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Current Drug Metabolism

Editor-in-Chief

ISSN (Print): 1389-2002
ISSN (Online): 1875-5453

Mini-Review Article

Methods to Improve the Stability of Nucleic Acid-Based Nanomaterials

Author(s): Xueping Xie, Wenjuan Ma, Yuxi Zhan, Qifeng Zhang, Chaowei Wang* and Huiyong Zhu*

Volume 24, Issue 5, 2023

Published on: 15 June, 2023

Page: [315 - 326] Pages: 12

DOI: 10.2174/1389200224666230601091346

Price: $65

Abstract

Nucleic acid strands can be synthesized into various nucleic acid-based nanomaterials (NANs) through strict base pairing. The self-assembled NANs are programmable, intelligent, biocompatible, non-immunogenic, and non-cytotoxic. With the rapid development of nanotechnology, the application of NANs in the biomedical fields, such as drug delivery and biological sensing, has attracted wide attention. However, the stability of NANs is often affected by the cation concentrations, enzymatic degradation, and organic solvents. This susceptibility to degradation is one of the most important factors that have restricted the application of NANs. NANs can be denatured or degraded under conditions of low cation concentrations, enzymatic presence, and organic solvents. To deal with this issue, a lot of methods have been attempted to improve the stability of NANs, including artificial nucleic acids, modification with specific groups, encapsulation with protective structures, etc. In this review, we summarized the relevant methods to have a deeper understanding of the stability of NANs.

