Rapid and annealing-free self-assembly of DNA building blocks for 3D hydrogel chaperoned by cationic comb-type copolymers

References

• Lanier LA, Bermudez H. DNA nanostructures: a shift from assembly to applications. Curr Opin Chem Eng. 2015;7:93–100.10.1016/j.coche.2015.01.001
   PubMed Web of Science ®Google Scholar
• Seeman NC. Nucleic acid junctions and lattices. J Theor Biol. 1982;99(2):237–247.10.1016/0022-5193(82)90002-9
   PubMed Web of Science ®Google Scholar
• Seeman NC, Kallenbach NR. Design of immobile nucleic acid junctions. Biophys J. 1983;44(2):201.10.1016/S0006-3495(83)84292-1
   PubMed Web of Science ®Google Scholar
• Wang Z-G, Ding B. Engineering DNA self-assemblies as templates for functional nanostructures. Acc Chem Res. 2014;47(6):1654–1662.10.1021/ar400305g
   PubMed Web of Science ®Google Scholar
• Wei B, Dai M, Yin P. Complex shapes self-assembled from single-stranded DNA tiles. Nature. 2012;485(7400):623. DOI:10.1038/nature11075. PubMed PMID: WOS:000304608000044.
   PubMed Web of Science ®Google Scholar
• Wei X, Nangreave J, Liu Y. Uncovering the self-assembly of DNA nanostructures by thermodynamics and kinetics. Acc Chem Res. 2014;47(6):1861–1870.10.1021/ar5000665
   PubMed Web of Science ®Google Scholar
• Cannon BL, Kellis DL, Davis PH, et al. Excitonic and logic gates on DNA brick nanobreadboards. ACS Photonics. 2015;2(3):398–404.10.1021/ph500444d
   PubMed Web of Science ®Google Scholar
• Li Y, Liu Z, Yu G, et al. Self-assembly of molecule-like nanoparticle clusters directed by DNA nanocages. J Am Chem Soc. 2015;137(13):4320–4323.10.1021/jacs.5b01196
   PubMed Web of Science ®Google Scholar
• Woo S, Rothemund PW. Programmable molecular recognition based on the geometry of DNA nanostructures. Nat Chem. 2011;3(8):620–627.10.1038/nchem.1070
   PubMed Web of Science ®Google Scholar
• Yang YR, Liu Y, Yan H. DNA nanostructures as programmable biomolecular scaffolds. Bioconjug Chem. 2015;26(8):1381–1395.10.1021/acs.bioconjchem.5b00194
   PubMed Web of Science ®Google Scholar
• Zhang T, Neumann A, Lindlau J, et al. DNA-based self-assembly of fluorescent nanodiamonds. J Am Chem Soc. 2015;137(31):9776–9779.10.1021/jacs.5b04857
   PubMed Web of Science ®Google Scholar
• Aghebat Rafat A, Pirzer T, Scheible MB, et al. Surface-assisted large-scale ordering of DNA origami tiles. Angew Chem Int Ed. 2014;53(29):7665–7668.10.1002/anie.201403965
   PubMed Web of Science ®Google Scholar
• Hung AM, Micheel CM, Bozano LD, et al. Large-area spatially ordered arrays of gold nanoparticles directed by lithographically confined DNA origami. Nat Nanotechnol. 2010;5(2):121–126.10.1038/nnano.2009.450
   PubMed Web of Science ®Google Scholar
• Marchi AN, Saaem I, Vogen BN, et al. Toward larger DNA origami. Nano Lett. 2014;14(10):5740–5747.10.1021/nl502626s
   PubMed Web of Science ®Google Scholar
• Suzuki Y, Endo M, Yang Y, et al. Dynamic assembly/disassembly processes of photoresponsive DNA origami nanostructures directly visualized on a lipid membrane surface. J Am Chem Soc. 2014;136(5):1714–1717.10.1021/ja4109819
   PubMed Web of Science ®Google Scholar
• Yang Y, Han D, Nangreave J, et al. DNA origami with double-stranded DNA as a unified scaffold. ACS Nano. 2012;6(9):8209–8215.10.1021/nn302896c
   PubMed Web of Science ®Google Scholar
• Nishida Y, Ohtsuki S, Araie Y, et al. Self-assembling DNA hydrogel-based delivery of immunoinhibitory nucleic acids to immune cells. Nanomed Nanotechnol Biol Med. 2016;12(1):123–130. DOI:10.1016/j.nano.2015.08.004
   PubMed Web of Science ®Google Scholar
• Wang Z, Xia J, Cai F, et al. Aptamer-functionalized hydrogel as effective anti-cancer drugs delivery agents. Colloids Surf, B. 2015;134:40–46. DOI:10.1016/j.colsurfb.2015.06.031. PubMed PMID: 26142627.
