew. Chem. 115 4478
[113]	Lubrich D, Lin J, Yan J 2008 Angew. Chem. Int. Ed. 47 7026
[114]	Goodman R P, Heilemann M, Doose S, Erben C M, Kapanidis A N, Turberfield A J 2008 Nat. Nanotechnol. 3 93
[115]	Dirks R M, Pierce N A 2004 Proc. Natl. Acad. Sci. U.S.A. 101 15275
[116]	Xing Y, Cheng E, Yang Y, Chen P, Zhang T, Sun Y, Yang Z, Liu D 2011 Adv. Mater. 23 1117
[117]	Xing Y, Yang Z, Liu D 2011 Angew. Chem. Int. Ed. 50 11934
[118]	Idili A, Porchetta A, Amodio A, Valle-Blisle A, Ricci F 2015 Nano Lett. 15 5539
[119]	Idili A, Valle-Blisle A, Ricci F 2014 J. Am. Chem. Soc. 136 5836
[120]	Yao D, Li H, Guo Y, Zhou X, Xiao S, Liang H 2016 Chem. Commun. 52 7556
[121]	Liu D, Cheng E, Yang Z 2011 NPG Asia Mater. 3 109
[122]	Dong Y, Yang Z, Liu D 2014 Acc. Chem. Res. 47 1853
[123]	Sherman W B, Seeman N C 2004 Nano Lett. 4 1203
[124]	Shin J S, Pierce N A 2004 J. Am. Chem. Soc. 126 10834
[125]	Gu H, Chao J, Xiao S J, Seeman N C 2010 Nature 465 202
[126]	You M, Chen Y, Zhang X, Liu H, Wang R, Wang K, Williams K R, Tan W 2012 Angew. Chem. Int. Ed. 51 2457
[127]	Yang Y, Goetzfried M A, Hidaka K, You M, Tan W, Sugiyama H, Endo M 2015 Nano Lett. 15 6672
[128]	Venkataraman S, Dirks R M, Rothemund P W K, Winfree E, Pierce N A 2007 Nat. Nanotechnol. 2 490
[129]	Lubrich D, Green S J, Turberfield A J 2009 J. Am. Chem. Soc. 131 2422
[130]	Xuan F, Hsing I M 2014 J. Am. Chem. Soc. 136 9810
[131]	Zhang D Y, Winfree E 2008 J. Am. Chem. Soc. 130 13921
[132]	Wang Y, Lin H X, Chen L, Ding S Y, Lei Z C, Liu D Y, Cao X Y, Liang H J, Jiang Y B, Tian Z Q 2014 Chem. Soc. Rev. 43 399
[133]	Song T, Xiao S, Yao D, Huang F, Hu M, Liang H 2014 Adv. Mater. 26 6181
[134]	Song T, Liang H 2012 J. Am. Chem. Soc. 134 10803
[135]	Bi S, Chen M, Jia X, Dong Y, Wang Z 2015 Angew. Chem. Int. Ed. 54 8144
[136]	Huang F, You M, Han D, Xiong X, Liang H, Tan W 2013 J. Am. Chem. Soc. 135 7967
[137]	Huang F, Xu H, Tan W, Liang H 2014 ACS Nano 8 6849
[138]	Huang F, Zhou X, Yao D, Xiao S, Liang H 2015 Small 11 5800
[139]	Yurke B, Mills A P, Lai Cheng S 1999 Biosystems 52 165
[140]	Dittmer W U, Reuter A, Simmel F C 2004 Angew. Chem. Int. Ed. 43 3550
[141]	Ko S H, Liu H, Chen Y, Mao C 2008 Biomacromolecules 9 3039
[142]	Mei Q, Wei X, Su F, Liu Y, Youngbull C, Johnson R, Lindsay S, Yan H, Meldrum D 2011 Nano Lett. 11 1477
[143]	Conway J W, McLaughlin C K, Castor K J, Sleiman H 2013 Chem. Commun. 49 1172
[144]	Hahn J, Wickham S F J, Shih W M, Perrault S D 2014 ACS Nano 8 8765
[145]	Castro C E, Kilchherr F, Kim D N, Shiao E L, Wauer T, Wortmann P, Bathe M, Dietz H 2011 Nat. Methods 8 221
[146]	Douglas S M, Bachelet I, Church G M 2012 Science 335 831
[147]	Rudchenko M, Taylor S, Pallavi P, Dechkovskaia A, Khan S, Butler V P, Rudchenko S, Stojanovic M N 2013 Nat. Nanotechnol. 8 580
[148]	You M, Zhu G, Chen T, Donovan M J, Tan W 2015 J. Am. Chem. Soc. 137 667
[149]	You M, Peng L, Shao N, Zhang L, Qiu L, Cui C, Tan W 2014 J. Am. Chem. Soc. 136 1256
[150]	Gartner Z J, Bertozzi C R 2009 Proc. Natl. Acad. Sci. U. S. A. 106 4606
[151]	Chandra R A, Douglas E S, Mathies R A, Bertozzi C R, Francis M B 2006 Angew. Chem. Int. Ed. 45 896
[152]	Modi S, M. G. S, Goswami D, Gupta G D, Mayor S, Krishnan Y 2009 Nat. Nanotechnol. 4 325
[153]	Modi S, Nizak C, Surana S, Halder S, Krishnan Y 2013 Nat. Nanotechnol. 8 459
[154]	Chen A K, Davydenko O, Behlke M A, Tsourkas A 2010 Nucleic Acids Res. 38 e148
[155]	Qiu L, Wu C, You M, Han D, Chen T, Zhu G, Jiang J, Yu R, Tan W 2013 J. Am. Chem. Soc. 135 12952
[156]	Tyagi S, Kramer F R 1996 Nat. Biotechnol. 14 303
[157]	Wu C, Cansiz S, Zhang L, Teng I T, Qiu L, Li J, Liu Y, Zhou C, Hu R, Zhang T, Cui C, Cui L, Tan W 2015 J. Am. Chem. Soc. 137 4900
[158]	Seferos D S, Giljohann D A, Hill H D, Prigodich A E, Mirkin C A 2007 J. Am. Chem. Soc. 129 15477
[159]	Prigodich A E, Seferos D S, Massich M D, Giljohann D A, Lane B C, Mirkin C A 2009 ACS Nano 3 2147
[160]	Massich M D, Giljohann D A, Schmucker A L, Patel P C, Mirkin C A 2010 ACS Nano 4 5641
[161]	Amir Y, Ben-Ishay E, Levner D, Ittah S, Abu-Horowitz A, Bachelet I 2014 Nat. Nanotechnol. 9 353
[162]	Hemphill J, Deiters A 2013 J. Am. Chem. Soc. 135 10512
[163]	Sponer J, Cang X, Cheatham T E 2012 Methods 57 25
[164]	poner J, Ban P, Jurečka P, Zgarbov M, Khrov P, Havrila M, Krepl M, Stadlbauer P, Otyepka M 2014 J. Phys. Chem. Lett. 5 1771

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