Graphical Abstract

[1]
Loescher, S.; Groeer, S.; Walther, A. 3D DNA origami nanoparticles: From basic design principles to emerging applications in soft matter and (bio-)nanosciences. Angew. Chem. Int. Ed., 2018, 57(33), 10436-10448.
[http://dx.doi.org/10.1002/anie.201801700] [PMID: 29676504]
[2]
Chidchob, P.; Sleiman, H.F. Recent advances in DNA nanotechnology. Curr. Opin. Chem. Biol., 2018, 46, 63-70.
[http://dx.doi.org/10.1016/j.cbpa.2018.04.012] [PMID: 29751162]
[3]
Zhang, T.; Tian, T.; Lin, Y. Functionalizing framework nucleic-acid-based nanostructures for biomedical application. Adv. Mater., 2022, 34(46), e2107820.
[http://dx.doi.org/10.1002/adma.202107820] [PMID: 34787933]
[4]
Hong, F.; Zhang, F.; Liu, Y.; Yan, H. DNA origami: Scaffolds for creating higher order structures. Chem. Rev., 2017, 117(20), 12584-12640.
[5]
Ramakrishnan, S.; Shen, B.; Kostiainen, M.A.; Grundmeier, G.; Keller, A.; Linko, V. Real-time observation of superstructure-dependent DNA origami digestion by DNase I using high-speed atomic force microscopy. ChemBioChem, 2019, 20(22), 2818-2823.
[http://dx.doi.org/10.1002/cbic.201900369] [PMID: 31163091]
[6]
Jiang, Y.; Li, S.; Zhang, T.; Zhang, M.; Chen, Y.; Wu, Y.; Liu, Y.; Liu, Z.; Lin, Y. Tetrahedral framework nucleic acids inhibit skin fibrosis via the pyroptosis pathway. ACS Appl. Mater. Interfaces, 2022, 14(13), 15069-15079.
[http://dx.doi.org/10.1021/acsami.2c02877] [PMID: 35319864]
[7]
Zhou, M.; Zhang, T.; Zhang, B.; Zhang, X.; Gao, S.; Zhang, T.; Li, S.; Cai, X.; Lin, Y. A DNA nanostructure-based neuroprotectant against neuronal apoptosis via inhibiting toll-like receptor 2 signaling pathway in acute ischemic stroke. ACS Nano, 2022, 16(1), 1456-1470.
[http://dx.doi.org/10.1021/acsnano.1c09626] [PMID: 34967217]
[8]
Zhu, J.; Yang, Y.; Ma, W.; Wang, Y.; Chen, L.; Xiong, H.; Yin, C.; He, Z.; Fu, W.; Xu, R.; Lin, Y. Antiepilepticus effects of tetrahedral framework nucleic acid via inhibition of gliosis-induced downregulation of glutamine synthetase and increased AMPAR internalization in the postsynaptic membrane. Nano Lett., 2022, 22(6), 2381-2390.
[http://dx.doi.org/10.1021/acs.nanolett.2c00025]
[9]
Li, J.; Yao, Y.; Wang, Y.; Xu, J.; Zhao, D.; Liu, M.; Shi, S.; Lin, Y. Modulation of the crosstalk between schwann cells and macrophages for nerve regeneration: a therapeutic strategy based on a multifunctional tetrahedral framework nucleic acids system. Adv. Mater., 2022, 34(46), 2202513.
[http://dx.doi.org/10.1002/adma.202202513] [PMID: 35483031]
[10]
Chen, Y.; Shi, S.; Li, B.; Lan, T.; Yuan, K.; Yuan, J.; Zhou, Y.; Song, J.; Lv, T.; Shi, Y.; Xiang, B.; Tian, T.; Zhang, T.; Yang, J.; Lin, Y. Therapeutic effects of self-assembled tetrahedral framework nucleic acids on liver regeneration in acute liver failure. ACS Appl. Mater. Interfaces, 2022, 14(11), 13136-13146.
[http://dx.doi.org/10.1021/acsami.2c02523] [PMID: 35285610]
[11]
Wang, Y.; Li, Y.; Gao, S.; Yu, X.; Chen, Y.; Lin, Y. Tetrahedral framework nucleic acids can alleviate taurocholate-induced severe acute pancreatitis and its subsequent multiorgan injury in mice. Nano Lett., 2022, 22(4), 1759-1768.
[http://dx.doi.org/10.1021/acs.nanolett.1c05003] [PMID: 35138113]
[12]
Chen, R.; Wen, D.; Fu, W.; Xing, L.; Ma, L.; Liu, Y.; Li, H.; You, C.; Lin, Y. Treatment effect of DNA framework nucleic acids on diffuse microvascular endothelial cell injury after subarachnoid hemorrhage. Cell Prolif., 2022, 55(4), e13206.
[http://dx.doi.org/10.1111/cpr.13206] [PMID: 35187748]
[13]
Li, J.; Lai, Y.; Li, M.; Chen, X.; Zhou, M.; Wang, W.; Li, J.; Cui, W.; Zhang, G.; Wang, K.; Liu, L.; Lin, Y. Repair of infected bone defect with Clindamycin-Tetrahedral DNA nanostructure Complex-loaded 3D bioprinted hybrid scaffold. Chem. Eng. J., 2022, 435, 134855.
[http://dx.doi.org/10.1016/j.cej.2022.134855]
[14]
Zhang, M.; Zhang, X.; Tian, T.; Zhang, Q.; Wen, Y.; Zhu, J.; Xiao, D.; Cui, W.; Lin, Y. Anti-inflammatory activity of curcumin-loaded tetrahedral framework nucleic acids on acute gouty arthritis. Bioact. Mater., 2022, 8, 368-380.
[http://dx.doi.org/10.1016/j.bioactmat.2021.06.003] [PMID: 34541407]
[15]
Zhao, D.; Xiao, D.; Liu, M.; Li, J.; Peng, S.; He, Q.; Sun, Y.; Xiao, J.; Lin, Y. Tetrahedral framework nucleic acid carrying angiogenic peptide prevents bisphosphonate-related osteonecrosis of the jaw by promoting angiogenesis. Int. J. Oral Sci., 2022, 14(1), 23.
