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Current Medicinal Chemistry

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ISSN (Print): 0929-8673
ISSN (Online): 1875-533X

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Review Article

Modified Nucleotides for Chemical and Enzymatic Synthesis of Therapeutic RNA

Author(s): Anna Graczyk, Ewa Radzikowska-Cieciura, Renata Kaczmarek, Roza Pawlowska and Arkadiusz Chworos*

Volume 30, Issue 11, 2023

Published on: 13 December, 2022

Page: [1320 - 1347] Pages: 28

DOI: 10.2174/0929867330666221014111403

Price: $65

Abstract

In recent years, RNA has emerged as a medium with a broad spectrum of therapeutic potential, however, for years, a group of short RNA fragments was studied and considered therapeutic molecules. In nature, RNA plays both functions, with coding and non-coding potential. For RNA, like any other therapeutic, to be used clinically, certain barriers must be crossed. Among them, there are biocompatibility, relatively low toxicity, bioavailability, increased stability, target efficiency and low off-target effects. In the case of RNA, most of these obstacles can be overcome by incorporating modified nucleotides into its structure. This may be achieved by both, in vitro and in vivo biosynthetic methods, as well as chemical synthesis. Some advantages and disadvantages of each approach are summarized here. The wide range of nucleotide analogues has been tested for their utility as monomers for RNA synthesis. Many of them have been successfully implemented, and a lot of pre-clinical and clinical studies involving modified RNA have been carried out. Some of these medications have already been introduced into clinics. After the huge success of RNA-based vaccines that were introduced into widespread use in 2020, and the introduction to the market of some RNA-based drugs, RNA therapeutics containing modified nucleotides appear to be the future of medicine.

« Previous
[1]
Freier, S.M.; Kierzek, R.; Jaeger, J.A.; Sugimoto, N.; Caruthers, M.H.; Neilson, T.; Turner, D.H. Improved free-energy parameters for predictions of RNA duplex stability. Proc. Natl. Acad. Sci. USA, 1986, 83(24), 9373-9377.
[http://dx.doi.org/10.1073/pnas.83.24.9373] [PMID: 2432595]
[2]
Egli, M.; Portmann, S.; Usman, N. RNA hydration: A detailed look. Biochemistry, 1996, 35(26), 8489-8494.
[http://dx.doi.org/10.1021/bi9607214] [PMID: 8679609]
[3]
Rich, A.; Davies, D.R. A new two-stranded helical structure: Polyadenylic acid and polyuridylic acid. J. Am. Chem. Soc., 1956, 78(14), 3548-3549.
[http://dx.doi.org/10.1021/ja01595a086]
[4]
Rich, A. A hybrid helix containing both deoxyribose and ribose polynucleotides and its relation to the transfer of information between the nucleic acids. Proc. Natl. Acad. Sci. USA, 1960, 46(8), 1044-1053.
[http://dx.doi.org/10.1073/pnas.46.8.1044] [PMID: 16590711]
[5]
Holley, R.W.; Apgar, J.; Everett, G.A.; Madison, J.T.; Marquisee, M.; Merrill, S.H.; Penswick, J.R.; Zamir, A. Structure of a ribonucleic acid. Science, 1965, 147(3664), 1462-1465.
[http://dx.doi.org/10.1126/science.147.3664.1462] [PMID: 14263761]
[6]
Suwara, J.; Radzikowska-Cieciura, E.; Chworos, A.; Pawlowska, R. The ATP-dependent pathways and human diseases. Curr. Med. Chem., 2022.
[http://dx.doi.org/10.2174/0929867329666220322104552] [PMID: 35319356]
[7]
Kornberg, R.D. The molecular basis of eukaryotic transcription. Proc. Natl. Acad. Sci. USA, 2007, 104(32), 12955-12961.
[http://dx.doi.org/10.1073/pnas.0704138104] [PMID: 17670940]
[8]
Spencer, M. The stereochemistry of deoxyribonucleic acid. II. Hydrogen-bonded pairs of bases. Acta Crystallogr., 1959, 12(1), 66-71.
[http://dx.doi.org/10.1107/S0365110X59000160]
[9]
Hermann, T.; Westhof, E. Non-Watson-Crick base pairs in RNA-protein recognition. Chem. Biol., 1999, 6(12), R335-R343.
[http://dx.doi.org/10.1016/S1074-5521(00)80003-4] [PMID: 10631510]
[10]
Hendrix, D.K.; Brenner, S.E.; Holbrook, S.R. RNA structural motifs: Building blocks of a modular biomolecule. Q. Rev. Biophys., 2005, 38(3), 221-243.
[http://dx.doi.org/10.1017/S0033583506004215] [PMID: 16817983]
[11]
Woodson, S.A. Recent insights on RNA folding mechanisms from catalytic RNA. Cell. Mol. Life Sci., 2000, 57(5), 796-808.
[http://dx.doi.org/10.1007/s000180050042] [PMID: 10892344]
[12]
Butcher, S.E.; Pyle, A.M. The molecular interactions that stabilize RNA tertiary structure: RNA motifs, patterns, and networks. Acc. Chem. Res., 2011, 44(12), 1302-1311.
[http://dx.doi.org/10.1021/ar200098t] [PMID: 21899297]
[13]
McCloskey, J.A.; Nishimura, S. Modified nucleosides in transfer RNA. Acc. Chem. Res., 1977, 10(11), 403-410.
[http://dx.doi.org/10.1021/ar50119a004]
[14]
Suzuki, T. The expanding world of tRNA modifications and their disease relevance. Nat. Rev. Mol. Cell Biol., 2021, 22(6), 375-392.
[http://dx.doi.org/10.1038/s41580-021-00342-0] [PMID: 33658722]
[15]
Moras, D.; Comarmond, M.B.; Fischer, J.; Weiss, R.; Thierry, J.C.; Ebel, J.P.; Giegé, R. Crystal structure of yeast tRNAAsp. Nature, 1980, 288(5792), 669-674.
[http://dx.doi.org/10.1038/288669a0] [PMID: 7005687]
[16]
O’Donoghue, P.; Ling, J.; Söll, D. Transfer RNA function and evolution. RNA Biol., 2018, 15(4-5), 423-426.
[http://dx.doi.org/10.1080/15476286.2018.1478942] [PMID: 30099966]
[17]
Moore, P.B.; Steitz, T.A. The involvement of RNA in ribosome function. Nature, 2002, 418(6894), 229-235.
[http://dx.doi.org/10.1038/418229a] [PMID: 12110899]
[18]
Mei, Y.; Stonestrom, A.; Hou, Y.M.; Yang, X. Apoptotic regulation and tRNA. Protein Cell, 2010, 1(9), 795-801.
[http://dx.doi.org/10.1007/s13238-010-0107-x] [PMID: 21113408]
[19]
Pawlowska, R.; Janicka, M.; Jedrzejczyk, D.; Chworos, A. RNA fragments mimicking tRNA analogs interact with cytochrome c. Mol. Biol. Rep., 2016, 43(4), 295-304.
[http://dx.doi.org/10.1007/s11033-016-3954-6] [PMID: 26892782]
[20]
Consortium, E.P. An integrated encyclopedia of DNA elements in the human genome. Nature, 2012, 489(7414), 57-74.
[http://dx.doi.org/10.1038/nature11247] [PMID: 22955616]
[21]
Yao, R.W.; Wang, Y.; Chen, L.L. Cellular functions of long noncoding RNAs. Nat. Cell Biol., 2019, 21(5), 542-551.
[http://dx.doi.org/10.1038/s41556-019-0311-8] [PMID: 31048766]
[22]
Statello, L.; Guo, C.J.; Chen, L.L.; Huarte, M. Gene regulation by long non-coding RNAs and its biological functions. Nat. Rev. Mol. Cell Biol., 2021, 22(2), 96-118.
[http://dx.doi.org/10.1038/s41580-020-00315-9] [PMID: 33353982]
[23]
Ma, L.; Cao, J.; Liu, L.; Du, Q.; Li, Z.; Zou, D.; Bajic, V.B.; Zhang, Z. LncBook: A curated knowledgebase of human long non-coding RNAs. Nucleic Acids Res., 2019, 47(D1), D128-D134.
[http://dx.doi.org/10.1093/nar/gky960] [PMID: 30329098]
[24]
Carninci, P.; Kasukawa, T.; Katayama, S.; Gough, J.; Frith, M.C.; Maeda, N.; Oyama, R.; Ravasi, T.; Lenhard, B.; Wells, C.; Kodzius, R.; Shimokawa, K.; Bajic, V.B.; Brenner, S.E.; Batalov, S.; Forrest, A.R.R.; Zavolan, M.; Davis, M.J.; Wilming, L.G.; Aidinis, V.; Allen, J.E.; Ambesi-Impiombato, A.; Apweiler, R.; Aturaliya, R.N.; Bailey, T.L.; Bansal, M.; Baxter, L.; Beisel, K.W.; Bersano, T.; Bono, H.; Chalk, A.M.; Chiu, K.P.; Choudhary, V.; Christoffels, A.; Clutterbuck, D.R.; Crowe, M.L.; Dalla, E.; Dalrymple, B.P.; de Bono, B.; Gatta, G.D.; di Bernardo, D.; Down, T.; Engstrom, P.; Fagiolini, M.; Faulkner, G.; Fletcher, C.F.; Fukushima, T.; Furuno, M.; Futaki, S.; Gariboldi, M.; Georgii-Hemming, P.; Gingeras, T.R.; Gojobori, T.; Green, R.E.; Gustincich, S.; Harbers, M.; Hayashi, Y.; Hensch, T.K.; Hirokawa, N.; Hill, D.; Huminiecki, L.; Iacono, M.; Ikeo, K.; Iwama, A.; Ishikawa, T.; Jakt, M.; Kanapin, A.; Katoh, M.; Kawasawa, Y.; Kelso, J.; Kitamura, H.; Kitano, H.; Kollias, G.; Krishnan, S.P.T.; Kruger, A.; Kummerfeld, S.K.; Kurochkin, I.V.; Lareau, L.F.; Lazarevic, D.; Lipovich, L.; Liu, J.; Liuni, S.; McWilliam, S.; Babu, M.M.; Madera, M.; Marchionni, L.; Matsuda, H.; Matsuzawa, S.; Miki, H.; Mignone, F.; Miyake, S.; Morris, K.; Mottagui-Tabar, S.; Mulder, N.; Nakano, N.; Nakauchi, H.; Ng, P.; Nilsson, R.; Nishiguchi, S.; Nishikawa, S.; Nori, F.; Ohara, O.; Okazaki, Y.; Orlando, V.; Pang, K.C.; Pavan, W.J.; Pavesi, G.; Pesole, G.; Petrovsky, N.; Piazza, S.; Reed, J.; Reid, J.F.; Ring, B.Z.; Ringwald, M.; Rost, B.; Ruan, Y.; Salzberg, S.L.; Sandelin, A.; Schneider, C.; Schönbach, C.; Sekiguchi, K.; Semple, C.A.M.; Seno, S.; Sessa, L.; Sheng, Y.; Shibata, Y.; Shimada, H.; Shimada, K.; Silva, D.; Sinclair, B.; Sperling, S.; Stupka, E.; Sugiura, K.; Sultana, R.; Takenaka, Y.; Taki, K.; Tammoja, K.; Tan, S.L.; Tang, S.; Taylor, M.S.; Tegner, J.; Teichmann, S.A.; Ueda, H.R.; van Nimwegen, E.; Verardo, R.; Wei, C.L.; Yagi, K.; Yamanishi, H.; Zabarovsky, E.; Zhu, S.; Zimmer, A.; Hide, W.; Bult, C.; Grimmond, S.M.; Teasdale, R.D.; Liu, E.T.; Brusic, V.; Quackenbush, J.; Wahlestedt, C.; Mattick, J.S.; Hume, D.A.; Kai, C.; Sasaki, D.; Tomaru, Y.; Fukuda, S.; Kanamori-Katayama, M.; Suzuki, M.; Aoki, J.; Arakawa, T.; Iida, J.; Imamura, K.; Itoh, M.; Kato, T.; Kawaji, H.; Kawagashira, N.; Kawashima, T.; Kojima, M.; Kondo, S.; Konno, H.; Nakano, K.; Ninomiya, N.; Nishio, T.; Okada, M.; Plessy, C.; Shibata, K.; Shiraki, T.; Suzuki, S.; Tagami, M.; Waki, K.; Watahiki, A.; Okamura-Oho, Y.; Suzuki, H.; Kawai, J.; Hayashizaki, Y. The transcriptional landscape of the mammalian genome. Science, 2005, 309(5740), 1559-1563.
