Читать книгу DNA- and RNA-Based Computing Systems - Группа авторов - Страница 51

References

Оглавление

1 1 Cinteza, L.O. (2010). Quantum dots in biomedical applications: advances and challenges. J. Nanophotonics 4 (Art. No.: 042503) https://doi.org/10.1117/1.3500388.

2 2 Wagner, A.M., Knipe, J.M., Orive, G., and Peppas, N.A. (2019). Quantum dots in biomedical applications. Acta Biomater. 94: 44–63. https://doi.org/10.1016/j.actbio.2019.05.022.

3 3 Jeevanandam, J., Barhoum, A., Chan, Y.S. et al. (2018). Review on nanoparticles and nanostructured materials: history, sources, toxicity and regulations. Beilstein J. Nanotechnol. 9: 1050–1074. https://doi.org/10.3762/bjnano.9.98.

4 4 Iriarte‐Mesa, C., Lopez, Y.C., Matos‐Peralta, Y. et al. (2020). Gold, silver and iron oxide nanoparticles: synthesis and bionanoconjugation strategies aimed at electrochemical applications. Top. Curr. Chem. (Cham) 378: 12. https://doi.org/10.1007/s41061-019-0275-y.

5 5 Mirahadi, M., Ghanbarzadeh, S., Ghorbani, M. et al. (2018). A review on the role of lipid‐based nanoparticles in medical diagnosis and imaging. Ther. Deliv. 9: 557–569. https://doi.org/10.4155/tde-2018-0020.

6 6 Chiu, M.L., Goulet, D.R., Teplyakov, A., and Gilliland, G.L. (2019). Antibody structure and function: the basis for engineering therapeutics. Antibodies (Basel) 8 https://doi.org/10.3390/antib8040055.

7 7 Fernandez, L.A. and Muyldermans, S. (2011). Recent developments in engineering and delivery of protein and antibody therapeutics. Curr. Opin. Biotechnol. 22: 839–842. https://doi.org/10.1016/j.copbio.2011.08.001.

8 8 Michelotti, N., Johnson‐Buck, A., Manzo, A.J., and Walter, N.G. (2012). Beyond DNA origami: the unfolding prospects of nucleic acid nanotechnology. Wiley Interdiscip. Rev. Nanomed. Nanobiotechnol. 4: 139–152. https://doi.org/10.1002/wnan.170.

9 9 Zuker, M. (2003). Mfold web server for nucleic acid folding and hybridization prediction. Nucleic Acids Res. 31: 3406–3415. https://doi.org/10.1093/nar/gkg595.

10 10 Zadeh, J.N., Steenberg, C.D., Bois, J.S. et al. (2011). NUPACK: analysis and design of nucleic acid systems. J. Comput. Chem. 32: 170–173. https://doi.org/10.1002/jcc.21596.

11 11 Turner, D.H. (1996). Thermodynamics of base pairing. Curr. Opin. Struct. Biol. 6: 299–304. https://doi.org/10.1016/s0959-440x(96)80047-9.

12 12 Petersheim, M. and Turner, D.H. (1983). Base‐stacking and base‐pairing contributions to helix stability: thermodynamics of double‐helix formation with CCGG, CCGGp, CCGGAp, ACCGGp, CCGGUp, and ACCGGUp. Biochemistry 22: 256–263. https://doi.org/10.1021/bi00271a004.

13 13 Leontis, N.B., Stombaugh, J., and Westhof, E. (2002). The non‐Watson‐Crick base pairs and their associated isostericity matrices. Nucleic Acids Res. 30: 3497–3531. https://doi.org/10.1093/nar/gkf481.

14 14 Sweeney, B.A., Roy, P., and Leontis, N.B. (2015). An introduction to recurrent nucleotide interactions in RNA. Wiley Interdiscip. Rev.: RNA 6: 17–45. https://doi.org/10.1002/wrna.1258.

15 15 Leontis, N.B. and Westhof, E. (2002). The annotation of RNA motifs. Comp. Funct. Genomics 3: 518–524. https://doi.org/10.1002/cfg.213.