[http://dx.doi.org/10.1038/s41368-022-00171-7] [PMID: 35477924]
[16]
Qin, X.; Xiao, L.; Li, N.; Hou, C.; Li, W.; Li, J.; Yan, N.; Lin, Y. Tetrahedral framework nucleic acids-based delivery of microRNA-155 inhibits choroidal neovascularization by regulating the polarization of macrophages. Bioact. Mater., 2022, 14, 134-144.
[http://dx.doi.org/10.1016/j.bioactmat.2021.11.031] [PMID: 35310341]
[17]
Gao, Y.; Chen, X.; Tian, T.; Zhang, T.; Gao, S.; Zhang, X.; Yao, Y.; Lin, Y.; Cai, X. A lysosome-activated tetrahedral nanobox for encapsulated siRNA delivery. Adv. Mater., 2022, 34(46), 2201731.
[http://dx.doi.org/10.1002/adma.202201731] [PMID: 35511782]
[18]
McKee, T.J.; Komarova, S.V. Is it time to reinvent basic cell culture medium? Am. J. Physiol. Cell Physiol., 2017, 312(5), C624-C626.
[http://dx.doi.org/10.1152/ajpcell.00336.2016] [PMID: 28228375]
[19]
Doye, J.P.K.; Ouldridge, T.E.; Louis, A.A.; Romano, F.; Šulc, P.; Matek, C.; Snodin, B.E.K.; Rovigatti, L.; Schreck, J.S.; Harrison, R.M.; Smith, W.P.J. Coarse-graining DNA for simulations of DNA nanotechnology. Phys. Chem. Chem. Phys., 2013, 15(47), 20395-20414.
[http://dx.doi.org/10.1039/c3cp53545b] [PMID: 24121860]
[20]
Kielar, C.; Xin, Y.; Shen, B.; Kostiainen, M.A.; Grundmeier, G.; Linko, V.; Keller, A. On the stability of DNA origami nanostructures in low-magnesium buffers. Angew. Chem. Int. Ed., 2018, 57(30), 9470-9474.
[http://dx.doi.org/10.1002/anie.201802890] [PMID: 29799663]
[21]
Gerling, T.; Kube, M.; Kick, B.; Dietz, H. Sequence-programmable covalent bonding of designed DNA assemblies. Sci. Adv., 2018, 4(8), eaau1157.
[http://dx.doi.org/10.1126/sciadv.aau1157] [PMID: 30128357]
[22]
Stephanopoulos, N. Strategies for stabilizing DNA nanostructures to biological conditions. ChemBioChem, 2019, 20(17), 2191-2197.
[http://dx.doi.org/10.1002/cbic.201900075] [PMID: 30875443]
[23]
Yang, H.; Xi, W. Nucleobase-containing polymers: structure, synthesis, and applications. Polymers (Basel), 2017, 9(12), 666.
[http://dx.doi.org/10.3390/polym9120666] [PMID: 30965964]
[24]
Ke, F.; Luu, Y.K.; Hadjiargyrou, M.; Liang, D. Characterizing DNA condensation and conformational changes in organic solvents. PLoS One, 2010, 5(10), e13308.
[25]
Sen, A.; Nielsen, P.E. On the stability of peptide nucleic acid duplexes in the presence of organic solvents. Nucleic Acids Res., 2007, 35(10), 3367-3374.
[http://dx.doi.org/10.1093/nar/gkm210] [PMID: 17478520]
[26]
Hahn, J.; Wickham, S.F.J.; Shih, W.M.; Perrault, S.D. Addressing the instability of DNA nanostructures in tissue culture. ACS Nano, 2014, 8(9), 8765-8775.
[http://dx.doi.org/10.1021/nn503513p] [PMID: 25136758]
[27]
Kim, Y.; Yang, C.J.; Tan, W. Superior structure stability and selectivity of hairpin nucleic acid probes with an L-DNA stem. Nucleic Acids Res., 2007, 35(21), 7279-7287.
[http://dx.doi.org/10.1093/nar/gkm771] [PMID: 17959649]
[28]
Wlotzka, B.; Leva, S.; Eschgfäller, B.; Burmeister, J.; Kleinjung, F.; Kaduk, C.; Muhn, P.; Hess-Stumpp, H.; Klussmann, S. In vivo properties of an anti-GnRH Spiegelmer: An example of an oligonucleotide-based therapeutic substance class. Proc. Natl. Acad. Sci. USA, 2002, 99(13), 8898-8902.
[http://dx.doi.org/10.1073/pnas.132067399] [PMID: 12070349]
[29]
Xu, Y.; Wei, Y.; Cheng, N.; Huang, K.; Wang, W.; Zhang, L.; Xu, W.; Luo, Y. Nucleic acid biosensor synthesis of an all-in-one universal blocking linker recombinase polymerase amplification with a peptide nucleic acid-based lateral flow device for ultrasensitive detection of food pathogens. Anal. Chem., 2018, 90(1), 708-715.
[http://dx.doi.org/10.1021/acs.analchem.7b01912] [PMID: 29202232]
[30]
Shakeel, S.; Karim, S.; Ali, A. Peptide nucleic acid (PNA)-A review. J. Chem. Technol. Biotechnol., 2006, 81(6), 892-899.
[http://dx.doi.org/10.1002/jctb.1505]
[31]
Ray, A.; Nordén, B. Peptide nucleic acid (PNA): Its medical and biotechnical applications and promise for the future. FASEB J., 2000, 14(9), 1041-1060.
[http://dx.doi.org/10.1096/fasebj.14.9.1041] [PMID: 10834926]
[32]
Murayama, K.; Kashida, H.; Asanuma, H. Acyclic L -threoninol nucleic acid (L -aTNA) with suitable structural rigidity cross-pairs with DNA and RNA. Chem. Commun., 2015, 51(30), 6500-6503.