[http://dx.doi.org/10.1126/science.1112014] [PMID: 16141072]
[25]
Ravasi, T.; Suzuki, H.; Pang, K.C.; Katayama, S.; Furuno, M.; Okunishi, R.; Fukuda, S.; Ru, K.; Frith, M.C.; Gongora, M.M.; Grimmond, S.M.; Hume, D.A.; Hayashizaki, Y.; Mattick, J.S. Experimental validation of the regulated expression of large numbers of non-coding RNAs from the mouse genome. Genome Res., 2006, 16(1), 11-19.
[http://dx.doi.org/10.1101/gr.4200206] [PMID: 16344565]
[26]
Morceau, F.; Chateauvieux, S.; Gaigneaux, A.; Dicato, M.; Diederich, M. Long and short non-coding RNAs as regulators of hematopoietic differentiation. Int. J. Mol. Sci., 2013, 14(7), 14744-14770.
[http://dx.doi.org/10.3390/ijms140714744] [PMID: 23860209]
[27]
Matera, A.G.; Terns, R.M.; Terns, M.P. Non-coding RNAs: Lessons from the small nuclear and small nucleolar RNAs. Nat. Rev. Mol. Cell Biol., 2007, 8(3), 209-220.
[http://dx.doi.org/10.1038/nrm2124] [PMID: 17318225]
[28]
Wightman, B.; Ha, I.; Ruvkun, G. Posttranscriptional regulation of the heterochronic gene lin-14 by lin-4 mediates temporal pattern formation in C. elegans. Cell, 1993, 75(5), 855-862.
[http://dx.doi.org/10.1016/0092-8674(93)90530-4] [PMID: 8252622]
[29]
Fire, A.; Xu, S.; Montgomery, M.K.; Kostas, S.A.; Driver, S.E.; Mello, C.C. Potent and specific genetic interference by double-stranded RNA in Caenorhabditis elegans. Nature, 1998, 391(6669), 806-811.
[http://dx.doi.org/10.1038/35888] [PMID: 9486653]
[30]
Hammond, S.M. An overview of microRNAs. Adv. Drug Deliv. Rev., 2015, 87, 3-14.
[http://dx.doi.org/10.1016/j.addr.2015.05.001] [PMID: 25979468]
[31]
Drak Alsibai, K.; Meseure, D. Tumor microenvironment and noncoding RNAs as co-drivers of epithelial-mesenchymal transition and cancer metastasis. Dev. Dyn., 2018, 247(3), 405-431.
[http://dx.doi.org/10.1002/dvdy.24548] [PMID: 28691356]
[32]
Erdmann, V.A.; Barciszewski, J. DNA and RNA Nanobiotechnologies in Medicine: Diagnosis and Treatment of Diseases; Springer Berlin, Heidelberg, 2013.
[http://dx.doi.org/10.1007/978-3-642-36853-0]
[33]
Carthew, R.W.; Sontheimer, E.J. Origins and mechanisms of miRNAs and siRNAs. Cell, 2009, 136(4), 642-655.
[http://dx.doi.org/10.1016/j.cell.2009.01.035] [PMID: 19239886]
[34]
Tomari, Y.; Zamore, P.D. Perspective: Machines for RNAi. Genes Dev., 2005, 19(5), 517-529.
[http://dx.doi.org/10.1101/gad.1284105] [PMID: 15741316]
[35]
Ozata, D.M.; Gainetdinov, I.; Zoch, A.; O’Carroll, D.; Zamore, P.D. PIWI-interacting RNAs: Small RNAs with big functions. Nat. Rev. Genet., 2019, 20(2), 89-108.
[http://dx.doi.org/10.1038/s41576-018-0073-3] [PMID: 30446728]
[36]
Seto, A.G.; Kingston, R.E.; Lau, N.C. The coming of age for Piwi proteins. Mol. Cell, 2007, 26(5), 603-609.
[http://dx.doi.org/10.1016/j.molcel.2007.05.021] [PMID: 17560367]
[37]
Duss, O.; Lukavsky, P.J.; Allain, F.H.T. Isotope labeling and segmental labeling of larger RNAs for NMR structural studies. Adv. Exp. Med. Biol., 2012, 992, 121-144.
[http://dx.doi.org/10.1007/978-94-007-4954-2_7] [PMID: 23076582]
[38]
Lodish, H.B.A.; Zipursky, S.L. Molecular Cell Biology, 4th ed; W.H. Freeman: New York, USA, 2000.
[39]
James, D. Richard Losick Molecular Biology of the Gene; Pearson: London, UK, 2013.
[40]
von Hippel, P.H. An integrated model of the transcription complex in elongation, termination, and editing. Science, 1998, 281(5377), 660-665.
[http://dx.doi.org/10.1126/science.281.5377.660] [PMID: 9685251]
[41]
Sanchez-Garcia, L.; Martín, L.; Mangues, R.; Ferrer-Miralles, N.; Vázquez, E.; Villaverde, A. Recombinant pharmaceuticals from microbial cells: A 2015 update. Microb. Cell Fact., 2016, 15(1), 33.
[http://dx.doi.org/10.1186/s12934-016-0437-3] [PMID: 26861699]
[42]
Rosano, G.L.; Ceccarelli, E.A. Recombinant protein expression in Escherichia coli: Advances and challenges. Front. Microbiol., 2014, 5, 172.
[http://dx.doi.org/10.3389/fmicb.2014.00172] [PMID: 24860555]
[43]
Meinnel, T.; Mechulam, Y.; Fayat, G. Fast purification of a functional elongator tRNA met expressed from a synthetic gene in vivo. Nucleic Acids Res., 1988, 16(16), 8095-8112.
[http://dx.doi.org/10.1093/nar/16.16.8095] [PMID: 3419903]
[44]
Moore, P.B.; Abo, S.; Freeborn, B.; Gewirth, D.T.; Leontis, N.B.; Sun, G. Preparation of 5S RNA-related materials for nuclear magnetic resonance and crystallography studies. Methods Enzymol., 1988, 164, 158-174.
[http://dx.doi.org/10.1016/S0076-6879(88)64041-9] [PMID: 3071660]
[45]
Perona, J.J.; Swanson, R.; Steitz, T.A.; Söll, D. Overproduction and purification of Escherichia coli tRNAGln2 and its use in crystallization of the glutaminyl-tRNA synthetase-tRNAGln complex. J. Mol. Biol., 1988, 202(1), 121-126.
[http://dx.doi.org/10.1016/0022-2836(88)90524-4] [PMID: 2459391]
[46]
Ponchon, L.; Dardel, F. Recombinant RNA technology: The tRNA scaffold. Nat. Methods, 2007, 4(7), 571-576.
[http://dx.doi.org/10.1038/nmeth1058] [PMID: 17558412]
[47]
Ponchon, L.; Beauvais, G.; Nonin-Lecomte, S.; Dardel, F. A generic protocol for the expression and purification of recombinant RNA in Escherichia coli using a tRNA scaffold. Nat. Protoc., 2009, 4(6), 947-959.
[http://dx.doi.org/10.1038/nprot.2009.67] [PMID: 19478810]
[48]
Zhang, X.; Potty, A.S.R.; Jackson, G.W.; Stepanov, V.; Tang, A.; Liu, Y.; Kourentzi, K.; Strych, U.; Fox, G.E.; Willson, R.C. Engineered 5S ribosomal RNAs displaying aptamers recognizing vascular endothelial growth factor and malachite green. J. Mol. Recognit., 2009, 22(2), 154-161.
[http://dx.doi.org/10.1002/jmr.917] [PMID: 19195013]
[49]
Srisawat, C.; Engelke, D.R. Streptavidin aptamers: Affinity tags for the study of RNAs and ribonucleoproteins. RNA, 2001, 7(4), 632-641.
[http://dx.doi.org/10.1017/S135583820100245X] [PMID: 11345441]
[50]
Yerramilli, V.S.; Kim, K.H. Labeling RNAs in live cells using malachite green aptamer scaffolds as fluorescent probes. ACS Synth. Biol., 2018, 7(3), 758-766.
[http://dx.doi.org/10.1021/acssynbio.7b00237] [PMID: 29513000]
[51]
Grate, D.; Wilson, C. Laser-mediated, site-specific inactivation of RNA transcripts. Proc. Natl. Acad. Sci. USA, 1999, 96(11), 6131-6136.
[http://dx.doi.org/10.1073/pnas.96.11.6131] [PMID: 10339553]
[52]
Shields, T.P.; Mollova, E.; Marie, L.S.; Hansen, M.R.; Pardi, A. High-performance liquid chromatography purification of homogenous-length RNA produced by trans cleavage with a hammerhead ribozyme. RNA, 1999, 5(9), 1259-1267.
[http://dx.doi.org/10.1017/S1355838299990945] [PMID: 10496226]
[53]
Avis, J.M.; Conn, G.L.; Walker, S.C. Cis-acting ribozymes for the production of RNA in vitro transcripts with defined 5′ and 3′ ends. Methods Mol. Biol., 2013, 941, 83-98.
[http://dx.doi.org/10.1007/978-1-62703-113-4_7] [PMID: 23065555]
[54]
Paillart, J.C.; Skripkin, E.; Ehresmann, B.; Ehresmann, C.; Marquet, R. A loop-loop “kissing” complex is the essential part of the dimer linkage of genomic HIV-1 RNA. Proc. Natl. Acad. Sci. USA, 1996, 93(11), 5572-5577.