16 16 Seeman, N.C. (1982). Nucleic acid junctions and lattices. J. Theor. Biol. 99: 237–247. https://doi.org/10.1016/0022-5193(82)90002-9.

17 17 Chen, J.H. and Seeman, N.C. (1991). Synthesis from DNA of a molecule with the connectivity of a cube. Nature 350: 631–633. https://doi.org/10.1038/350631a0.

18 18 Pinheiro, A.V., Han, D., Shih, W.M., and Yan, H. (2011). Challenges and opportunities for structural DNA nanotechnology. Nat. Nanotechnol. 6: 763–772. https://doi.org/10.1038/nnano.2011.187.

19 19 Chen, T., Ren, L., Liu, X. et al. (2018). DNA nanotechnology for cancer diagnosis and therapy. Int. J. Mol. Sci. 19 https://doi.org/10.3390/ijms19061671.

20 20 Cox, A.J., Bengtson, H.N., Rohde, K.H., and Kolpashchikov, D.M. (2016). DNA nanotechnology for nucleic acid analysis: multifunctional molecular DNA machine for RNA detection. Chem. Commun. (Camb) 52: 14318–14321. https://doi.org/10.1039/c6cc06889h.

21 21 Afonin, K.A., Schultz, D., Jaeger, L. et al. (2015). Silver nanoclusters for RNA nanotechnology: steps towards visualization and tracking of RNA nanoparticle assemblies. Methods Mol. Biol. 1297: 59–66. https://doi.org/10.1007/978-1-4939-2562-9_4.

22 22 Bui, M.N., Brittany Johnson, M., Viard, M. et al. (2017). Versatile RNA tetra‐U helix linking motif as a toolkit for nucleic acid nanotechnology. Nanomedicine 13: 1137–1146. https://doi.org/10.1016/j.nano.2016.12.018.

23 23 Guo, P. (2010). The emerging field of RNA nanotechnology. Nat. Nanotechnol. 5: 833–842. https://doi.org/10.1038/nnano.2010.231.

24 24 Shukla, G.C., Haque, F., Tor, Y. et al. (2011). A boost for the emerging field of RNA nanotechnology. ACS Nano 5: 3405–3418. https://doi.org/10.1021/nn200989r.

25 25 Rothemund, P.W. (2006). Folding DNA to create nanoscale shapes and patterns. Nature 440: 297–302. https://doi.org/10.1038/nature04586.

26 26 Woo, S. and Rothemund, P.W. (2014). Self‐assembly of two‐dimensional DNA origami lattices using cation‐controlled surface diffusion. Nat. Commun. 5: 4889. https://doi.org/10.1038/ncomms5889.

27 27 Andersen, E.S., Dong, M., Nielsen, M.M. et al. (2008). DNA origami design of dolphin‐shaped structures with flexible tails. ACS Nano 2: 1213–1218. https://doi.org/10.1021/nn800215j.

28 28 Grabow, W.W. and Jaeger, L. (2014). RNA self‐assembly and RNA nanotechnology. Acc. Chem. Res. 47: 1871–1880. https://doi.org/10.1021/ar500076k.

29 29 Sparvath, S.L., Geary, C.W., and Andersen, E.S. (2017). Computer‐aided design of RNA origami structures. Methods Mol. Biol. 1500: 51–80. https://doi.org/10.1007/978-1-4939-6454-3_5.

30 30 Parlea, L.G., Sweeney, B.A., Hosseini‐Asanjan, M. et al. (2016). The RNA 3D Motif Atlas: computational methods for extraction, organization and evaluation of RNA motifs. Methods 103: 99–119. https://doi.org/10.1016/j.ymeth.2016.04.025.

31 31 Kaplan, W. and Littlejohn, T.G. (2001). Swiss‐PDB viewer (deep view). Briefings Bioinf. 2: 195–197. https://doi.org/10.1093/bib/2.2.195.

32 32 Jasinski, D., Haque, F., Binzel, D.W., and Guo, P. (2017). Advancement of the emerging field of RNA nanotechnology. ACS Nano 11: 1142–1164. https://doi.org/10.1021/acsnano.6b05737.