[http://dx.doi.org/10.1039/C4CC09244A] [PMID: 25633432]
[33]
Pasternak, A.; Wengel, J. Modulation of i-motif thermodynamic stability by the introduction of UNA (unlocked nucleic acid) monomers. Bioorg. Med. Chem. Lett., 2011, 21(2), 752-755.
[http://dx.doi.org/10.1016/j.bmcl.2010.11.106] [PMID: 21185179]
[34]
Pasternak, A.; Wengel, J. Thermodynamics of RNA duplexes modified with unlocked nucleic acid nucleotides. Nucleic Acids Res., 2010, 38(19), 6697-6706.
[http://dx.doi.org/10.1093/nar/gkq561] [PMID: 20562222]
[35]
Jensen, T.B.; Henriksen, J.R.; Rasmussen, B.E.; Rasmussen, L.M.; Andresen, T.L.; Wengel, J.; Pasternak, A. Thermodynamic and biological evaluation of a thrombin binding aptamer modified with several unlocked nucleic acid (UNA) monomers and a 2′-C-piperazino-UNA monomer. Bioorg. Med. Chem., 2011, 19(16), 4739-4745.
[http://dx.doi.org/10.1016/j.bmc.2011.06.087] [PMID: 21795054]
[36]
Shrestha, A.R.; Kotobuki, Y.; Hari, Y.; Obika, S. Guanidine bridged nucleic acid (GuNA): An effect of a cationic bridged nucleic acid on DNA binding affinity. Chem. Commun., 2014, 50(5), 575-577.
[http://dx.doi.org/10.1039/C3CC46017G] [PMID: 24270219]
[37]
Shimo, T.; Nakatsuji, Y.; Tachibana, K.; Obika, S. Design and in vitro evaluation of splice-switching oligonucleotides bearing locked nucleic acids, amido-bridged nucleic acids, and guanidine-bridged nucleic acids. Int. J. Mol. Sci., 2021, 22(7), 3526.
[http://dx.doi.org/10.3390/ijms22073526] [PMID: 33805378]
[38]
Saccà, B.; Lacroix, L.; Mergny, J.L. The effect of chemical modifications on the thermal stability of different G-quadruplex-forming oligonucleotides. Nucleic Acids Res., 2005, 33(4), 1182-1192.
[http://dx.doi.org/10.1093/nar/gki257] [PMID: 15731338]
[39]
Pedersen, E.B.; Nielsen, J.T.; Nielsen, C.; Filichev, V.V. Enhanced anti-HIV-1 activity of G-quadruplexes comprising locked nucleic acids and intercalating nucleic acids. Nucleic Acids Res., 2011, 39(6), 2470-2481.
[http://dx.doi.org/10.1093/nar/gkq1133] [PMID: 21062811]
[40]
Kim, K.R.; Lee, T.; Kim, B.S.; Ahn, D.R. Utilizing the bioorthogonal base-pairing system of L -DNA to design ideal DNA nanocarriers for enhanced delivery of nucleic acid cargos. Chem. Sci., 2014, 5(4), 1533-1537.
[http://dx.doi.org/10.1039/C3SC52601A]
[41]
Kim, K.R.; Kim, H.Y.; Lee, Y.D.; Ha, J.S.; Kang, J.H.; Jeong, H.; Bang, D.; Ko, Y.T.; Kim, S.; Lee, H.; Ahn, D.R. Self-assembled mirror DNA nanostructures for tumor-specific delivery of anticancer drugs. J. Control. Release, 2016, 243, 121-131.
[http://dx.doi.org/10.1016/j.jconrel.2016.10.015] [PMID: 27746274]
[42]
Kim, K.R.; Hwang, D.; Kim, J.; Lee, C.Y.; Lee, W.; Yoon, D.S.; Shin, D.; Min, S.J.; Kwon, I.C.; Chung, H.S.; Ahn, D.R. Streptavidin-mirror DNA tetrahedron hybrid as a platform for intracellular and tumor delivery of enzymes. J. Control. Release, 2018, 280(280), 1-10.
[http://dx.doi.org/10.1016/j.jconrel.2018.04.051] [PMID: 29723615]
[43]
Chu, TW; Feng, J; Yang, J Kopeček, J. Hybrid polymeric hydrogels via peptide nucleic acid (PNA)/DNA complexation. J Control Release, 2015, 220(Pt B), 608-616.
[http://dx.doi.org/10.1016/j.jconrel.2015.09.035]
[44]
Nielsen, P.E.; Egholm, M. An introduction to peptide nucleic acid. Curr. Issues Mol. Biol., 1999, 1(1-2), 89-104.
[PMID: 11475704]
[45]
Zhang, Y.; Zhu, L.; Tian, J.; Zhu, L.; Ma, X.; He, X.; Huang, K.; Ren, F.; Xu, W. Smart and functionalized development of nucleic acid-based hydrogels: Assembly strategies, recent advances, and challenges. Adv. Sci., 2021, 8(14), 2100216.
[http://dx.doi.org/10.1002/advs.202100216] [PMID: 34306976]
[46]
Kumar, S.; Pearse, A.; Liu, Y.; Taylor, R.E. Modular self-assembly of gamma-modified peptide nucleic acids in organic solvent mixtures. Nat. Commun., 2020, 11(1), 2960.
[http://dx.doi.org/10.1038/s41467-020-16759-8] [PMID: 32528008]
[47]
Zhang, Y.; Ma, W.; Zhu, Y.; Shi, S.; Li, Q.; Mao, C.; Zhao, D.; Zhan, Y.; Shi, J.; Li, W.; Wang, L.; Fan, C.; Lin, Y. Inhibiting methicillin-resistant Staphylococcus aureus by tetrahedral DNA nanostructure-enabled antisense peptide nucleic acid delivery. Nano Lett., 2018, 18(9), 5652-5659.
[http://dx.doi.org/10.1021/acs.nanolett.8b02166] [PMID: 30088771]
[48]