[http://dx.doi.org/10.1073/pnas.93.11.5572] [PMID: 8643617]
[55]
Tisné, C.; Rigourd, M.; Marquet, R.; Ehresmann, C.; Dardel, F. NMR and biochemical characterization of recombinant human tRNA3 Lys expressed in Escherichia coli: Identification of posttranscriptional nucleotide modifications required for efficient initiation of HIV-1 reverse transcription. RNA, 2000, 6(10), 1403-1412.
[http://dx.doi.org/10.1017/S1355838200000947] [PMID: 11073216]
[56]
Lu, K.; Miyazaki, Y.; Summers, M.F. Isotope labeling strategies for NMR studies of RNA. J. Biomol. NMR, 2010, 46(1), 113-125.
[http://dx.doi.org/10.1007/s10858-009-9375-2] [PMID: 19789981]
[57]
Nelissen, F.H.T.; Leunissen, E.H.P.; van de Laar, L.; Tessari, M.; Heus, H.A.; Wijmenga, S.S. Fast production of homogeneous recombinant RNA-towards large-scale production of RNA. Nucleic Acids Res., 2012, 40(13), e102.
[http://dx.doi.org/10.1093/nar/gks292] [PMID: 22457065]
[58]
Umekage, S.; Kikuchi, Y. In vitro and in vivo production and purification of circular RNA aptamer. J. Biotechnol., 2009, 139(4), 265-272.
[http://dx.doi.org/10.1016/j.jbiotec.2008.12.012] [PMID: 19138712]
[59]
Petkovic, S.; Müller, S. RNA circularization strategies in vivo and in vitro. Nucleic Acids Res., 2015, 43(4), 2454-2465.
[http://dx.doi.org/10.1093/nar/gkv045] [PMID: 25662225]
[60]
Noto, J.J.; Schmidt, C.A.; Matera, A.G. Engineering and expressing circular RNAs via tRNA splicing. RNA Biol., 2017, 14(8), 978-984.
[http://dx.doi.org/10.1080/15476286.2017.1317911] [PMID: 28402213]
[61]
Schmidt, C.A.; Noto, J.J.; Filonov, G.S.; Matera, A.G. A Method for expressing and imaging abundant, stable, circular rnas in vivo using tRNA splicing. Methods Enzymol., 2016, 572, 215-236.
[http://dx.doi.org/10.1016/bs.mie.2016.02.018] [PMID: 27241756]
[62]
Baronti, L.; Karlsson, H.; Marušič, M.; Petzold, K. A guide to large-scale RNA sample preparation. Anal. Bioanal. Chem., 2018, 410(14), 3239-3252.
[http://dx.doi.org/10.1007/s00216-018-0943-8] [PMID: 29546546]
[63]
Chen, Z.; Schneider, T.D. Information theory based T7- like promoter models: Classification of bacteriophages and differential evolution of promoters and their polymerases. Nucleic Acids Res., 2005, 33(19), 6172-6187.
[http://dx.doi.org/10.1093/nar/gki915] [PMID: 16260472]
[64]
Pokrovskaya, I.D.; Gurevich, V.V. In vitro transcription: Preparative RNA yields in analytical scale reactions. Anal. Biochem., 1994, 220(2), 420-423.
[http://dx.doi.org/10.1006/abio.1994.1360] [PMID: 7526740]
[65]
Yang, H.; Ma, Y.; Wang, Y.; Yang, H.; Shen, W.; Chen, X. Transcription regulation mechanisms of bacteriophages. Bioengineered, 2014, 5(5), 300-304.
[http://dx.doi.org/10.4161/bioe.32110] [PMID: 25482231]
[66]
Beckert, B.; Masquida, B. Synthesis of RNA by in vitro transcription. Methods Mol. Biol., 2011, 703, 29-41.
[http://dx.doi.org/10.1007/978-1-59745-248-9_3] [PMID: 21125481]
[67]
Mcallister, W.T.; Küpper, H.; Bautz, E.K.F. Kinetics of transcription by the bacteriophage-T3 RNA polymerase in vitro. Eur. J. Biochem., 1973, 34(3), 489-501.
[http://dx.doi.org/10.1111/j.1432-1033.1973.tb02785.x] [PMID: 4577197]
[68]
Steinberger, J.; Shen, L.; J Kiniry, S.; Naineni, S.K.; Cencic, R.; Amiri, M.; Aboushawareb, S.A.E.; Chu, J.; Maïga, R.I.; Yachnin, B.J.; Robert, F.; Sonenberg, N.; Baranov, P.V.; Pelletier, J. Identification and characterization of hippuristanol-resistant mutants reveals eIF4A1 dependencies within mRNA 5′ leader regions. Nucleic Acids Res., 2020, 48(17), 9521-9537.
[http://dx.doi.org/10.1093/nar/gkaa662] [PMID: 32766783]
[69]
Zhang, F.; Hao, Y.; Li, X.; Li, Y.; Ye, D.; Zhang, R.; Wang, X.; He, M.; Wang, H.; Zhu, Z. Surrogate production of genome-edited sperm from a different subfamily by spermatogonial stem cell transplantation. Sci. China Life Sci., 2021, 65(5), 969-987.
[PMID: 34586576]
[70]
Krieg, P.A.; Melton, D.A. In vitro RNA synthesis with SP6 RNA polymerase. Methods Enzymol., 1987, 155, 397-415.
[http://dx.doi.org/10.1016/0076-6879(87)55027-3] [PMID: 2828872]
[71]
Stump, W.T.; Hall, K.B. SP6 RNA polymerase efficiently synthesizes RNA from short double-stranded DNA templates. Nucleic Acids Res., 1993, 21(23), 5480-5484.
[http://dx.doi.org/10.1093/nar/21.23.5480] [PMID: 7505427]
[72]
Taylor, D.R.; Mathews, M.B. Transcription by SP6 RNA polymerase exhibits an ATP dependence that is influenced by promoter topology. Nucleic Acids Res., 1993, 21(8), 1927-1933.
[http://dx.doi.org/10.1093/nar/21.8.1927] [PMID: 8493106]
[73]
Chamberlin, M.; McGrath, J.; Waskell, L. New RNA polymerase from Escherichia coli infected with bacteriophage T7. Nature, 1970, 228(5268), 227-231.
[http://dx.doi.org/10.1038/228227a0] [PMID: 4920917]
[74]
Davanloo, P.; Rosenberg, A.H.; Dunn, J.J.; Studier, F.W. Cloning and expression of the gene for bacteriophage T7 RNA polymerase. Proc. Natl. Acad. Sci. USA, 1984, 81(7), 2035-2039.
[http://dx.doi.org/10.1073/pnas.81.7.2035] [PMID: 6371808]
[75]
Wang, W.; Li, Y.; Wang, Y.; Shi, C.; Li, C.; Li, Q.; Linhardt, R.J. Bacteriophage T7 transcription system: An enabling tool in synthetic biology. Biotechnol. Adv., 2018, 36(8), 2129-2137.
[http://dx.doi.org/10.1016/j.biotechadv.2018.10.001] [PMID: 30290194]
[76]
Gallo, S.; Furler, M.; Sigel, R.K.O. In vitro transcription and purification of RNAs of different size. Chimia (Aarau), 2005, 59(11), 812-816.
[http://dx.doi.org/10.2533/000942905777675589]
[77]
Milligan, J.F.; Uhlenbeck, O.C. Synthesis of small RNAs using T7 RNA polymerase. Methods Enzymol., 1989, 180, 51-62.
[http://dx.doi.org/10.1016/0076-6879(89)80091-6] [PMID: 2482430]
[78]
Milligan, J.F.; Groebe, D.R.; Witherell, G.W.; Uhlenbeck, O.C. Oligoribonucleotide synthesis using T7 RNA polymerase and synthetic DNA templates. Nucleic Acids Res., 1987, 15(21), 8783-8798.
[http://dx.doi.org/10.1093/nar/15.21.8783] [PMID: 3684574]
[79]
Chen, Z.; Zhang, Y. Dimethyl sulfoxide targets phage RNA polymerases to promote transcription. Biochem. Biophys. Res. Commun., 2005, 333(3), 664-670.
[http://dx.doi.org/10.1016/j.bbrc.2005.05.166] [PMID: 15975554]
[80]
Kao, C.; Zheng, M.; Rüdisser, S. A simple and efficient method to reduce nontemplated nucleotide addition at the 3′ terminus of RNAs transcribed by T7 RNA polymerase. RNA, 1999, 5(9), 1268-1272.
[http://dx.doi.org/10.1017/S1355838299991033] [PMID: 10496227]
[81]
Helmling, C.; Keyhani, S.; Sochor, F.; Fürtig, B.; Hengesbach, M.; Schwalbe, H. Rapid NMR screening of RNA secondary structure and binding. J. Biomol. NMR, 2015, 63(1), 67-76.
[http://dx.doi.org/10.1007/s10858-015-9967-y] [PMID: 26188386]
[82]
Lapham, J.; Crothers, D.M. RNase H cleavage for processing of in vitro transcribed RNA for NMR studies and RNA ligation. RNA, 1996, 2(3), 289-296.
[PMID: 8608452]
[83]
Ferré-D’Amaré, A.R.; Doudna, J.A. Use of cis- and trans-ribozymes to remove 5′ and 3′ heterogeneities from milligrams of in vitro transcribed RNA. Nucleic Acids Res., 1996, 24(5), 977-978.
[http://dx.doi.org/10.1093/nar/24.5.977] [PMID: 8600468]
[84]
Das, U.; Shuman, S. Mechanism of RNA 2′,3′-cyclic phosphate end healing by T4 polynucleotide kinase–phosphatase. Nucleic Acids Res., 2013, 41(1), 355-365.
[http://dx.doi.org/10.1093/nar/gks977] [PMID: 23118482]
[85]
Easton, L.E.; Shibata, Y.; Lukavsky, P.J. Rapid, nondenaturing RNA purification using weak anion-exchange fast performance liquid chromatography. RNA, 2010, 16(3), 647-653.
[http://dx.doi.org/10.1261/rna.1862210] [PMID: 20100812]
[86]
Zhang, Q.; Lv, H.; Wang, L.; Chen, M.; Li, F.; Liang, C.; Yu, Y.; Jiang, F.; Lu, A.; Zhang, G. Recent methods for purification and structure determination of oligonucleotides. Int. J. Mol. Sci., 2016, 17(12), 2134.
[http://dx.doi.org/10.3390/ijms17122134] [PMID: 27999357]
[87]
Vaught, J.D.; Dewey, T.; Eaton, B.E. T7 RNA polymerase transcription with 5-position modified UTP derivatives. J. Am. Chem. Soc., 2004, 126(36), 11231-11237.
[http://dx.doi.org/10.1021/ja049009h] [PMID: 15355104]
[88]
Baladi, T.; Nilsson, J.R.; Gallud, A.; Celauro, E.; Gasse, C.; Levi-Acobas, F.; Sarac, I.; Hollenstein, M.R.; Dahlén, A.; Esbjörner, E.K.; Wilhelmsson, L.M. Stealth fluorescence labeling for live microscopy imaging of mRNA delivery. J. Am. Chem. Soc., 2021, 143(14), 5413-5424.