33 33 Shu, Y., Haque, F., Shu, D. et al. (2013). Fabrication of 14 different RNA nanoparticles for specific tumor targeting without accumulation in normal organs. RNA 19: 767–777. https://doi.org/10.1261/rna.037002.112.

34 34 Afonin, K.A., Bindewald, E., Kireeva, M., and Shapiro, B.A. (2015). Computational and experimental studies of reassociating RNA/DNA hybrids containing split functionalities. Methods Enzymol. 553: 313–334. https://doi.org/10.1016/bs.mie.2014.10.058.

35 35 Halman, J.R., Satterwhite, E., Roark, B. et al. (2017). Functionally‐interdependent shape‐switching nanoparticles with controllable properties. Nucleic Acids Res. 45: 2210–2220. https://doi.org/10.1093/nar/gkx008.

36 36 Hong, E., Halman, J.R., Shah, A.B. et al. (2018). Structure and composition define immunorecognition of nucleic acid nanoparticles. Nano Lett. 18: 4309–4321. https://doi.org/10.1021/acs.nanolett.8b01283.

37 37 Parlea, L., Bindewald, E., Sharan, R. et al. (2016). Ring catalog: a resource for designing self‐assembling RNA nanostructures. Methods 103: 128–137. https://doi.org/10.1016/j.ymeth.2016.04.016.

38 38 Jasinski, D.L., Khisamutdinov, E.F., Lyubchenko, Y.L., and Guo, P. (2014). Physicochemically tunable polyfunctionalized RNA square architecture with fluorogenic and ribozymatic properties. ACS Nano 8: 7620–7629. https://doi.org/10.1021/nn502160s.

39 39 Khisamutdinov, E.F., Jasinski, D.L., and Guo, P. (2014). RNA as a boiling‐resistant anionic polymer material to build robust structures with defined shape and stoichiometry. ACS Nano 8: 4771–4781. https://doi.org/10.1021/nn5006254.

40 40 Khisamutdinov, E.F., Jasinski, D.L., Li, H. et al. (2016). Fabrication of RNA 3D nanoprisms for loading and protection of small RNAs and model drugs. Adv. Mater. 28: 10079–10087. https://doi.org/10.1002/adma.201603180.

41 41 Guo, P., Haque, F., Hallahan, B. et al. (2012). Uniqueness, advantages, challenges, solutions, and perspectives in therapeutics applying RNA nanotechnology. Nucleic Acid Ther. 22: 226–245. https://doi.org/10.1089/nat.2012.0350.

42 42 Shu, D., Shu, Y., Haque, F. et al. (2011). Thermodynamically stable RNA three‐way junction for constructing multifunctional nanoparticles for delivery of therapeutics. Nat. Nanotechnol. 6: 658–667. https://doi.org/10.1038/nnano.2011.105.

43 43 Shu, D., Khisamutdinov, E.F., Zhang, L., and Guo, P.X. (2014). Programmable folding of fusion RNA in vivo and in vitro driven by pRNA 3WJ motif of phi29 DNA packaging motor. Nucleic Acids Res. 42 (Art. No.: e10) https://doi.org/10.1093/nar/gkt885.

44 44 Guet, D., Burns, L.T., Maji, S. et al. (2015). Combining Spinach‐tagged RNA and gene localization to image gene expression in live yeast. Nat. Commun. 6: 8882. https://doi.org/10.1038/ncomms9882.

45 45 Shen, H., Wang, Y., Wang, J. et al. (2019). Emerging biomimetic applications of DNA nanotechnology. ACS Appl. Mater. Interfaces 11: 13859–13873. https://doi.org/10.1021/acsami.8b06175.

46 46 Goldsworthy, V., LaForce, G., Abels, S., and Khisamutdinov, E.E. (2018). Fluorogenic RNA aptamers: a nano‐platform for fabrication of simple and combinatorial logic gates. Nanomaterials (Basel) 8 (Art. No.: 984) https://doi.org/10.3390/nano8120984.

47 47 Kang, K.N. and Lee, Y.S. (2013). RNA aptamers: a review of recent trends and applications. Adv. Biochem. Eng./Biotechnol. 131: 153–169. https://doi.org/10.1007/10_2012_136.