Märcher, A.; Kumar, V.; Andersen, V.L.; El-Chami, K.; Nguyen, T.J.D.; Skaanning, M.K.; Rudnik-Jansen, I.; Nielsen, J.S.; Howard, K.A.; Kjems, J.; Gothelf, K.V. Functionalized acyclic (L)-threoninol nucleic acid four-way junction with high stability in vitro and in vivo. Angew. Chem. Int. Ed., 2022, 61(24), e202115275.
[http://dx.doi.org/10.1002/anie.202115275] [PMID: 35352451]
[49]
Taylor, A.I.; Beuron, F.; Peak-Chew, S.Y.; Morris, E.P.; Herdewijn, P.; Holliger, P. Nanostructures from synthetic genetic polymers. ChemBioChem, 2016, 17(12), 1107-1110.
[http://dx.doi.org/10.1002/cbic.201600136] [PMID: 26992063]
[50]
Zhou, L.; Sun, N.; Xu, L.; Chen, X.; Cheng, H.; Wang, J.; Pei, R. Dual signal amplification by an “on-command” pure DNA hydrogel encapsulating HRP for colorimetric detection of ochratoxin A. RSC Advances, 2016, 6(115), 114500-114504.
[http://dx.doi.org/10.1039/C6RA23462C]
[51]
Huang, Y.; Xu, W.; Liu, G.; Tian, L. A pure DNA hydrogel with stable catalytic ability produced by one-step rolling circle amplification. Chem. Commun., 2017, 53(21), 3038-3041.
[http://dx.doi.org/10.1039/C7CC00636E] [PMID: 28239729]
[52]
Fluiter, K.; Mook, O.R.F.; Vreijling, J.; Langkjær, N.; Højland, T.; Wengel, J.; Baas, F. Filling the gap in LNA antisense oligo gapmers: The effects of unlocked nucleic acid (UNA) and 4′-C-hydroxymethyl-DNA modifications on RNase H recruitment and efficacy of an LNA gapmer. Mol. Biosyst., 2009, 5(8), 838-843.
[http://dx.doi.org/10.1039/b903922h] [PMID: 19603119]
[53]
Nielsen, J.T.; Arar, K.; Petersen, M. NMR solution structures of LNA (locked nucleic acid) modified quadruplexes. Nucleic Acids Res., 2006, 34(7), 2006-2014.
[http://dx.doi.org/10.1093/nar/gkl144] [PMID: 16614450]
[54]
Nielsen, J.T.; Arar, K.; Petersen, M. Solution structure of a locked nucleic acid modified quadruplex: introducing the V4 folding topology. Angew. Chem. Int. Ed., 2009, 48(17), 3099-3103.
[http://dx.doi.org/10.1002/anie.200806244] [PMID: 19308940]
[55]
Pal, R.; Deb, I.; Sarzynska, J.; Lahiri, A. LNA-induced dynamic stability in a therapeutic aptamer: insights from molecular dynamics simulations. J. Biomol. Struct. Dyn., 2022, 1-10.
[http://dx.doi.org/10.1080/07391102.2022.2029567] [PMID: 35100936]
[56]
Seth, P.P.; Allerson, C.R.; Siwkowski, A.; Vasquez, G.; Berdeja, A.; Migawa, M.T.; Gaus, H.; Prakash, T.P.; Bhat, B.; Swayze, E.E. Configuration of the 5′-methyl group modulates the biophysical and biological properties of locked nucleic acid (LNA) oligonucleotides. J. Med. Chem., 2010, 53(23), 8309-8318.
[http://dx.doi.org/10.1021/jm101207e] [PMID: 21058707]
[57]
Yahara, A.; Shrestha, A.R.; Yamamoto, T.; Hari, Y.; Osawa, T.; Yamaguchi, M.; Nishida, M.; Kodama, T.; Obika, S. Amido-bridged nucleic acids (AmNAs): Synthesis, duplex stability, nuclease resistance, and in vitro antisense potency. ChemBioChem, 2012, 13(17), 2513-2516.
[http://dx.doi.org/10.1002/cbic.201200506] [PMID: 23081931]
[58]
Goswami, A.; Prasad, A.K.; Maity, J.; Khaneja, N. Synthesis and applications of bicyclic sugar modified locked nucleic acids: A review. Nucleosides Nucleotides Nucleic Acids, 2022, 41(5-6), 503-529.
[http://dx.doi.org/10.1080/15257770.2022.2052316]
[59]
Meanwell, M.; Silverman, S.M.; Lehmann, J.; Adluri, B.; Wang, Y.; Cohen, R.; Campeau, L.C.; Britton, R. A short de novo synthesis of nucleoside analogs. Science, 2020, 369(6504), 725-730.
[http://dx.doi.org/10.1126/science.abb3231] [PMID: 32764073]
[60]
Pozmogova, G.E.; Zaitseva, M.A.; Smirnov, I.P.; Shvachko, A.G.; Murina, M.A.; Sergeenko, V.I. Anticoagulant effects of thioanalogs of thrombin-binding DNA-aptamer and their stability in the plasma. Bull. Exp. Biol. Med., 2010, 150(2), 180-184.
[http://dx.doi.org/10.1007/s10517-010-1099-5] [PMID: 21240367]
[61]
Jie, J.; Xia, Y.; Huang, C.H.; Zhao, H.; Yang, C.; Liu, K.; Song, D.; Zhu, B.Z.; Su, H. Sulfur-centered hemi-bond radicals as active intermediates in S-DNA phosphorothioate oxidation. Nucleic Acids Res., 2019, 47(22), gkz987.
[http://dx.doi.org/10.1093/nar/gkz987] [PMID: 31724721]
[62]
Zhou, J.; Li, T.; Geng, X.; Sui, L.; Wang, F. Antisense oligonucleotide repress telomerase activity via manipulating alternative splicing or translation. Biochem. Biophys. Res. Commun., 2021, 582, 118-124.
[http://dx.doi.org/10.1016/j.bbrc.2021.10.034] [PMID: 34710826]
[63]