[http://dx.doi.org/10.1021/jacs.1c00014] [PMID: 33797236]
[89]
Milisavljevič, N.; Perlíková, P.; Pohl, R.; Hocek, M. Enzymatic synthesis of base-modified RNA by T7 RNA polymerase. A systematic study and comparison of 5-substituted pyrimidine and 7-substituted 7-deazapurine nucleoside triphosphates as substrates. Org. Biomol. Chem., 2018, 16(32), 5800-5807.
[http://dx.doi.org/10.1039/C8OB01498A] [PMID: 30063056]
[90]
Bornewasser, L.; Domnick, C.; Kath-Schorr, S. Stronger together for in-cell translation: Natural and unnatural base modified mRNA. RSC Chem. Sci, 2022, 13(17), 4753-4761.
[91]
Chelliserrykattil, J.; Ellington, A.D. Evolution of a T7 RNA polymerase variant that transcribes 2′-O-methyl RNA. Nat. Biotechnol., 2004, 22(9), 1155-1160.
[http://dx.doi.org/10.1038/nbt1001] [PMID: 15300257]
[92]
Ibach, J.; Dietrich, L.; Koopmans, K.R.M.; Nöbel, N.; Skoupi, M.; Brakmann, S. Identification of a T7 RNA polymerase variant that permits the enzymatic synthesis of fully 2′-O-methyl-modified RNA. J. Biotechnol., 2013, 167(3), 287-295.
[http://dx.doi.org/10.1016/j.jbiotec.2013.07.005] [PMID: 23871655]
[93]
Zhu, B.; Hernandez, A.; Tan, M.; Wollenhaupt, J.; Tabor, S.; Richardson, C.C. Synthesis of 2′-Fluoro RNA by Syn5 RNA polymerase. Nucleic Acids Res., 2015, 43(14), e94.
[http://dx.doi.org/10.1093/nar/gkv367] [PMID: 25897116]
[94]
Meyer, A.J.; Garry, D.J.; Hall, B.; Byrom, M.M.; McDonald, H.G.; Yang, X.; Yin, Y.W.; Ellington, A.D. Transcription yield of fully 2′-modified RNA can be increased by the addition of thermostabilizing mutations to T7 RNA polymerase mutants. Nucleic Acids Res., 2015, 43(15), 7480-7488.
[http://dx.doi.org/10.1093/nar/gkv734] [PMID: 26209133]
[95]
Ohashi, S.; Hashiya, F.; Abe, H. Variety of nucleotide polymerase mutants aiming to synthesize modified RNA. ChemBioChem, 2021, 22(14), 2398-2406.
[http://dx.doi.org/10.1002/cbic.202100004] [PMID: 33822453]
[96]
Pardi, N.; Hogan, M.J.; Porter, F.W.; Weissman, D. mRNA vaccines - a new era in vaccinology. Nat. Rev. Drug Discov., 2018, 17(4), 261-279.
[http://dx.doi.org/10.1038/nrd.2017.243] [PMID: 29326426]
[97]
Nance, K.D.; Meier, J.L. Modifications in an emergency: The Role of n1-methylpseudouridine in COVID-19 vaccines. ACS Cent. Sci., 2021, 7(5), 748-756.
[http://dx.doi.org/10.1021/acscentsci.1c00197] [PMID: 34075344]
[98]
Corbett, K.S.; Edwards, D.K.; Leist, S.R.; Abiona, O.M.; Boyoglu-Barnum, S.; Gillespie, R.A.; Himansu, S.; Schäfer, A.; Ziwawo, C.T.; DiPiazza, A.T.; Dinnon, K.H.; Elbashir, S.M.; Shaw, C.A.; Woods, A.; Fritch, E.J.; Martinez, D.R.; Bock, K.W.; Minai, M.; Nagata, B.M.; Hutchinson, G.B.; Wu, K.; Henry, C.; Bahl, K.; Garcia-Dominguez, D.; Ma, L.; Renzi, I.; Kong, W.P.; Schmidt, S.D.; Wang, L.; Zhang, Y.; Phung, E.; Chang, L.A.; Loomis, R.J.; Altaras, N.E.; Narayanan, E.; Metkar, M.; Presnyak, V.; Liu, C.; Louder, M.K.; Shi, W.; Leung, K.; Yang, E.S.; West, A.; Gully, K.L.; Stevens, L.J.; Wang, N.; Wrapp, D.; Doria-Rose, N.A.; Stewart-Jones, G.; Bennett, H.; Alvarado, G.S.; Nason, M.C.; Ruckwardt, T.J.; McLellan, J.S.; Denison, M.R.; Chappell, J.D.; Moore, I.N.; Morabito, K.M.; Mascola, J.R.; Baric, R.S.; Carfi, A.; Graham, B.S. SARS-CoV-2 mRNA vaccine design enabled by prototype pathogen preparedness. Nature, 2020, 586(7830), 567-571.
[http://dx.doi.org/10.1038/s41586-020-2622-0] [PMID: 32756549]
[99]
Liu, Y.; Holmstrom, E.; Zhang, J.; Yu, P.; Wang, J.; Dyba, M.A.; De Chen; Ying, J.; Lockett, S.; Nesbitt, D.J.; Ferré-D’Amaré, A.R.; Sousa, R.; Stagno, J.R.; Wang, Y.X. Synthesis and applications of RNAs with position-selective labelling and mosaic composition. Nature, 2015, 522(7556), 368-372.
[http://dx.doi.org/10.1038/nature14352] [PMID: 25938715]
[100]
Xia, G.; Chen, L.; Sera, T.; Fa, M.; Schultz, P.G.; Romesberg, F.E. Directed evolution of novel polymerase activities: Mutation of a DNA polymerase into an efficient RNA polymerase. Proc. Natl. Acad. Sci. USA, 2002, 99(10), 6597-6602.
[http://dx.doi.org/10.1073/pnas.102577799] [PMID: 12011423]
[101]
Ong, J.L.; Loakes, D.; Jaroslawski, S.; Too, K.; Holliger, P. Directed evolution of DNA polymerase, RNA polymerase and reverse transcriptase activity in a single polypeptide. J. Mol. Biol., 2006, 361(3), 537-550.
[http://dx.doi.org/10.1016/j.jmb.2006.06.050] [PMID: 16859707]
[102]
Chen, T.; Romesberg, F.E. Polymerase chain transcription: Exponential synthesis of RNA and modified RNA. J. Am. Chem. Soc., 2017, 139(29), 9949-9954.
[http://dx.doi.org/10.1021/jacs.7b03981] [PMID: 28715205]
[103]
Laos, R.; Thomson, J.M.; Benner, S.A. DNA polymerases engineered by directed evolution to incorporate non-standard nucleotides. Front. Microbiol., 2014, 5, 565.
[http://dx.doi.org/10.3389/fmicb.2014.00565] [PMID: 25400626]
[104]
Weimann, B.J.; Lohrmann, R.; Orgel, L.E.; Schneider-Bernloehr, H.; Sulston, J.E. Template-directed synthesis with adenosine-5′-phosphorimidazolide. Science, 1968, 161(3839), 387.
[http://dx.doi.org/10.1126/science.161.3839.387] [PMID: 5661298]
[105]
Orgel, L.E. Molecular replication. Nature, 1992, 358(6383), 203-209.
[http://dx.doi.org/10.1038/358203a0] [PMID: 1630488]
[106]
Leslie E, O. Prebiotic chemistry and the origin of the RNA world. Crit. Rev. Biochem. Mol. Biol., 2004, 39(2), 99-123.
[http://dx.doi.org/10.1080/10409230490460765] [PMID: 15217990]
[107]
Zhang, W.; Pal, A.; Ricardo, A.; Szostak, J.W. Template-directed nonenzymatic primer extension using 2-methylimidazole-activated morpholino derivatives of guanosine and cytidine. J. Am. Chem. Soc., 2019, 141(30), 12159-12166.
[http://dx.doi.org/10.1021/jacs.9b06453] [PMID: 31298852]
[108]
Kim, S.C.; O’Flaherty, D.K.; Giurgiu, C.; Zhou, L.; Szostak, J.W. The emergence of RNA from the heterogeneous products of prebiotic nucleotide synthesis. J. Am. Chem. Soc., 2021, 143(9), 3267-3279.
[http://dx.doi.org/10.1021/jacs.0c12955] [PMID: 33636080]
[109]
Depmeier, H.; Hoffmann, E.; Bornewasser, L.; Kath-Schorr, S. Strategies for covalent labeling of long RNAs. ChemBioChem, 2021, 22(19), 2826-2847.
[http://dx.doi.org/10.1002/cbic.202100161] [PMID: 34043861]
[110]
Beaucage, S.L. Solid-phase synthesis of siRNA oligonucleotides. Curr. Opin. Drug Discov. Devel., 2008, 11(2), 203-216.
[PMID: 18283608]
[111]
Beaucage, S.L.; Reese, C.B. Recent advances in the chemical synthesis of RNA. Curr. Protoc. Nucleic Acid Chem., 2009, 2, Unit 2.16 1-31.
[http://dx.doi.org/10.1002/0471142700.nc0216s38]
[112]
Semenyuk, A.; Földesi, A.; Johansson, T.; Estmer-Nilsson, C.; Blomgren, P.; Brännvall, M.; Kirsebom, L.A.; Kwiatkowski, M. Synthesis of RNA using 2′-O-DTM protection. J. Am. Chem. Soc., 2006, 128(38), 12356-12357.
[http://dx.doi.org/10.1021/ja0636587] [PMID: 16984152]
[113]
Obika, S.; Sekine, M. Synthesis of therapeutic oligonucleotides; Elsevier: Amsterdam, 2018.
[http://dx.doi.org/10.1007/978-981-13-1912-9]
[114]
Germer, K.; Leonard, M.; Zhang, X. RNA aptamers and their therapeutic and diagnostic applications. Int. J. Biochem. Mol. Biol., 2013, 4(1), 27-40.
[PMID: 23638319]
[115]
Dana, H.; Chalbatani, G.M.; Mahmoodzadeh, H.; Karimloo, R.; Rezaiean, O.; Moradzadeh, A.; Mehmandoost, N.; Moazzen, F.; Mazraeh, A.; Marmari, V.; Ebrahimi, M.; Rashno, M.M.; Abadi, S.J.; Gharagouzlo, E. Molecular mechanisms and biological functions of siRNA. Int. J. Biomed. Sci., 2017, 13(2), 48-57.
[PMID: 28824341]
[116]
Hu, B.; Zhong, L.P.; Weng, Y.H.; Peng, L.; Huang, Y.Y.; Zhao, Y.X.; Liang, X.J. Therapeutic siRNA: State of the art. Signal. Transduct. Tar., 2020, 5(1), 101.
[117]
Beaucage, S.L.; Caruthers, M.H. Deoxynucleoside phosphoramidites-A new class of key intermediates for deoxypolynucleotide synthesis. Tetrahedron Lett., 1981, 22(20), 1859-1862.
