pH-Responsive Reversible DNA Self-assembly Mediated by Zwitterion

Abstract

pH-Responsive DNA assembles have drawn growing attentions owing to their great potential in diverse areas. However, pH-responsive motifs are limited to specific DNA sequences and annealing is usually needed for DNA assemblies; therefore, sequence-independent pH-responsive DNA assembly at room temperature is highly desired as a more general way. Here, we propose a reversible pH-responsive DNA assembly strategy at room-temperature using zwitterion, glycine betaine(GB), as charge-regulation molecules. The reversible assembly and disassembly of DNA nanostructures could be achieved by alternatively regulating the acidic and basic environments in the presence of GB, respectively. In an acidic environment, carboxylate group in GB was protonated and GB was positively charged, which facilitated to shield the inherent electrostatic repulsion of DNA strands. Molecular simulation showed that the newly formed carboxyl group in protonated GB could form hydrogen bonds with bases in DNA to promote the assembly of DNA strands. In a basic solution, carboxylate group in GB was deprotonated and GB was neutral, thus inducing the dissociation of DNA assembly.

Keywords

DNA nanotechnology / Dynamic assembly / pH responsiveness / Zwitterion

References

[1] Zhang D Y, Seelig G. Nat. Chem., 2011, 3(2): 103.

[2] Liu X, Lu C H, Willner I. Acc. Chem. Res., 2014, 47(6): 1673.

[3] Modi S, Nizak C, Surana S, Halder S, Krishnan Y. Nat. Nanotechnol., 2013, 8(6): 459.

[4] Han X G, Zhou Z H, Yang F, Deng Z X. J. Am. Chem. Soc., 2008, 130(44): 14414.

[5] Wang C, Ren J, Qu X. Chem. Commun., 2011, 47(5): 1428.

[6] Wang Z G, Elbaz J, Willner I. Nano Lett., 2011, 11(1): 304.

[7] Qi X J, Lu C H, Liu X, Shimron S, Yang H H, Willner I. Nano Lett., 2013, 13(10): 4920.

[8] Amodio A, Adedeji A F, Castronovo M, Franco E, Ricci F. J. Am. Chem. Soc., 201, 138(39): 12735.

[9] Green L N, Amodio A, Subramanian H K K, Ricci F, Franco E. Nano Lett., 2017, 17(12): 7283.

[10] Guo W, Lu C H, Orbach R, Wang F, Qi X J, Cecconello A, Seliktar D, Willner I. Adv. Mater., 2015, 27(1): 73.

[11] Hu Y, Guo W, Kahn J S, Aleman-Garcia M A, Willner I. Angew. Chem. Int. Ed., 201, 55(13): 4210.

[12] Cheng E, Xing Y, Chen P, Yang Y, Sun Y, Zhou D, Xu L, Fan Q, Liu D. Angew. Chem. Int. Ed., 2009, 48(41): 7660.

[13] Idili A, Vallee-Belisle A, Ricci F. J. Am. Chem. Soc., 2014, 136(16): 5836.

[14] Li F., Tang J., Geng J., Luo D., Yang D., Prog. Polym. Sci., 2019, 98

[15] Fu W, Tang L, Wei G, Fang L, Zeng J, Zhan R, Liu X, Zuo H, Huang C Z, Mao C. Angew. Chem. Int. Ed., 2019, 58(46): 16405.

[16] Chen H, Zhang H, Pan J, Cha T G, Li S, Andreasson J, Choi J H. ACS Nano, 201, 10(5): 4989.

[17] Jungmann R, Liedl T, Sobey T L, Shih W, Simmel F C. J. Am. Chem. Soc., 2008, 130(31): 10062.

[18] Zhang Z, Song J, Besenbacher F, Dong M, Gothelf K V. Angew. Chem. Int. Ed., 2013, 52(35): 9219.

[19] Rees W A, Yager T D, Korte J, von Hippel P H. Biochemistry, 1993, 32(1): 137.

[20] Henke W, Herdel K, Jung K, Schnorr D, Loening S A. Nucleic Acids Res., 1997, 25(19): 3957.

[21] Kopielski A, Schneider A, Csaki A, Fritzsche W. Nanoscale, 2015, 7(5): 2102.

[22] Li Y, Song L, Wang B, He J, Li Y, Deng Z, Mao C. Angew. Chem. Int. Ed., 2018, 57(23): 6892.

[23] Govrin R, Tcherner S, Obstbaum T, Sivan U. J. Am. Chem. Soc., 2018, 140(43): 14206.

[24] Zipper H, Brunner H, Bernhagen J, Vitzthum F. Nucleic Acids Res., 2004, 32(12): e103.

[25] Yang L, Yao C, Li F, Dong Y, Zhang Z, Yang D. Small, 2018, 14(16): e1800185.

[26] Li F, Dong Y, Zhang Z, Lv M, Wang Z, Ruan X, Yang D. Biosens. Bioelectron., 2018, 117: 562.

[27] Dong Y, Yao C, Wang Z, Luo D, Yang D. Science, 2019, 21: 228.

[28] Colotte M, Coudy D, Tuffet S, Bonnet J. Biopreserv. Biobank., 2011, 9(1): 47.

[29] Ma C, Wang Y, Zhang P, Shi C. Anal. Biochem., 2017, 530: 1.

[30] Guinn E J, Pegram L M, Capp M W, Pollock M N, Record M T Jr. Proc. Natl. Acad. Sci. USA, 2011, 108(41): 16932.

[31] Shao Q, Jiang S. Adv. Mater., 2015, 27(1): 15.

[32] Portella G, Germann M W, Hud N V, Orozco M. J. Am. Chem. Soc., 2014, 136(8): 3075.

[33] Nakano M, Tateishi-Karimata H, Tanaka S, Sugimoto N. J. Phys. Chem. B, 2014, 118(2): 379.

[34] Sarkar S, Maity A, Sarma Phukon A, Ghosh S, Chakrabarti R. J. Phys. Chem. B, 2019, 123(1): 47.