Su, Y.; Fujii, H.; Burakova, E.A.; Chelobanov, B.P.; Fujii, M.; Stetsenko, D.A.; Filichev, V.V. Neutral and negatively charged phosphate modifications altering thermal stability, kinetics of formation and monovalent ion dependence of DNA G‐. Quadruplexes. Chem. Asian J., 2019, 14(8), 1212-1220.
[http://dx.doi.org/10.1002/asia.201801757] [PMID: 30600926]
[64]
Kumar, P.; Caruthers, M.H. DNA analogues modified at the nonlinking positions of phosphorus. Acc. Chem. Res., 2020, 53(10), 2152-2166.
[http://dx.doi.org/10.1021/acs.accounts.0c00078] [PMID: 32885957]
[65]
Su, Y.; Edwards, P.J.B.; Stetsenko, D.A.; Filichev, V.V. The importance of phosphates for DNA G-Quadruplex Formation: Evaluation of Zwitterionic G-Rich Oligodeoxynucleotides. ChemBioChem, 2020, 21(17), 2455-2466.
[http://dx.doi.org/10.1002/cbic.202000110] [PMID: 32281223]
[66]
Su, Y.; Bayarjargal, M.; Hale, T.K.; Filichev, V.V. DNA with zwitterionic and negatively charged phosphate modifications: Formation of DNA triplexes, duplexes and cell uptake studies. Beilstein J. Org. Chem., 2021.
[67]
Schön, A.; Kaminska, E.; Schelter, F.; Ponkkonen, E.; Korytiaková, E.; Schiffers, S.; Carell, T. Analysis of an active deformylation mechanism of 5-formyl-deoxycytidine (fdc) in stem cells. Angew. Chem. Int. Ed., 2020, 59(14), 5591-5594.
[http://dx.doi.org/10.1002/anie.202000414] [PMID: 31999041]
[68]
Flodman, K.; Corrêa, I.R., Jr; Dai, N.; Weigele, P.; Xu, S. In vitro Type II restriction of bacteriophage DNA with modified pyrimidines. Front. Microbiol., 2020, 11, 604618.
[http://dx.doi.org/10.3389/fmicb.2020.604618] [PMID: 33193286]
[69]
Hutinet, G.; Lee, Y.J.; de Crécy-Lagard, V.; Weigele, P.R. Hypermodified DNA in viruses of E.coli and Salmonella. Ecosal. Plus, 2021, 9(2), eESP-0028-2019.
[http://dx.doi.org/10.1128/ecosalplus.ESP-0028-2019] [PMID: 34910575]
[70]
Kieft, R.; Zhang, Y.; Marand, A.P.; Moran, J.D.; Bridger, R.; Wells, L.; Schmitz, R.J.; Sabatini, R. Identification of a novel base J binding protein complex involved in RNA polymerase II transcription termination in trypanosomes. PLoS Genet., 2020, 16(2), e1008390.
[71]
Chakrapani, A.; Ruiz-Larrabeiti, O.; Pohl, R.; Svoboda, M.; Krásný, L.; Hocek, M. Glucosylated 5-hydroxymethylpyrimidines as epigenetic DNA bases regulating transcription and restriction cleavage. Chemistry, 2022, 28(31), e202200911.
[http://dx.doi.org/10.1002/chem.202200911] [PMID: 35355345]
[72]
Shigdar, S.; Macdonald, J.; O’Connor, M.; Wang, T.; Xiang, D.; Al Shamaileh, H.; Qiao, L.; Wei, M.; Zhou, S.F.; Zhu, Y.; Kong, L.; Bhattacharya, S.; Li, C.; Duan, W. Aptamers as theranostic agents: Modifications, serum stability and functionalisation. Sensors, 2013, 13(10), 13624-13637.
[http://dx.doi.org/10.3390/s131013624] [PMID: 24152925]
[73]
Johnson, B.M.; Shu, Y.Z.; Zhuo, X.; Meanwell, N.A. Metabolic and pharmaceutical aspects of fluorinated compounds. J. Med. Chem., 2020, 63(12), 6315-6386.
[74]
Pal, S.; Chandra, G.; Patel, S.; Singh, S. Fluorinated nucleosides: Synthesis, modulation in conformation and therapeutic application. Chem. Rec., 2022, 22(5), e202100335.
[http://dx.doi.org/10.1002/tcr.202100335] [PMID: 35253973]
[75]
Okamura, H.; Trinh, G.H.; Dong, Z.; Masaki, Y.; Seio, K.; Nagatsugi, F. Selective and stable base pairing by alkynylated nucleosides featuring a spatially-separated recognition interface. Nucleic Acids Res., 2022, 50(6), 3042-3055.
[http://dx.doi.org/10.1093/nar/gkac140] [PMID: 35234916]
[76]
Conway, J.W.; McLaughlin, C.K.; Castor, K.J.; Sleiman, H. DNA nanostructure serum stability: greater than the sum of its parts. Chem. Commun., 2013, 49(12), 1172-1174.
[http://dx.doi.org/10.1039/c2cc37556g] [PMID: 23287884]
[77]
Chakraborty, G.; Balinin, K.; Portale, G.; Loznik, M.; Polushkin, E.; Weil, T.; Herrmann, A. Electrostatically PEGylated DNA enables salt-free hybridization in water. Chem. Sci., 2019, 10(43), 10097-10105.
[http://dx.doi.org/10.1039/C9SC02598G] [PMID: 32055364]
[78]
Mikkilä, J.; Eskelinen, A.P.; Niemelä, E.H.; Linko, V.; Frilander, M.J.; Törmä, P.; Kostiainen, M.A. Virus-encapsulated DNA origami nanostructures for cellular delivery. Nano Lett., 2014, 14(4), 2196-2200.
[http://dx.doi.org/10.1021/nl500677j] [PMID: 24627955]
[79]
Kiviaho, J.K.; Linko, V.; Ora, A.; Tiainen, T.; Järvihaavisto, E.; Mikkilä, J.; Tenhu, H.; Nonappa, N.; Kostiainen, M.A. Cationic polymers for DNA origami coating – examining their binding efficiency and tuning the enzymatic reaction rates. Nanoscale, 2016, 8(22), 11674-11680.