[http://dx.doi.org/10.1016/S0040-4039(01)90461-7]
[118]
Letsinger, R.L.; Caruthers, M.H.; Jerina, D.M. Reactions of nucleosides on polymer supports. Synthesis of thymidylylthymidylylthymidine. Biochemistry, 1967, 6(5), 1379-1388.
[http://dx.doi.org/10.1021/bi00857a021] [PMID: 6036831]
[119]
Letsinger, R.L.; Caruthers, M.H.; Miller, P.S.; Ogilvie, K.K. Oligonucleotide syntheses utilizing beta benzoylpropionyl, a blocking group with a trigger for selective cleavage. J. Am. Chem. Soc., 1967, 89(26), 7146-7147.
[http://dx.doi.org/10.1021/ja01002a074] [PMID: 6064358]
[120]
Rublack, N.; Nguyen, H.; Appel, B.; Springstubbe, D.; Strohbach, D.; Müller, S. Synthesis of specifically modified oligonucleotides for application in structural and functional analysis of RNA. J. Nucleic Acids, 2011, 2011, 1-19.
[http://dx.doi.org/10.4061/2011/805253] [PMID: 22013508]
[121]
Baevcage SL. Current Protocols in Nucleic Acid Chemistry; Wiley: USA, 2022.
[122]
Letsinger, R.L.; Mahadevan, V. Oligonucleotide synthesis on a polymer support1,2. J. Am. Chem. Soc., 1965, 87(15), 3526-3527.
[http://dx.doi.org/10.1021/ja01093a058] [PMID: 14322545]
[123]
Matteucci, M.D.; Caruthers, M.H. Synthesis of deoxyoligonucleotides on a polymer support. Biotechnology, 1992, 24, 92-98.
[PMID: 1422073]
[124]
Breslow, R. Kinetics and mechanism in RNA cleavage. Proc. Natl. Acad. Sci. USA, 1993, 90(4), 1208-1211.
[http://dx.doi.org/10.1073/pnas.90.4.1208] [PMID: 7679493]
[125]
Hakimelahi, G.H.; Proba, Z.A.; Ogilvie, K.K. New catalysts and procedures for the dimethoxytritylation and selective silylation of ribonucleosides. Can. J. Chem., 1982, 60(9), 1106-1113.
[http://dx.doi.org/10.1139/v82-165]
[126]
Scaringe, S.A.; Wincott, F.E.; Caruthers, M.H. Novel RNA synthesis method using 5 '-O-silyl-2 '-O-orthoester protecting groups. J. Am. Chem. Soc., 1998, 120(45), 11820-11821.
[http://dx.doi.org/10.1021/ja980730v]
[127]
Schwartz, M.E.; Breaker, R.R.; Asteriadis, G.T.; deBear, J.S.; Gough, G.R. Rapid synthesis of oligoribonucleotides using 2′-O-(o-nitrobenzyloxymethyl)-protected monomers. Bioorg. Med. Chem. Lett., 1992, 2(9), 1019-1024.
[http://dx.doi.org/10.1016/S0960-894X(00)80610-1]
[128]
Saneyoshi, H.; Ando, K.; Seio, K.; Sekine, M. Chemical synthesis of RNA via 2′-O-cyanoethylated intermediates. Tetrahedron, 2007, 63(45), 11195-11203.
[http://dx.doi.org/10.1016/j.tet.2007.07.102]
[129]
Somoza, Á. Protecting groups for RNA synthesis: An increasing need for selective preparative methods. Chem. Soc. Rev., 2008, 37(12), 2668-2675.
[http://dx.doi.org/10.1039/b809851d] [PMID: 19020680]
[130]
Zon, G. Commercialization of automated RNA synthesis - Twenty years on. Can. J. Chem., 2007, 85(4), 257-260.
[http://dx.doi.org/10.1139/v07-005]
[131]
Welz, R.; Müller, S. 5-(Benzylmercapto)-1 H -tetrazole as activator for 2′-O-TBDMS phosphoramidite building blocks in RNA synthesis. Tetrahedron Lett., 2002, 43(5), 795-797.
[http://dx.doi.org/10.1016/S0040-4039(01)02274-2]
[132]
Schulhof, J.C.; Molko, D.; Teoule, R. The final deprotection step in oligonucleotide synthesis is reduced to a mild and rapid ammonia treatment by using labile base-protecting groups. Nucleic Acids Res., 1987, 15(2), 397-416.
[http://dx.doi.org/10.1093/nar/15.2.397] [PMID: 3822812]
[133]
Sinha, N.; Davis, P.; Usman, N.; Pérez, J.; Hodge, R.; Kremsky, J.; Casale, R. Labile exocyclic amine protection of nucleosides in DNA, RNA and oligonucleotide analog synthesis facililating N-deacylation, minimizing depurination and chain degradation. Biochimie, 1993, 75(1-2), 13-23.
[http://dx.doi.org/10.1016/0300-9084(93)90019-O] [PMID: 7684933]
[134]
Meher, G.; Meher, N.K.; Iyer, R.P. Nucleobase protection of deoxyribo and ribonucleosides. Curr. Protoc. Nucleic Acid Chem., 2017, 69, 2.
[135]
Lönnberg, H. Synthesis of oligonucleotides on a soluble support. Beilstein J. Org. Chem., 2017, 13, 1368-1387.
[http://dx.doi.org/10.3762/bjoc.13.134] [PMID: 28781703]
[136]
Iyer, R.P.; Egan, W.; Regan, J.B.; Beaucage, S.L. 3H-1,2-Benzodithiole-3-one 1,1-dioxide as an improved sulfurizing reagent in the solid-phase synthesis of oligodeoxyribonucleoside phosphorothioates. J. Am. Chem. Soc., 1990, 112(3), 1253-1254.
[http://dx.doi.org/10.1021/ja00159a059]
[137]
Nukaga, Y.; Yamada, K.; Ogata, T.; Oka, N.; Wada, T. Stereocontrolled solid-phase synthesis of phosphorothioate oligoribonucleotides using 2′-O-(2-cyanoethoxymethyl)-nucleoside 3′-O-oxazaphospholidine monomers. J. Org. Chem., 2012, 77(18), 7913-7922.
[http://dx.doi.org/10.1021/jo301052v] [PMID: 22931131]
[138]
Wan, W.B.; Migawa, M.T.; Vasquez, G.; Murray, H.M.; Nichols, J.G.; Gaus, H.; Berdeja, A.; Lee, S.; Hart, C.E.; Lima, W.F.; Swayze, E.E.; Seth, P.P. Synthesis, biophysical properties and biological activity of second generation antisense oligonucleotides containing chiral phosphorothioate linkages. Nucleic Acids Res., 2014, 42(22), 13456-13468.
[http://dx.doi.org/10.1093/nar/gku1115] [PMID: 25398895]
[139]
Krasheninina, O.A.; Fishman, V.S.; Lomzov, A.A.; Ustinov, A.V.; Venyaminova, A.G. Postsynthetic on-column 2′ functionalization of RNA by convenient versatile method. Int. J. Mol. Sci., 2020, 21(14), 5127.
[http://dx.doi.org/10.3390/ijms21145127] [PMID: 32698484]
[140]
Lee, Y.H.; Yu, E.; Park, C.M. Programmable site-selective labeling of oligonucleotides based on carbene catalysis. Nat. Commun., 2021, 12(1), 1681.
[http://dx.doi.org/10.1038/s41467-021-21839-4] [PMID: 33727561]
[141]
Corey, D.R. Chemical modification: The key to clinical application of RNA interference? J. Clin. Invest., 2007, 117(12), 3615-3622.
[http://dx.doi.org/10.1172/JCI33483] [PMID: 18060019]
[142]
Gao, M.; Zhang, Q.; Feng, X.H.; Liu, J. Synthetic modified messenger RNA for therapeutic applications. Acta Biomater., 2021, 131, 1-15.
[http://dx.doi.org/10.1016/j.actbio.2021.06.020] [PMID: 34133982]
[143]
Jemielity, J.; Kowalska, J.; Rydzik, A.M.; Darzynkiewicz, E. Synthetic mRNA cap analogs with a modified triphosphate bridge – synthesis, applications and prospects. New J. Chem., 2010, 34(5), 829.
[http://dx.doi.org/10.1039/c0nj00041h]
[144]
Guo, Y.E.; Steitz, J.A. 3′-Biotin-tagged microRNA-27 does not associate with Argonaute proteins in cells. RNA, 2014, 20(7), 985-988.
[http://dx.doi.org/10.1261/rna.045054.114] [PMID: 24821854]
[145]
Hendrix, C.; Rosemeyer, H.; Verheggen, I.; Van Aerschot, A.; Seela, F.; Herdewijn, P. 1′, 5′ -anhydrohexitol oligonucleotides: synthesis, base pairing and recognition by regular oligodeoxyribonucleotides and oligoribonucleotides. Chemistry, 1997, 3(1), 110-120.
[http://dx.doi.org/10.1002/chem.19970030118]
[146]
Habibian, M.; Martínez-Montero, S.; Portella, G.; Chua, Z.; Bohle, D.S.; Orozco, M.; Damha, M.J. Seven-membered ring nucleoside analogues: Stereoselective synthesis and studies on their conformational properties. Org. Lett., 2015, 17(21), 5416-5419.
[http://dx.doi.org/10.1021/acs.orglett.5b02769] [PMID: 26492193]
[147]
Allerson, C.R.; Sioufi, N.; Jarres, R.; Prakash, T.P.; Naik, N.; Berdeja, A.; Wanders, L.; Griffey, R.H.; Swayze, E.E.; Bhat, B. Fully 2′-modified oligonucleotide duplexes with improved in vitro potency and stability compared to unmodified small interfering RNA. J. Med. Chem., 2005, 48(4), 901-904.
[http://dx.doi.org/10.1021/jm049167j] [PMID: 15715458]
[148]
Hagedorn, P.H.; Persson, R.; Funder, E.D.; Albæk, N.; Diemer, S.L.; Hansen, D.J.; Møller, M.R.; Papargyri, N.; Christiansen, H.; Hansen, B.R.; Hansen, H.F.; Jensen, M.A.; Koch, T. Locked nucleic acid: Modality, diversity, and drug discovery. Drug Discov. Today, 2018, 23(1), 101-114.
[http://dx.doi.org/10.1016/j.drudis.2017.09.018] [PMID: 28988994]
[149]
Braasch, D.A.; Corey, D.R. Locked nucleic acid (LNA): Fine-tuning the recognition of DNA and RNA. Chem. Biol., 2001, 8(1), 1-7.
[http://dx.doi.org/10.1016/S1074-5521(00)00058-2] [PMID: 11182314]
[150]
Elm n, J.; Thonberg, H.; Ljungberg, K.; Frieden, M.; Westergaard, M.; Xu, Y.; Wahren, B.; Liang, Z.; Ørum, H.; Koch, T.; Wahlestedt, C. Locked nucleic acid (LNA) mediated improvements in siRNA stability and functionality. Nucleic Acids Res., 2005, 33(1), 439-447.