48 48 Tuerk, C. and Gold, L. (1990). Systematic evolution of ligands by exponential enrichment: RNA ligands to bacteriophage T4 DNA polymerase. Science 249: 505–510. https://doi.org/10.1126/science.2200121.

49 49 Ellington, A.D. and Szostak, J.W. (1990). In vitro selection of RNA molecules that bind specific ligands. Nature 346: 818–822. https://doi.org/10.1038/346818a0.

50 50 Iliuk, A.B., Hu, L., and Tao, W.A. (2011). Aptamer in bioanalytical applications. Anal. Chem. 83: 4440–4452. https://doi.org/10.1021/ac201057w.

51 51 Panigaj, M., Johnson, M.B., Ke, W. et al. (2019). Aptamers as modular components of therapeutic nucleic acid nanotechnology. ACS Nano 13: 12301–12321. https://doi.org/10.1021/acsnano.9b06522.

52 52 Goud, K.Y., Reddy, K.K., Satyanarayana, M. et al. (2019). A review on recent developments in optical and electrochemical aptamer‐based assays for mycotoxins using advanced nanomaterials. Mikrochim. Acta 187: 29. https://doi.org/10.1007/s00604-019-4034-0.

53 53 Li, F., Yu, Z., Han, X., and Lai, R.Y. (2019). Electrochemical aptamer‐based sensors for food and water analysis: a review. Anal. Chim. Acta 1051: 1–23. https://doi.org/10.1016/j.aca.2018.10.058.

54 54 Pehlivan, Z.S., Torabfam, M., Kurt, H. et al. (2019). Aptamer and nanomaterial based FRET biosensors: a review on recent advances (2014–2019). Mikrochim. Acta 186: 563. https://doi.org/10.1007/s00604-019-3659-3.

55 55 Seelig, G., Soloveichik, D., Zhang, D.Y., and Winfree, E. (2006). Enzyme‐free nucleic acid logic circuits. Science 314: 1585–1588. https://doi.org/10.1126/science.1132493.

56 56 Bao, G., Rhee, W.J., and Tsourkas, A. (2009). Fluorescent probes for live‐cell RNA detection. Annu. Rev. Biomed. Eng. 11: 25–47. https://doi.org/10.1146/annurev-bioeng-061008-124920.

57 57 Benenson, Y., Gil, B., Ben‐Dor, U. et al. (2004). An autonomous molecular computer for logical control of gene expression. Nature 429: 423–429. https://doi.org/10.1038/nature02551.

58 58 Zhang, X., Potty, A.S., Jackson, G.W. et al. (2009). Engineered 5S ribosomal RNAs displaying aptamers recognizing vascular endothelial growth factor and malachite green. J. Mol. Recognit. 22: 154–161. https://doi.org/10.1002/jmr.917.

59 59 Masuda, I., Igarashi, T., Sakaguchi, R. et al. (2017). A genetically encoded fluorescent tRNA is active in live‐cell protein synthesis. Nucleic Acids Res. 45: 4081–4093. https://doi.org/10.1093/nar/gkw1229.

60 60 Culler, S.J., Hoff, K.G., and Smolke, C.D. (2010). Reprogramming cellular behavior with RNA controllers responsive to endogenous proteins. Science 330: 1251–1255. https://doi.org/10.1126/science.1192128.

61 61 Tan, X., Constantin, T.P., Sloane, K.L. et al. (2017). Fluoromodules consisting of a promiscuous RNA aptamer and red or blue fluorogenic cyanine dyes: selection, characterization, and bioimaging. J. Am. Chem. Soc. 139: 9001–9009. https://doi.org/10.1021/jacs.7b04211.

62 62 Paige, J.S., Wu, K.Y., and Jaffrey, S.R. (2011). RNA mimics of green fluorescent protein. Science 333: 642–646. https://doi.org/10.1126/science.1207339.

63 63 Song, W., Strack, R.L., Svensen, N., and Jaffrey, S.R. (2014). Plug‐and‐play fluorophores extend the spectral properties of Spinach. J. Am. Chem. Soc. 136: 1198–1201. https://doi.org/10.1021/ja410819x.