[http://dx.doi.org/10.1039/C5NR08355A] [PMID: 27219684]
[80]
Perrault, S.D.; Shih, W.M. Virus-inspired membrane encapsulation of DNA nanostructures to achieve in vivo stability. ACS Nano, 2014, 8(5), 5132-5140.
[http://dx.doi.org/10.1021/nn5011914] [PMID: 24694301]
[81]
Agarwal, N.P.; Matthies, M.; Gür, F.N.; Osada, K.; Schmidt, T.L. Block copolymer micellization as a protection strategy for DNA origami. Angew. Chem. Int. Ed., 2017, 56(20), 5460-5464.
[http://dx.doi.org/10.1002/anie.201608873] [PMID: 28295864]
[82]
Ramakrishnan, S.; Ijäs, H.; Linko, V.; Keller, A. Structural stability of DNA origami nanostructures under application-specific conditions. Comput. Struct. Biotechnol. J., 2018, 16, 342-349.
[http://dx.doi.org/10.1016/j.csbj.2018.09.002] [PMID: 30305885]
[83]
Peng, Q.; Wei, X.Q.; Yang, Q.; Zhang, S.; Zhang, T.; Shao, X.R.; Cai, X.X.; Zhang, Z.R.; Lin, Y.F. Enhanced biostability of nanoparticle-based drug delivery systems by albumin corona. Nanomedicine (Lond.), 2015, 10(2), 205-214.
[http://dx.doi.org/10.2217/nnm.14.86] [PMID: 25600966]
[84]
Auvinen, H.; Zhang, H. Nonappa; Kopilow, A.; Niemelä, E.H.; Nummelin, S.; Correia, A.; Santos, H.A.; Linko, V.; Kostiainen, M.A. Protein coating of DNA nanostructures for enhanced stability and immunocompatibility. Adv. Healthc. Mater., 2017, 6(18), 1700692.
[http://dx.doi.org/10.1002/adhm.201700692] [PMID: 28738444]
[85]
Tian, T.; Zhang, T.; Zhou, T.; Lin, S.; Shi, S.; Lin, Y. Synthesis of an ethyleneimine/tetrahedral DNA nanostructure complex and its potential application as a multi-functional delivery vehicle. Nanoscale, 2017, 9(46), 18402-18412.
[http://dx.doi.org/10.1039/C7NR07130B] [PMID: 29147695]
[86]
Ahmadi, Y.; De Llano, E.; Barišić, I. (Poly)cation-induced protection of conventional and wireframe DNA origami nanostructures. Nanoscale, 2018, 10(16), 7494-7504.
[http://dx.doi.org/10.1039/C7NR09461B] [PMID: 29637957]
[87]
Ge, Y.; Tian, T.; Shao, X.; Lin, S.; Zhang, T.; Lin, Y.; Cai, X. PEGylated protamine-based adsorbing improves the biological properties and stability of tetrahedral framework nucleic acids. ACS Appl. Mater. Interfaces, 2019, 11(31), 27588-27597.
[http://dx.doi.org/10.1021/acsami.9b09243] [PMID: 31298033]
[88]
Ponnuswamy, N.; Bastings, M.M.C.; Nathwani, B.; Ryu, J.H.; Chou, L.Y.T.; Vinther, M.; Li, W.A.; Anastassacos, F.M.; Mooney, D.J.; Shih, W.M. Oligolysine-based coating protects DNA nanostructures from low-salt denaturation and nuclease degradation. Nat. Commun., 2017, 8(1), 15654.
[http://dx.doi.org/10.1038/ncomms15654] [PMID: 28561045]
[89]
Bertosin, E.; Stömmer, P.; Feigl, E.; Wenig, M.; Honemann, M.N.; Dietz, H. Cryo-electron microscopy and mass analysis of oligolysine-coated DNA nanostructures. ACS Nano, 2021, 15(6), 9391-9403.
[http://dx.doi.org/10.1021/acsnano.0c10137] [PMID: 33724780]
[90]
Anastassacos, F.M.; Zhao, Z.; Zeng, Y.; Shih, W.M. glutaraldehyde cross-linking of oligolysines coating DNA origami greatly reduces susceptibility to nuclease degradation. J. Am. Chem. Soc., 2020, 142(7), 3311-3315.
[http://dx.doi.org/10.1021/jacs.9b11698] [PMID: 32011869]
[91]
Kim, Y.; Yin, P. Enhancing biocompatible stability of DNA nanostructures using dendritic oligonucleotides and brick motifs. Angew. Chem. Int. Ed., 2020, 59(2), 700-703.
[http://dx.doi.org/10.1002/anie.201911664] [PMID: 31595637]
[92]
Feng, Y.; Tang, F.; Li, S.; Wu, D.; Liu, Q.; Li, H.; Zhang, X.; Liu, Z.; Zhang, L.; Feng, H. Mannose-modified erythrocyte membrane-encapsulated chitovanic nanoparticles as a DNA vaccine carrier against reticuloendothelial tissue hyperplasia virus. Front. Immunol., 2023, 13, 1066268.
[http://dx.doi.org/10.3389/fimmu.2022.1066268] [PMID: 36776397]
[93]
Ma, W.; Yang, Y.; Zhu, J.; Jia, W.; Zhang, T.; Liu, Z.; Chen, X.; Lin, Y. Biomimetic nanoerythrosome-coated aptamer–DNA tetrahedron/maytansine conjugates: pH-Responsive and targeted cytotoxicity for HER2-positive breast cancer. Adv. Mater., 2022, 34(46), 2109609.
[http://dx.doi.org/10.1002/adma.202109609] [PMID: 35064993]
[94]
Ma, W.; Zhan, Y.; Zhang, Y.; Shao, X.; Xie, X.; Mao, C.; Cui, W.; Li, Q.; Shi, J.; Li, J.; Fan, C.; Lin, Y. An intelligent DNA nanorobot with in vitro enhanced protein lysosomal degradation of her2. Nano Lett., 2019, 19(7), 4505-4517.