[http://dx.doi.org/10.1093/nar/gki193] [PMID: 15653644]
[151]
Castanotto, D.; Zhang, X.; Rüger, J.; Alluin, J.; Sharma, R.; Pirrotte, P.; Joenson, L.; Ioannou, S.; Nelson, M.S.; Vikeså, J.; Hansen, B.R.; Koch, T.; Jensen, M.A.; Rossi, J.J.; Stein, C.A. A multifunctional LNA oligonucleotide-based strategy blocks AR expression and transactivation activity in PCa cells. Mol. Ther. Nucleic Acids, 2021, 23, 63-75.
[http://dx.doi.org/10.1016/j.omtn.2020.10.032] [PMID: 33335793]
[152]
Zhang, Y.; Qu, Z.; Kim, S.; Shi, V.; Liao, B.; Kraft, P.; Bandaru, R.; Wu, Y.; Greenberger, L.M.; Horak, I.D. Down-modulation of cancer targets using locked nucleic acid (LNA)-based antisense oligonucleotides without transfection. Gene Ther., 2011, 18(4), 326-333.
[http://dx.doi.org/10.1038/gt.2010.133] [PMID: 21179173]
[153]
Kasuya, T.; Hori, S.; Watanabe, A.; Nakajima, M.; Gahara, Y.; Rokushima, M.; Yanagimoto, T.; Kugimiya, A. Ribonuclease H1-dependent hepatotoxicity caused by locked nucleic acid-modified gapmer antisense oligonucleotides. Sci. Rep., 2016, 6(1), 30377.
[http://dx.doi.org/10.1038/srep30377] [PMID: 27461380]
[154]
Martín-Pintado, N.; Yahyaee-Anzahaee, M.; Campos-Olivas, R.; Noronha, A.M.; Wilds, C.J.; Damha, M.J.; González, C. The solution structure of double helical arabino nucleic acids (ANA and 2′F-ANA): Effect of arabinoses in duplex-hairpin interconversion. Nucleic Acids Res., 2012, 40(18), 9329-9339.
[http://dx.doi.org/10.1093/nar/gks672] [PMID: 22798499]
[155]
Wilds, C.J.; Damha, M.J. 2′-Deoxy-2′-fluoro-beta-D-arabinonucleosides and oligonucleotides (2'F-ANA): Synthesis and physicochemical studies. Nucleic Acids Res., 2000, 28(18), 3625-3635.
[http://dx.doi.org/10.1093/nar/28.18.3625] [PMID: 10982885]
[156]
Sandoval-Mojica, A.F.; Hunter, W.B.; Aishwarya, V.; Bonilla, S.; Pelz-Stelinski, K.S. Antibacterial FANA oligonucleotides as a novel approach for managing the Huanglongbing pathosystem. Sci. Rep., 2021, 11(1), 2760.
[http://dx.doi.org/10.1038/s41598-021-82425-8] [PMID: 33531619]
[157]
Seth, P.P.; Vasquez, G.; Allerson, C.A.; Berdeja, A.; Gaus, H.; Kinberger, G.A.; Prakash, T.P.; Migawa, M.T.; Bhat, B.; Swayze, E.E. Synthesis and biophysical evaluation of 2′,4′-constrained 2‘-O-methoxyethyl and 2’,4′-constrained 2'-O-ethyl nucleic acid analogues. J. Org. Chem., 2010, 75(5), 1569-1581.
[http://dx.doi.org/10.1021/jo902560f] [PMID: 20136157]
[158]
Pallan, P.S.; Allerson, C.R.; Berdeja, A.; Seth, P.P.; Swayze, E.E.; Prakash, T.P.; Egli, M. Structure and nuclease resistance of 2′,4′-constrained 2′-O-methoxyethyl (cMOE) and 2′-O-ethyl (cEt) modified DNAs. Chem. Commun. (Camb.), 2012, 48(66), 8195-8197.
[http://dx.doi.org/10.1039/c2cc32286b] [PMID: 22614180]
[159]
Anderson, B.A.; Freestone, G.C.; Low, A.; De-Hoyos, C.L.; Iii, W.J.D.; Østergaard, M.E.; Migawa, M.T.; Fazio, M.; Wan, W.B.; Berdeja, A.; Scandalis, E.; Burel, S.A.; Vickers, T.A.; Crooke, S.T.; Swayze, E.E.; Liang, X.; Seth, P.P. Towards next generation antisense oligonucleotides: Mesylphosphoramidate modification improves therapeutic index and duration of effect of gapmer antisense oligonucleotides. Nucleic Acids Res., 2021, 49(16), 9026-9041.
[http://dx.doi.org/10.1093/nar/gkab718] [PMID: 34417625]
[160]
Kumar, P.; Madsen, C.S.; Nielsen, P. Synthesis of 2′-O-(thymin-1-yl)methyluridine and its incorporation into secondary nucleic acid structures. Bioorg. Med. Chem. Lett., 2013, 23(24), 6847-6850.
[http://dx.doi.org/10.1016/j.bmcl.2013.10.006] [PMID: 24432386]
[161]
Kumar, P.; Sharma, P.K.; Nielsen, P. Double-headed nucleotides with arabino configuration: Synthesis and hybridization properties. J. Org. Chem., 2014, 79(23), 11534-11540.
[http://dx.doi.org/10.1021/jo502189h] [PMID: 25375974]
[162]
Mattelaer, C.A.; Maiti, M.; Smets, L.; Maiti, M.; Schepers, G.; Mattelaer, H.P.; Rosemeyer, H.; Herdewijn, P.; Lescrinier, E. Stable hairpin structures formed by xylose-based nucleic acids. ChemBioChem, 2021, 22(9), 1638-1645.
[http://dx.doi.org/10.1002/cbic.202000803] [PMID: 33427360]
[163]
Hendrix, C.; Rosemeyer, H.; De Bouvere, B.; Van Aerschot, A.; Seela, F.; Herdewijn, P. 1′,5′-anhydrohexitol oligonucleotides: Hybridisation and strand displacement with oligoribonucleotides, interaction with RNase H and HIV reverse transcriptase. Chemistry, 1997, 3(9), 1513-1520.
[http://dx.doi.org/10.1002/chem.19970030920]
[164]
Jana, S.K.; Harikrishna, S.; Sudhakar, S.; El-Khoury, R.; Pradeepkumar, P.I.; Damha, M.J. Nucleoside analogues with a seven-membered sugar ring: Synthesis and structural compatibility in DNA–RNA hybrids. J. Org. Chem., 2022, 87(5), 2367-2379.
[http://dx.doi.org/10.1021/acs.joc.1c02254] [PMID: 35133166]
[165]
Pochet, S.; Kaminski, P.A.; Van Aerschot, A.; Herdewijn, P.; Marlière, P. Replication of hexitol oligonucleotides as a prelude to the propagation of a third type of nucleic acid in vivo. C. R. Biol., 2003, 326(12), 1175-1184.
[http://dx.doi.org/10.1016/j.crvi.2003.10.004] [PMID: 14746272]
[166]
Dande, P.; Prakash, T.P.; Sioufi, N.; Gaus, H.; Jarres, R.; Berdeja, A.; Swayze, E.E.; Griffey, R.H.; Bhat, B. Improving RNA interference in mammalian cells by 4′-thio-modified small interfering RNA (siRNA): Effect on siRNA activity and nuclease stability when used in combination with 2′-O-alkyl modifications. J. Med. Chem., 2006, 49(5), 1624-1634.
[http://dx.doi.org/10.1021/jm050822c] [PMID: 16509579]
[167]
Herdewijn, P. Nucleic acids with a six-membered ‘carbohydrate’ mimic in the backbone. Chem. Biodivers., 2010, 7(1), 1-59.
[http://dx.doi.org/10.1002/cbdv.200900185] [PMID: 20087996]
[168]
Uehara, T.; Choong, C.J.; Nakamori, M.; Hayakawa, H.; Nishiyama, K.; Kasahara, Y.; Baba, K.; Nagata, T.; Yokota, T.; Tsuda, H.; Obika, S.; Mochizuki, H. Amido-bridged nucleic acid (AmNA)-modified antisense oligonucleotides targeting α-synuclein as a novel therapy for Parkinson’s disease. Sci. Rep., 2019, 9(1), 7567.
[http://dx.doi.org/10.1038/s41598-019-43772-9] [PMID: 31110191]
[169]
Habuchi, T.; Yamaguchi, T.; Obika, S. Thioamide-Bridged Nucleic Acid (thioAmNA) Containing Thymine or 2-Thiothymine: Duplex-Forming ability, base discrimination, and enzymatic stability. ChemBioChem, 2019, 20(8), 1060-1067.
[http://dx.doi.org/10.1002/cbic.201800702] [PMID: 30552742]
[170]
Egli, M.; Pallan, P.S.; Allerson, C.R.; Prakash, T.P.; Berdeja, A.; Yu, J.; Lee, S.; Watt, A.; Gaus, H.; Bhat, B.; Swayze, E.E.; Seth, P.P. Synthesis, improved antisense activity and structural rationale for the divergent RNA affinities of 3′-fluoro hexitol nucleic acid (FHNA and Ara-FHNA) modified oligonucleotides. J. Am. Chem. Soc., 2011, 133(41), 16642-16649.
[http://dx.doi.org/10.1021/ja207086x] [PMID: 21919455]
[171]
Langkjær, N.; Pasternak, A.; Wengel, J. UNA (unlocked nucleic acid): A flexible RNA mimic that allows engineering of nucleic acid duplex stability. Bioorg. Med. Chem., 2009, 17(15), 5420-5425.
[http://dx.doi.org/10.1016/j.bmc.2009.06.045] [PMID: 19604699]
[172]
Pasternak, A.; Wengel, J. Unlocked nucleic acid - an RNA modification with broad potential. Org. Biomol. Chem., 2011, 9(10), 3591-3597.
[http://dx.doi.org/10.1039/c0ob01085e] [PMID: 21431171]
[173]
Zhang, L.; Peritz, A.; Meggers, E. A simple glycol nucleic acid. J. Am. Chem. Soc., 2005, 127(12), 4174-4175.
[http://dx.doi.org/10.1021/ja042564z] [PMID: 15783191]
[174]
Mutisya, D.; Selvam, C.; Kennedy, S.D.; Rozners, E. Synthesis and properties of triazole-linked RNA. Bioorg. Med. Chem. Lett., 2011, 21(11), 3420-3422.
[http://dx.doi.org/10.1016/j.bmcl.2011.03.111] [PMID: 21524577]
[175]
Crooke, S.T.; Vickers, T.A.; Liang, X. Phosphorothioate modified oligonucleotide–protein interactions. Nucleic Acids Res., 2020, 48(10), 5235-5253.
[http://dx.doi.org/10.1093/nar/gkaa299] [PMID: 32356888]
[176]
Jahns, H.; Roos, M.; Imig, J.; Baumann, F.; Wang, Y.; Gilmour, R.; Hall, J. Stereochemical bias introduced during RNA synthesis modulates the activity of phosphorothioate siRNAs. Nat. Commun., 2015, 6(1), 6317.