   PubMed Web of Science ®Google Scholar
• Song J, Im K, Hwang S, et al. DNA hydrogel delivery vehicle for light-triggered and synergistic cancer therapy. Nanoscale. 2015;7(21):9433–9437. DOI:10.1039/c5nr00858a. PubMed PMID: 25959856.
   PubMed Web of Science ®Google Scholar
• Ren J, Hu Y, Lu C-H, et al. pH-responsive and switchable triplex-based DNA hydrogels. Chem Sci. 2015;6(7):4190–4195. DOI:10.1039/c5sc00594a
   Web of Science ®Google Scholar
• Li J, Zheng C, Cansiz S, et al. Self-assembly of DNA nanohydrogels with controllable size and stimuli-responsive property for targeted gene regulation therapy. J Am Chem Soc. 2015;137(4):1412–1415. DOI:10.1021/ja512293f. PubMed PMID: 25581100; PubMed Central PMCID: PMC4449038.
   PubMed Web of Science ®Google Scholar
• Guo WW, Lu CH, Orbach R, et al. pH-stimulated DNA hydrogels exhibiting shape-memory properties. Adv Mater. 2015;27(1):73–78. DOI:10.1002/adma.201403702. PubMed PMID: WOS:000347239600010.
   PubMed Web of Science ®Google Scholar
• Lu C-H, Qi X-J, Orbach R, et al. Switchable catalytic acrylamide hydrogels cross-linked by Hemin/G-Quadruplexes. Nano Lett. 2013;13(3):1298–1302.10.1021/nl400078g
   PubMed Web of Science ®Google Scholar
• Li C, Faulkner-Jones A, Dun AR, et al. Rapid formation of a supramolecular polypeptide–DNA hydrogel for in situ three-dimensional multilayer bioprinting. Angew Chem Int Ed. 2015;54(13):3957–3961.10.1002/anie.201411383
   PubMed Web of Science ®Google Scholar
• Li C, Chen P, Shao Y, et al. A writable polypeptide–DNA hydrogel with rationally designed multi-modification sites. Small. 2015;11(9–10):1138–1143. DOI:10.1002/smll.201401906
   PubMed Web of Science ®Google Scholar
• Xing Y, Cheng E, Yang Y, et al. Self-assembled DNA hydrogels with designable thermal and enzymatic responsiveness. Adv Mater. 2011;23(9):1117–1121.10.1002/adma.201003343
   PubMed Web of Science ®Google Scholar
• Cheng E, Xing Y, Chen P, et al. A pH-triggered, fast-responding DNA hydrogel. Angew Chem. 2009;121(41):7796–7799.10.1002/ange.v121:41
   Google Scholar
• Jakob U, Gaestel M, Engel K, et al. Small heat shock proteins are molecular chaperones. J Biol Chem. 1993;268(3):1517–1520.
   PubMed Web of Science ®Google Scholar
• Choi SW, Makita N, Kano A, et al. DNA nanomachine switching improved by cationic comb-type copolymer. Macromol Symp. 2007;249–250(1):317–321. DOI:10.1002/masy.200750352
   Google Scholar
• Choi SW, Makita N, Inoue S, et al. Cationic comb-type copolymers for boosting DNA-fueled nanomachines. Nano Lett. 2007;7(1):172–178.10.1021/nl0626232
   PubMed Web of Science ®Google Scholar
• Sato Y, Kobayashi Y, Kamiya T, et al. The effect of backbone structure on polycation comb-type copolymer/DNA interactions and the molecular assembly of DNA. Biomaterials. 2005;26(7):703–711. DOI:10.1016/j.biomaterials.2004.03.018. PubMed PMID: 15350774.
   PubMed Web of Science ®Google Scholar
• Maruyama A, Ueda M, Kim WJ, et al. Design of polymer materials enhancing nucleotide hybridization for anti-gene technology. Adv Drug Deliv Rev. 2001;52(3):227–233.10.1016/S0169-409X(01)00208-3
   PubMed Web of Science ®Google Scholar
• Torigoe H, Ferdous A, Watanabe H, et al. Poly (l-lysine)-graft-dextran copolymer promotes pyrimidine motif triplex DNA formation at physiological pH thermodynamic and kinetic studies. J Biol Chem. 1999;274(10):6161–6167.10.1074/jbc.274.10.6161
   PubMed Web of Science ®Google Scholar
• Maruyama A, Ohnishi Y-I, Watanabe H, et al. Polycation comb-type copolymer reduces counterion condensation effect to stabilize DNA duplex and triplex formation. Colloids Surf, B. 1999;16(1):273–280.10.1016/S0927-7765(99)00078-8
   Web of Science ®Google Scholar
• Choi SW, Kano A, Maruyama A. Activation of DNA strand exchange by cationic comb-type copolymers: effect of cationic moieties of the copolymers. Nucleic Acids Res. 2008;36(1):342–351. DOI:10.1093/nar/gkm1035. PubMed PMID: 18033803; PubMed Central PMCID: PMC2248768.