[http://dx.doi.org/10.1021/acs.nanolett.9b01320] [PMID: 31185573]
[95]
Chen, X.; Lu, Y. Circular RNA: Biosynthesis in vitro. Front. Bioeng. Biotechnol., 2021, 9, 787881.
[http://dx.doi.org/10.3389/fbioe.2021.787881] [PMID: 34917603]
[96]
O’Neill, P.; Rothemund, P.W.K.; Kumar, A.; Fygenson, D.K. Sturdier DNA nanotubes via ligation. Nano Lett., 2006, 6(7), 1379-1383.
[http://dx.doi.org/10.1021/nl0603505] [PMID: 16834415]
[97]
Rajendran, A.; Krishnamurthy, K.; Giridasappa, A.; Nakata, E.; Morii, T. Stabilization and structural changes of 2D DNA origami by enzymatic ligation. Nucleic Acids Res., 2021, 49(14), 7884-7900.
[http://dx.doi.org/10.1093/nar/gkab611] [PMID: 34289063]
[98]
Rajendran, A.; Magesh, C.J.; Perumal, P.T. DNA-DNA cross-linking mediated by bifunctional [SalenAlIII]+ complex. Biochim. Biophys. Acta, Gen. Subj., 2008, 1780(2), 282-288.
[http://dx.doi.org/10.1016/j.bbagen.2007.11.012] [PMID: 18155173]
[99]
Rajendran, A.; Endo, M.; Katsuda, Y.; Hidaka, K.; Sugiyama, H. Photo-cross-linking-assisted thermal stability of DNA origami structures and its application for higher-temperature self-assembly. J. Am. Chem. Soc., 2011, 133(37), 14488-14491.
[http://dx.doi.org/10.1021/ja204546h] [PMID: 21859143]
[100]
Benson, E.; Mohammed, A.; Gardell, J.; Masich, S.; Czeizler, E.; Orponen, P.; Högberg, B. DNA rendering of polyhedral meshes at the nanoscale. Nature, 2015, 523(7561), 441-444.
[http://dx.doi.org/10.1038/nature14586] [PMID: 26201596]
[101]
Veneziano, R.; Ratanalert, S.; Zhang, K.; Zhang, F.; Yan, H.; Chiu, W.; Bathe, M. Designer nanoscale DNA assemblies programmed from the top down. Science, 2016, 352(6293), 1534.
[http://dx.doi.org/10.1126/science.aaf4388] [PMID: 27229143]
[102]
Kroener, F.; Traxler, L.; Heerwig, A.; Rant, U.; Mertig, M. Magnesium-dependent electrical actuation and stability of DNA origami rods. ACS Appl. Mater. Interfaces, 2019, 11(2), 2295-2301.
[http://dx.doi.org/10.1021/acsami.8b18611] [PMID: 30584763]
[103]
Liu, S.; Jiang, Q.; Wang, Y.; Ding, B. Biomedical applications of DNA-based molecular devices. Adv. Healthc. Mater., 2019, 8(10), 1801658.
[http://dx.doi.org/10.1002/adhm.201801658] [PMID: 30938489]
[104]
Liu, N.; Zhang, X.; Li, N.; Zhou, M.; Zhang, T.; Li, S.; Cai, X.; Ji, P.; Lin, Y. Tetrahedral framework nucleic acids promote corneal epithelial wound healing in vitro and in vivo. Small, 2019, 15(31), 1901907.
[http://dx.doi.org/10.1002/smll.201901907] [PMID: 31192537]
[105]
Shi, S.; Lin, S.; Li, Y.; Zhang, T.; Shao, X.; Tian, T.; Zhou, T.; Li, Q.; Lin, Y. Effects of tetrahedral DNA nanostructures on autophagy in chondrocytes. Chem. Commun., 2018, 54(11), 1327-1330.
[http://dx.doi.org/10.1039/C7CC09397G] [PMID: 29349457]
[106]
Xie, X.; Shao, X.; Ma, W.; Zhao, D.; Shi, S.; Li, Q.; Lin, Y. Overcoming drug-resistant lung cancer by paclitaxel loaded tetrahedral DNA nanostructures. Nanoscale, 2018, 10(12), 5457-5465.
[http://dx.doi.org/10.1039/C7NR09692E] [PMID: 29484330]
[107]
Liu, M.; Ma, W.; Li, Q.; Zhao, D.; Shao, X.; Huang, Q.; Hao, L.; Lin, Y. Aptamer-targeted DNA nanostructures with doxorubicin to treat protein tyrosine kinase 7-positive tumours. Cell Prolif., 2019, 52(1), e12511.
[http://dx.doi.org/10.1111/cpr.12511] [PMID: 30311693]
[108]
Kostiainen, M.A.; Linko, V. DNA origami nanophotonics and plasmonics at interfaces. Langmuir, 2018, 34(46), 14911-14920.
[109]
Green, C.M.; Mathur, D.; Medintz, I.L. Understanding the fate of DNA nanostructures inside the cell. J. Mater. Chem. B Mater. Biol. Med., 2020, 8(29), 6170-6178.
[http://dx.doi.org/10.1039/D0TB00395F] [PMID: 32239041]
[110]
Surana, S.; Shenoy, A.R.; Krishnan, Y. Designing DNA nanodevices for compatibility with the immune system of higher organisms. Nat. Nanotechnol., 2015, 10(9), 741-747.
[http://dx.doi.org/10.1038/nnano.2015.180] [PMID: 26329110]
[111]
Jiang, D.; Ge, Z. Im, H.J.; England, C.G.; Ni, D.; Hou, J.; Zhang, L.; Kutyreff, C.J.; Yan, Y.; Liu, Y.; Cho, S.Y.; Engle, J.W.; Shi, J.; Huang, P.; Fan, C.; Yan, H.; Cai, W. DNA origami nanostructures can exhibit preferential renal uptake and alleviate acute kidney injury. Nat. Biomed. Eng., 2018, 2(11), 865-877.
[http://dx.doi.org/10.1038/s41551-018-0317-8] [PMID: 30505626]

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