[http://dx.doi.org/10.1038/ncomms7317] [PMID: 25744034]
[177]
Jahns, H.; Taneja, N.; Willoughby, J.L.S.; Akabane-Nakata, M.; Brown, C.R.; Nguyen, T.; Bisbe, A.; Matsuda, S.; Hettinger, M.; Manoharan, R.M.; Rajeev, K.G.; Maier, M.A.; Zlatev, I.; Charisse, K.; Egli, M.; Manoharan, M. Chirality matters: stereo-defined phosphorothioate linkages at the termini of small interfering RNAs improve pharmacology in vivo. Nucleic Acids Res., 2022, 50(3), 1221-1240.
[http://dx.doi.org/10.1093/nar/gkab544] [PMID: 34268578]
[178]
Wu, Y.; Tang, Y.; Dong, X.; Zheng, Y.Y.; Haruehanroengra, P.; Mao, S.; Lin, Q.; Sheng, J. RNA phosphorothioate modification in prokaryotes and eukaryotes. ACS Chem. Biol., 2020, 15(6), 1301-1305.
[http://dx.doi.org/10.1021/acschembio.0c00163] [PMID: 32275390]
[179]
Kim, J.; Hu, C.; Moufawad El Achkar, C.; Black, L.E.; Douville, J.; Larson, A.; Pendergast, M.K.; Goldkind, S.F.; Lee, E.A.; Kuniholm, A.; Soucy, A.; Vaze, J.; Belur, N.R.; Fredriksen, K.; Stojkovska, I.; Tsytsykova, A.; Armant, M.; DiDonato, R.L.; Choi, J.; Cornelissen, L.; Pereira, L.M.; Augustine, E.F.; Genetti, C.A.; Dies, K.; Barton, B.; Williams, L.; Goodlett, B.D.; Riley, B.L.; Pasternak, A.; Berry, E.R.; Pflock, K.A.; Chu, S.; Reed, C.; Tyndall, K.; Agrawal, P.B.; Beggs, A.H.; Grant, P.E.; Urion, D.K.; Snyder, R.O.; Waisbren, S.E.; Poduri, A.; Park, P.J.; Patterson, A.; Biffi, A.; Mazzulli, J.R.; Bodamer, O.; Berde, C.B.; Yu, T.W. Patient-customized oligonucleotide therapy for a rare genetic disease. N. Engl. J. Med., 2019, 381(17), 1644-1652.
[http://dx.doi.org/10.1056/NEJMoa1813279] [PMID: 31597037]
[180]
Hall, A.H.S.; Wan, J.; Spesock, A.; Sergueeva, Z.; Shaw, B.R.; Alexander, K.A. High potency silencing by single-stranded boranophosphate siRNA. Nucleic Acids Res., 2006, 34(9), 2773-2781.
[http://dx.doi.org/10.1093/nar/gkl339] [PMID: 16717282]
[181]
Carrasco, N.; Caton-Williams, J.; Brandt, G.; Wang, S.; Huang, Z. Efficient enzymatic synthesis of phosphoroselenoate RNA by using adenosine 5′-(alpha-P-seleno)triphosphate. Angew. Chem. Int. Ed., 2006, 45(1), 94-97.
[http://dx.doi.org/10.1002/anie.200502215] [PMID: 16304655]
[182]
Fujino, T.; Kogashi, K.; Okada, K.; Mattarella, M.; Suzuki, T.; Yasumoto, K.; Sogawa, K.; Isobe, H. Chimeric RNA oligonucleotides with triazole and phosphate linkages: Synthesis and RNA interference. Chem. Asian J., 2015, 10(12), 2683-2688.
[http://dx.doi.org/10.1002/asia.201500765] [PMID: 26248050]
[183]
Harcourt, E.M.; Kietrys, A.M.; Kool, E.T. Chemical and structural effects of base modifications in messenger RNA. Nature, 2017, 541(7637), 339-346.
[http://dx.doi.org/10.1038/nature21351] [PMID: 28102265]
[184]
Miao, S.; Liang, Y.; Rundell, S.; Bhunia, D.; Devari, S.; Munyaradzi, O.; Bong, D. Unnatural bases for recognition of noncoding nucleic acid interfaces. Biopolymers, 2021, 112(1), e23399.
[http://dx.doi.org/10.1002/bip.23399] [PMID: 32969496]
[185]
Peacock, H.; Fucini, R.V.; Jayalath, P.; Ibarra-Soza, J.M.; Haringsma, H.J.; Flanagan, W.M.; Willingham, A.; Beal, P.A. Nucleobase and ribose modifications control immunostimulation by a microRNA-122-mimetic RNA. J. Am. Chem. Soc., 2011, 133(24), 9200-9203.
[http://dx.doi.org/10.1021/ja202492e] [PMID: 21612237]
[186]
Phelps, K.J.; Ibarra-Soza, J.M.; Tran, K.; Fisher, A.J.; Beal, P.A. Click modification of RNA at adenosine: Structure and reactivity of 7-ethynyl- and 7-triazolyl-8-aza-7-deazaadenosine in RNA. ACS Chem. Biol., 2014, 9(8), 1780-1787.
[http://dx.doi.org/10.1021/cb500270x] [PMID: 24896732]
[187]
Suter, S.R.; Ball-Jones, A.; Mumbleau, M.M.; Valenzuela, R.; Ibarra-Soza, J.; Owens, H.; Fisher, A.J.; Beal, P.A. Controlling miRNA-like off-target effects of an siRNA with nucleobase modifications. Org. Biomol. Chem., 2017, 15(47), 10029-10036.
[http://dx.doi.org/10.1039/C7OB02654D] [PMID: 29164215]
[188]
Srivatsan, S.G.; Sawant, A.A. Fluorescent ribonucleoside analogues as probes for investigating RNA structure and function. J. Pure Appl. Chem., 2010, 83, 213-232.
[189]
Boo, S.H.; Kim, Y.K. The emerging role of RNA modifications in the regulation of mRNA stability. Exp. Mol. Med., 2020, 52(3), 400-408.
[http://dx.doi.org/10.1038/s12276-020-0407-z] [PMID: 32210357]
[190]
Song, J.; Yi, C. Chemical modifications to RNA: A new layer of gene expression regulation. ACS Chem. Biol., 2017, 12(2), 316-325.
[http://dx.doi.org/10.1021/acschembio.6b00960] [PMID: 28051309]
[191]
Delaunay, S.; Frye, M. RNA modifications regulating cell fate in cancer. Nat. Cell Biol., 2019, 21(5), 552-559.
[http://dx.doi.org/10.1038/s41556-019-0319-0] [PMID: 31048770]
[192]
Roundtree, I.A.; Evans, M.E.; Pan, T.; He, C. Dynamic RNA modifications in gene expression regulation. Cell, 2017, 169(7), 1187-1200.
[http://dx.doi.org/10.1016/j.cell.2017.05.045] [PMID: 28622506]
[193]
Leszczynska, G.; Sadowska, K.; Bartos, P.; Nawrot, B.; Sochacka, E. S -geranylated 2-thiouridines of bacterial tRNAs: Chemical synthesis and physicochemical properties. Eur. J. Org. Chem., 2016, 2016(21), 3482-3485.
[http://dx.doi.org/10.1002/ejoc.201600519]
[194]
Bartosik, K.; Debiec, K.; Czarnecka, A.; Sochacka, E.; Leszczynska, G. Synthesis of nucleobase-modified RNA oligonucleotides by post-synthetic approach. Molecules, 2020, 25(15), 3344.
[http://dx.doi.org/10.3390/molecules25153344] [PMID: 32717917]
[195]
Höbartner, C.; Kreutz, C.; Flecker, E. The Synthesis of 2′-o-[(triisopropylsilyl)oxy] methyl (TOM) phosphoramidites of methylated ribonucleosides (m 1 G, m 2 G, m 2 2 G, m 1 I, m 3 U, m 4 C, m 6 A, m 6 2 A) for use in automated RNA solid-phase synthesis. Monatsh. Chem., 2003, 34, 851-873.
[http://dx.doi.org/10.1007/s00706-003-0592-1]
[196]
Mikhailov, S.N.; Rozenski, J.; Efimtseva, E.V.; Busson, R.; Van Aerschot, A.; Herdewijn, P. Chemical incorporation of 1-methyladenosine into oligonucleotides. Nucleic Acids Res., 2002, 30(5), 1124-1131.
[http://dx.doi.org/10.1093/nar/30.5.1124] [PMID: 11861902]
[197]
Chen, S.; Le, B.T.; Chakravarthy, M.; Kosbar, T.R.; Veedu, R.N. Systematic evaluation of 2′-Fluoro modified chimeric antisense oligonucleotide-mediated exon skipping in vitro. Sci. Rep., 2019, 9(1), 6078.
[http://dx.doi.org/10.1038/s41598-019-42523-0] [PMID: 30988454]
[198]
Kumar, P.; El-Sagheer, A.H.; Truong, L.; Brown, T. Locked nucleic acid (LNA) enhances binding affinity of triazole-linked DNA towards RNA. Chem. Commun. (Camb.), 2017, 53(63), 8910-8913.
[http://dx.doi.org/10.1039/C7CC05159J] [PMID: 28748236]
[199]
Li, Q.; Maola, V.A.; Chim, N.; Hussain, J.; Lozoya-Colinas, A.; Chaput, J.C. Synthesis and polymerase recognition of threose nucleic acid triphosphates equipped with diverse chemical functionalities. J. Am. Chem. Soc., 2021, 143(42), 17761-17768.
[http://dx.doi.org/10.1021/jacs.1c08649] [PMID: 34637287]
[200]
Renders, M.; Dumbre, S.; Abramov, M.; Kestemont, D.; Margamuljana, L.; Largy, E.; Cozens, C.; Vandenameele, J.; Pinheiro, V.B.; Toye, D.; Frère, J.M.; Herdewijn, P. Kinetic analysis of N-alkylaryl carboxamide hexitol nucleotides as substrates for evolved polymerases. Nucleic Acids Res., 2019, 47(5), 2160-2168.
[http://dx.doi.org/10.1093/nar/gkz008] [PMID: 30698800]
[201]
Li, Q. Nusinersen as a therapeutic agent for spinal muscular atrophy. Yonsei Med. J., 2020, 61(4), 273-283.
[http://dx.doi.org/10.3349/ymj.2020.61.4.273] [PMID: 32233169]
[202]
Roberts, T.C.; Langer, R.; Wood, M.J.A. Advances in oligonucleotide drug delivery. Nat. Rev. Drug Discov., 2020, 19(10), 673-694.