   PubMed Web of Science ®Google Scholar
• Wu L, Shimada N, Kano A, et al. Poly(l-lysine)-graft-dextran copolymer accelerates DNA hybridization by two orders. Soft Matter. 2008;4(4):744. DOI:10.1039/b717478k
   Web of Science ®Google Scholar
• Kim WJ, Sato Y, Akaike T, et al. Cationic comb-type copolymers for DNA analysis. Nat Mater. 2003;2(12):815–820. DOI:10.1038/nmat1021. PubMed PMID: 14634643.
   PubMed Web of Science ®Google Scholar
• Kano A, Moriyama K, Yamano T, et al. Grafting of poly(ethylene glycol) to poly-lysine augments its lifetime in blood circulation and accumulation in tumors without loss of the ability to associate with siRNA. J Controlled Release. 2011;149(1):2–7. DOI:10.1016/j.jconrel.2009.12.007. PubMed PMID: 20005270.
   PubMed Web of Science ®Google Scholar
• Gao J, Shimada N, Maruyama A. MNAzyme-catalyzed nucleic acid detection enhanced by a cationic copolymer. Biomater Sci. 2015;3(5):716–720. DOI:10.1039/c4bm00449c. PubMed PMID: 26222590.
   PubMed Web of Science ®Google Scholar
• Zhang L, Lei J, Liu L, et al. Self-assembled DNA hydrogel as switchable material for aptamer-based fluorescent detection of protein. Anal Chem. 2013;85(22):11077–11082. DOI:10.1021/ac4027725. PubMed PMID: 24138007.
   PubMed Web of Science ®Google Scholar
• Lu C-H, Qi X-J, Li J, et al. Aptamer-based hydrogels and their applications. Aptamers selected by cell-SELEX for theranostics. Berlin Heidelberg: Springer; 2015. p. 163–195.
   Google Scholar
• Tran TNN, Cui J, Hartman MR, et al. A universal DNA-based protein detection system. J Am Chem Soc. 2013;135(38):14008–14011. DOI:10.1021/ja405872g
   PubMed Web of Science ®Google Scholar
• Maruyama A, Katoh M, Ishihara T, et al. Comb-type polycations effectively stabilize DNA triplex. Bioconjug Chem. 1997;8(1):3–6.10.1021/bc960071g
   PubMed Web of Science ®Google Scholar
• Asayama S, Nogawa M, Takei Y, et al. Synthesis of novel polyampholyte comb-type copolymers consisting of a poly(L-lysine) backbone and hyaluronic acid side chains for a DNA carrier. Bioconjug Chem. 1998;9(4):476–481. DOI:10.1021/bc970213m. PubMed PMID: 9667949.
   PubMed Web of Science ®Google Scholar
• Ferdous A, Watanabe H, Akaike T, et al. Poly (L-lysine)-graft-dextran copolymer: amazing effects on triplex stabilization under physiological pH and ionic conditions (in vitro). Nucleic Acids Res. 1998;26(17):3949–3954.10.1093/nar/26.17.3949
   PubMed Web of Science ®Google Scholar
• Jeong B, Bae YH, Kim SW. Thermoreversible gelation of PEG–PLGA–PEG triblock copolymer aqueous solutions. Macromolecules. 1999;32(21):7064–7069. DOI:10.1021/ma9908999
   Web of Science ®Google Scholar
• Green SJ, Lubrich D, Turberfield AJ. DNA hairpins: fuel for autonomous DNA devices. Biophys J. 2006;91(8):2966–2975. DOI:10.1529/biophysj.106.084681. PubMed PMID: 16861269; PubMed Central PMCID: PMC1578469.
   PubMed Web of Science ®Google Scholar
• Douglas SM, Dietz H, Liedl T, et al. Self-assembly of DNA into nanoscale three-dimensional shapes. Nature. 2009;459(7245):414–418. Available from: http://www.nature.com/nature/journal/v459/n7245/suppinfo/nature08016_S1.html10.1038/nature08016
   PubMed Web of Science ®Google Scholar