64 64 Dolgosheina, E.V., Jeng, S.C., Panchapakesan, S.S. et al. (2014). RNA mango aptamer‐fluorophore: a bright, high‐affinity complex for RNA labeling and tracking. ACS Chem. Biol. 9: 2412–2420. https://doi.org/10.1021/cb500499x.

65 65 Song, W., Filonov, G.S., Kim, H. et al. (2017). Imaging RNA polymerase III transcription using a photostable RNA‐fluorophore complex. Nat. Chem. Biol. 13: 1187–1194. https://doi.org/10.1038/nchembio.2477.

66 66 Constantin, T.P., Silva, G.L., Robertson, K.L. et al. (2008). Synthesis of new fluorogenic cyanine dyes and incorporation into RNA fluoromodules. Org. Lett. 10: 1561–1564. https://doi.org/10.1021/ol702920e.

67 67 Babendure, J.R., Adams, S.R., and Tsien, R.Y. (2003). Aptamers switch on fluorescence of triphenylmethane dyes. J. Am. Chem. Soc. 125: 14716–14717. https://doi.org/10.1021/ja037994o.

68 68 Bouhedda, F., Autour, A., and Ryckelynck, M. (2017). Light‐up RNA aptamers and their cognate fluorogens: from their development to their applications. Int. J. Mol. Sci. 19 https://doi.org/10.3390/ijms19010044.

69 69 Ouellet, J. (2016). RNA fluorescence with light‐up aptamers. Front. Chem. 4: 29. https://doi.org/10.3389/fchem.2016.00029.

70 70 Grate, D. and Wilson, C. (1999). Laser‐mediated, site‐specific inactivation of RNA transcripts. Proc. Natl. Acad. Sci. U.S.A. 96: 6131–6136. https://doi.org/10.1073/pnas.96.11.6131.

71 71 Khisamutdinov, E.F., Li, H., Jasinski, D.L. et al. (2014). Enhancing immunomodulation on innate immunity by shape transition among RNA triangle, square and pentagon nanovehicles. Nucleic Acids Res. 42: 9996–10004. https://doi.org/10.1093/nar/gku516.

72 72 Warner, K.D., Chen, M.C., Song, W. et al. (2014). Structural basis for activity of highly efficient RNA mimics of green fluorescent protein. Nat. Struct. Mol. Biol. 21: 658–663. https://doi.org/10.1038/nsmb.2865.

73 73 Kellenberger, C.A., Chen, C., Whiteley, A.T. et al. (2015). RNA‐based fluorescent biosensors for live cell imaging of second messenger cyclic di‐AMP. J. Am. Chem. Soc. 137: 6432–6435. https://doi.org/10.1021/jacs.5b00275.

74 74 Filonov, G.S., Moon, J.D., Svensen, N., and Jaffrey, S.R. (2014). Broccoli: rapid selection of an RNA mimic of green fluorescent protein by fluorescence‐based selection and directed evolution. J. Am. Chem. Soc. 136: 16299–16308. https://doi.org/10.1021/ja508478x.

75 75 Breaker, R.R. (2002). Engineered allosteric ribozymes as biosensor components. Curr. Opin. Biotechnol. 13: 31–39. https://doi.org/10.1016/s0958-1669(02)00281-1.

76 76 Zivarts, M., Liu, Y., and Breaker, R.R. (2005). Engineered allosteric ribozymes that respond to specific divalent metal ions. Nucleic Acids Res. 33: 622–631. https://doi.org/10.1093/nar/gki182.

77 77 Kolpashchikov, D.M. (2005). Binary malachite green aptamer for fluorescent detection of nucleic acids. J. Am. Chem. Soc. 127: 12442–12443. https://doi.org/10.1021/ja0529788.

78 78 Stojanovic, M.N. and Kolpashchikov, D.M. (2004). Modular aptameric sensors. J. Am. Chem. Soc. 126: 9266–9270. https://doi.org/10.1021/ja032013t.

79 79 Song, W., Strack, R.L., and Jaffrey, S.R. (2013). Imaging bacterial protein expression using genetically encoded RNA sensors. Nat. Methods 10: 873–875. https://doi.org/10.1038/nmeth.2568.