[http://dx.doi.org/10.1038/s41573-020-0075-7] [PMID: 32782413]
[203]
Wu, S.Y.; Yang, X.; Gharpure, K.M.; Hatakeyama, H.; Egli, M.; McGuire, M.H.; Nagaraja, A.S.; Miyake, T.M.; Rupaimoole, R.; Pecot, C.V.; Taylor, M.; Pradeep, S.; Sierant, M.; Rodriguez-Aguayo, C.; Choi, H.J.; Previs, R.A.; Armaiz-Pena, G.N.; Huang, L.; Martinez, C.; Hassell, T.; Ivan, C.; Sehgal, V.; Singhania, R.; Han, H.D.; Su, C.; Kim, J.H.; Dalton, H.J.; Kovvali, C.; Keyomarsi, K.; McMillan, N.A.J.; Overwijk, W.W.; Liu, J.; Lee, J.S.; Baggerly, K.A.; Lopez-Berestein, G.; Ram, P.T.; Nawrot, B.; Sood, A.K. 2′-OMe-phosphorodithioate-modified siRNAs show increased loading into the RISC complex and enhanced anti-tumour activity. Nat. Commun., 2014, 5(1), 3459.
[http://dx.doi.org/10.1038/ncomms4459] [PMID: 24619206]
[204]
Jastrzębska, K.; Mikołajczyk, B.; Guga, P. LNA units present in [RP-PS]-(DNA#LNA) chimeras enhance the thermal stability of parallel duplexes and triplexes formed with (2′-OMe)-RNA strands. RSC Advances, 2020, 10(38), 22370-22376.
[http://dx.doi.org/10.1039/D0RA03934A] [PMID: 35514591]
[205]
Flamme, M.; Hanlon, S.; Iding, H.; Puentener, K.; Sladojevich, F.; Hollenstein, M. Towards the enzymatic synthesis of phosphorothioate containing LNA oligonucleotides. Bioorg. Med. Chem. Lett., 2021, 48, 128242.
[http://dx.doi.org/10.1016/j.bmcl.2021.128242] [PMID: 34217829]
[206]
Sharma, V.K.; Singh, S.K.; Krishnamurthy, P.M.; Alterman, J.F.; Haraszti, R.A.; Khvorova, A.; Prasad, A.K.; Watts, J.K. Synthesis and biological properties of triazole-linked locked nucleic acid. Chem. Commun. (Camb.), 2017, 53(63), 8906-8909.
[http://dx.doi.org/10.1039/C7CC04092J] [PMID: 28736781]
[207]
Perrone, D.; Marchesi, E.; Preti, L.; Navacchia, M.L. Modified nucleosides, nucleotides and nucleic acids via click azide-alkyne cycloaddition for pharmacological applications. Molecules, 2021, 26(11), 3100.
[http://dx.doi.org/10.3390/molecules26113100] [PMID: 34067312]
[208]
Winkle, M.; El-Daly, S.M.; Fabbri, M.; Calin, G.A. Noncoding RNA therapeutics - challenges and potential solutions. Nat. Rev. Drug Discov., 2021, 20(8), 629-651.
[http://dx.doi.org/10.1038/s41573-021-00219-z] [PMID: 34145432]
[209]
Chaytow, H.; Faller, K.M.E.; Huang, Y.T.; Gillingwater, T.H. Spinal muscular atrophy: From approved therapies to future therapeutic targets for personalized medicine. Cell Rep Med , 2021, 2(7), 100346.
[http://dx.doi.org/10.1016/j.xcrm.2021.100346] [PMID: 34337562]
[210]
Sahin, U.; Karikó, K.; Türeci, Ö. mRNA-based therapeutics - developing a new class of drugs. Nat. Rev. Drug Discov., 2014, 13(10), 759-780.
[http://dx.doi.org/10.1038/nrd4278] [PMID: 25233993]
[211]
Pardi, N.; Hogan, M.J.; Pelc, R.S.; Muramatsu, H.; Andersen, H.; DeMaso, C.R.; Dowd, K.A.; Sutherland, L.L.; Scearce, R.M.; Parks, R.; Wagner, W.; Granados, A.; Greenhouse, J.; Walker, M.; Willis, E.; Yu, J.S.; McGee, C.E.; Sempowski, G.D.; Mui, B.L.; Tam, Y.K.; Huang, Y.J.; Vanlandingham, D.; Holmes, V.M.; Balachandran, H.; Sahu, S.; Lifton, M.; Higgs, S.; Hensley, S.E.; Madden, T.D.; Hope, M.J.; Karikó, K.; Santra, S.; Graham, B.S.; Lewis, M.G.; Pierson, T.C.; Haynes, B.F.; Weissman, D. Zika virus protection by a single low-dose nucleoside-modified mRNA vaccination. Nature, 2017, 543(7644), 248-251.
[http://dx.doi.org/10.1038/nature21428] [PMID: 28151488]
[212]
Polack, F.P.; Thomas, S.J.; Kitchin, N.; Absalon, J.; Gurtman, A.; Lockhart, S.; Perez, J.L.; Pérez Marc, G.; Moreira, E.D.; Zerbini, C.; Bailey, R.; Swanson, K.A.; Roychoudhury, S.; Koury, K.; Li, P.; Kalina, W.V.; Cooper, D.; Frenck, R.W., Jr; Hammitt, L.L.; Türeci, Ö.; Nell, H.; Schaefer, A.; Ünal, S.; Tresnan, D.B.; Mather, S.; Dormitzer, P.R.; Şahin, U.; Jansen, K.U.; Gruber, W.C. Safety and efficacy of the BNT162b2 mRNA COVID-19 vaccine. N. Engl. J. Med., 2020, 383(27), 2603-2615.
[http://dx.doi.org/10.1056/NEJMoa2034577] [PMID: 33301246]
[213]
Baden, L.R.; El Sahly, H.M.; Essink, B.; Kotloff, K.; Frey, S.; Novak, R.; Diemert, D.; Spector, S.A.; Rouphael, N.; Creech, C.B.; McGettigan, J.; Khetan, S.; Segall, N.; Solis, J.; Brosz, A.; Fierro, C.; Schwartz, H.; Neuzil, K.; Corey, L.; Gilbert, P.; Janes, H.; Follmann, D.; Marovich, M.; Mascola, J.; Polakowski, L.; Ledgerwood, J.; Graham, B.S.; Bennett, H.; Pajon, R.; Knightly, C.; Leav, B.; Deng, W.; Zhou, H.; Han, S.; Ivarsson, M.; Miller, J.; Zaks, T. Efficacy and safety of the mRNA-1273 SARS-CoV-2 vaccine. N. Engl. J. Med., 2021, 384(5), 403-416.
[http://dx.doi.org/10.1056/NEJMoa2035389] [PMID: 33378609]
[214]
Wolff, J.A.; Malone, R.W.; Williams, P.; Chong, W.; Acsadi, G.; Jani, A.; Felgner, P.L. Direct gene transfer into mouse muscle in vivo. Science, 1990, 247(4949), 1465-1468.
[http://dx.doi.org/10.1126/science.1690918] [PMID: 1690918]
[215]
Kim, S.C.; Sekhon, S.S.; Shin, W.R.; Ahn, G.; Cho, B.K.; Ahn, J.Y.; Kim, Y.H. Modifications of mRNA vaccine structural elements for improving mRNA stability and translation efficiency. Mol. Cell. Toxicol., 2022, 18(1), 1-8.
[http://dx.doi.org/10.1007/s13273-021-00171-4] [PMID: 34567201]
[216]
Muttach, F.; Muthmann, N.; Rentmeister, A. Synthetic mRNA capping. Beilstein J. Org. Chem., 2017, 13, 2819-2832.
[http://dx.doi.org/10.3762/bjoc.13.274] [PMID: 30018667]
[217]
Mollocana-Lara, E.C.; Ni, M.; Agathos, S.N.; Gonzales-Zubiate, F.A. The infinite possibilities of RNA therapeutics. J. Ind. Microbiol. Biotechnol., 2021, 48(9-10), kuab063.
[http://dx.doi.org/10.1093/jimb/kuab063] [PMID: 34463324]
[218]
Grudzien-Nogalska, E.; Kowalska, J.; Su, W.; Kuhn, A.N.; Slepenkov, S.V.; Darzynkiewicz, E.; Sahin, U.; Jemielity, J.; Rhoads, R.E. Synthetic mRNAs with superior translation and stability properties. Methods Mol. Biol., 2013, 969, 55-72.
[http://dx.doi.org/10.1007/978-1-62703-260-5_4] [PMID: 23296927]
[219]
Stepinski, J.; Waddell, C.; Stolarski, R.; Darzynkiewicz, E.; Rhoads, R.E. Synthesis and properties of mRNAs containing the novel “anti-reverse” cap analogs 7-methyl(3′-O-methyl)GpppG and 7-methyl (3′-deoxy)GpppG. RNA, 2001, 7(10), 1486-1495.
[PMID: 11680853]
[220]
Sikorski, P.J.; Warminski, M.; Kubacka, D.; Ratajczak, T.; Nowis, D.; Kowalska, J.; Jemielity, J. The identity and methylation status of the first transcribed nucleotide in eukaryotic mRNA 5′ cap modulates protein expression in living cells. Nucleic Acids Res., 2020, 48(4), 1607-1626.
[http://dx.doi.org/10.1093/nar/gkaa032] [PMID: 31984425]
[221]
Urbina, F.; Morales-Pison, S.; Maldonado, E. Enzymatic protein biopolymers as a tool to synthetize eukaryotic messenger ribonucleic acid (mRNA) with uses in vaccination, immunotherapy and nanotechnology. Polymers (Basel), 2020, 12(8), 1633.
[http://dx.doi.org/10.3390/polym12081633] [PMID: 32717794]
[222]
Morais, P.; Adachi, H.; Yu, Y.T. The critical contribution of pseudouridine to mRNA COVID-19 vaccines. Front. Cell Dev. Biol., 2021, 9, 789427.
[http://dx.doi.org/10.3389/fcell.2021.789427] [PMID: 34805188]
[223]
Whitley, J.; Zwolinski, C.; Denis, C.; Maughan, M.; Hayles, L.; Clarke, D.; Snare, M.; Liao, H.; Chiou, S.; Marmura, T. Development of mRNA manufacturing for vaccines and therapeutics: mRNA platform requirements and development of a scalable production process to support early phase clinical trials. Transl. Res., 2021. [Epub ahead of print].
[PMID: 34871810]
[224]
Jedrzejczyk, D.; Gendaszewska-Darmach, E.; Pawlowska, R.; Chworos, A. Designing synthetic RNA for delivery by nanoparticles. J. Phys. Condens. Matter, 2017, 29(12), 123001.
[http://dx.doi.org/10.1088/1361-648X/aa5561] [PMID: 28004640]
[225]
Graczyk, A.; Pawlowska, R.; Jedrzejczyk, D.; Chworos, A. Gold nanoparticles in conjunction with nucleic acids as a modern molecular system for cellular delivery. Molecules, 2020, 25(1), 204.
[http://dx.doi.org/10.3390/molecules25010204] [PMID: 31947834]
[226]
Graczyk, A.; Pawlowska, R.; Chworos, A. Gold nanoparticles as carriers for functional RNA nanostructures. Bioconjug. Chem., 2021, 32(8), 1667-1674.
[http://dx.doi.org/10.1021/acs.bioconjchem.1c00211] [PMID: 34323473]
[227]
Graczyk, A.; Pawlowska, R.; Chworos, A. Functional RNA-AuNP conjugates for gene expression regulation based on the GFP example. FEBS Open Bio., 2021, 11, 127-127.

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