80 80 Sharma, S., Zaveri, A., Visweswariah, S.S., and Krishnan, Y. (2014). A fluorescent nucleic acid nanodevice quantitatively images elevated cyclic adenosine monophosphate in membrane‐bound compartments. Small 10: 4276–4280. https://doi.org/10.1002/smll.201400833.

81 81 Paige, J.S., Nguyen‐Duc, T., Song, W., and Jaffrey, S.R. (2012). Fluorescence imaging of cellular metabolites with RNA. Science 335: 1194. https://doi.org/10.1126/science.1218298.

82 82 Su, Y., Hickey, S.F., Keyser, S.G., and Hammond, M.C. (2016). In vitro and in vivo enzyme activity screening via RNA‐based fluorescent biosensors for S‐adenosyl‐l‐homocysteine (SAH). J. Am. Chem. Soc. 138: 7040–7047. https://doi.org/10.1021/jacs.6b01621.

83 83 You, M., Litke, J.L., and Jaffrey, S.R. (2015). Imaging metabolite dynamics in living cells using a Spinach‐based riboswitch. Proc. Natl. Acad. Sci. U.S.A. 112: E2756–E2765. https://doi.org/10.1073/pnas.1504354112.

84 84 Ilgu, M., Ray, J., Bendickson, L. et al. (2016). Light‐up and FRET aptamer reporters; evaluating their applications for imaging transcription in eukaryotic cells. Methods 98: 26–33. https://doi.org/10.1016/j.ymeth.2015.12.009.

85 85 Saurabh, S., Perez, A.M., Comerci, C.J. et al. (2016). Super‐resolution imaging of live bacteria cells using a genetically directed, highly photostable fluoromodule. J. Am. Chem. Soc. 138: 10398–10401. https://doi.org/10.1021/jacs.6b05943.

86 86 Pothoulakis, G., Ceroni, F., Reeve, B., and Ellis, T. (2014). The spinach RNA aptamer as a characterization tool for synthetic biology. ACS Synth. Biol. 3: 182–187. https://doi.org/10.1021/sb400089c.

87 87 Strack, R.L., Disney, M.D., and Jaffrey, S.R. (2013). A superfolding Spinach2 reveals the dynamic nature of trinucleotide repeat‐containing RNA. Nat. Methods 10: 1219–1224. https://doi.org/10.1038/nmeth.2701.

88 88 Tregubov, A.A., Nikitin, P.I., and Nikitin, M.P. (2018). Advanced smart nanomaterials with integrated logic‐gating and biocomputing: dawn of theranostic nanorobots. Chem. Rev. 118: 10294–10348. https://doi.org/10.1021/acs.chemrev.8b00198.

89 89 Chandler, M., Lyalina, T., Halman, J. et al. (2018). Broccoli fluorets: split aptamers as a user‐friendly fluorescent toolkit for dynamic RNA nanotechnology. Molecules 23 https://doi.org/10.3390/molecules23123178.

90 90 Kikuchi, N. and Kolpashchikov, D.M. (2016). Split spinach aptamer for highly selective recognition of DNA and RNA at ambient temperatures. ChemBioChem 17: 1589–1592. https://doi.org/10.1002/cbic.201600323.

91 91 Kikuchi, N. and Kolpashchikov, D.M. (2017). A universal split spinach aptamer (USSA) for nucleic acid analysis and DNA computation. Chem. Commun. (Camb) 53: 4977–4980. https://doi.org/10.1039/c7cc01540b.

92 92 Rogers, T.A., Andrews, G.E., Jaeger, L., and Grabow, W.W. (2015). Fluorescent monitoring of RNA assembly and processing using the split‐spinach aptamer. ACS Synth. Biol. 4: 162–166. https://doi.org/10.1021/sb5000725.

93 93 Alam, K.K., Tawiah, K.D., Lichte, M.F. et al. (2017). A fluorescent split aptamer for visualizing RNA‐RNA assembly in vivo. ACS Synth. Biol. 6: 1710–1721. https://doi.org/10.1021/acssynbio.7b00059.

DNA- and RNA-Based Computing Systems

Подняться наверх