Abstract
Recent studies on the chemical synthesis of RNA and related derivatives are reviewed. In particular, a variety of new 2′-hydroxyl protecting groups that are developed during the past decade are described and compared with the conventional ones from the organochemical point of view. Great improvements in the coupling efficiency and suppression of side reactions during RNA synthesis cycles are described in great detail. The methods and associated problems for constructing the key synthetic intermediates, i.e., 2′-O-protected ribonucleoside 3′-phosphoramidite building blocks, are also discussed.
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References
Fire A, Xu S, Montgomery MK et al (1998) Potent and specific genetic interference by double-stranded RNA in Caenorhabditis elegans. Nature 391:806–811
Elbashir SM, Harborth J, Lendeckel W et al (2001) Duplexes of 21-nucleotide RNAs mediate RNA interference in cultured mammalian cells. Nature 411:494–498
Manoharan M (2002) Oligonucleotide conjugates as potential antisense drugs with improved uptake, biodistribution, targeted delivery, and mechanism of action. Antisense Nucleic Acid Drug Dev 12:103–128
Amarzguioui M, Lundberg P, Cantin E et al (2006) Rational design and in vitro and in vivo delivery of Dicer substrate siRNA. Nat Protoc 1:508–517
Ozcan G, Ozpolat B, Coleman RL, Sood AK, Lopez-Berestein G (2015) Preclinical and clinical development of siRNA-based therapeutics. Adv Drug Deliv Rev 87:108–119
Behlke MA (2008) Chemical modification of siRNAs for in vivo use. Oligonucleotides 18:305–319
Lewis BP, Burge CB, Bartel DP (2005) Conserved seed pairing, often flanked by adenosines, indicates that thousands of human genes are microRNA targets. Cell 120:15–20
Esau CC, Monia BP (2007) Therapeutic potential for microRNAs. Adv Drug Deliv Rev 59:101–114
Chua JH, Armugam A, Jeyaseelan K (2009) MicroRNAs: biogenesis, function and applications. Curr Opin Mol Ther 11:189–199
Liao W, Dong J, Peh HY, Tan LH, Lim KS, Li L, Wong WF (2017) Oligonucleotide therapy for obstructive and restrictive respiratory diseases. Molecules 22:139
Siolas D, Lerner C, Burchard J et al (2005) Synthetic shRNAs as potent RNAi triggers. Nat Biotechnol 23:227–231
Ge Q, Dallas A, Ilves H et al (2010) Effects of chemical modification on the potency, serum stability, and immunostimulatory properties of short shRNAs. RNA 16:118–130
Waterston RH, Lindblad-Toh K, Birney E et al (2002) Initial sequencing and comparative analysis of the mouse genome. Nature 420:520–562
Storz G, Altuvia S, Wassarman KM (2005) An abundance of RNA regulators. Annu Rev Biochem 74:199–217
Eddy SR (2001) Non-coding RNA genes and the modern RNA world. Nat Rev Genet 2:919–929
Vogel J (2009) A rough guide to the non-coding RNA world of salmonella. Mol Microbiol 71:1–11
Mehler MF, Mattick JS (2007) Noncoding RNAs and RNA editing in brain development, functional diversification, and neurological disease. Physiol Rev 87:799–823
Watts JK, Deleavey GF, Damha MJ (2008) Chemically modified siRNA: tools and applications. Drug Discov Today 13:842–855
Beaucage SL (2008) Solid-phase synthesis of siRNA oligonucleotides. Curr Opin Drug Discov Dev 11:203–216
Lönnberg H (2009) Solid-phase synthesis of oligonucleotide conjugates useful for delivery and targeting of potential nucleic acid therapeutics. Bioconjug Chem 20:1065–1094
Reese CB (2002) The chemical synthesis of oligo- and poly-nucleotides: a personal commentary. Tetrahedron 58:8893–8920
Reese CB (2005) Oligo- and poly-nucleotides: 50 years of chemical synthesis. Org Biomol Chem 3:3851–3868
Beaucage SL, Reese C (2009) Recent advances in the chemical synthesis of RNA. In: Beaucage SL, Bergstrom DE, Glick GD et al (eds) Current protocols in nucleic acid chemistry. Wiley, New York, pp 2.16.1–2.2.31
Beaucage SL, Caruthers MH (2000) In: Beaucage SL, Bergstrom DE, Glick GD et al (eds) Current protocols in nucleic acid chemistry, vol I. Wiley, New York, pp 3.3.1–3.3.20
Beaucage SL, Iyer RP (1993) The synthesis of modified oligonucleotides by the phosphoramidite approach and their applications. Tetrahedron 49:6123–6194
Beaucage SL, Iyer RP (1992) Advances in the synthesis of oligonucleotides by the phosphoramidite approach. Tetrahedron 48:2223–2311
Bornscheuer U (2010) The first artificial cell-A revolutionary step in synthetic biology? Angew Chem Int Ed 49:5228–5230
Gibson DG (2008) Complete chemical synthesis, assembly, and cloning of a mycoplasma genitalium genome. Science 319:1215–1220
Smith M, Rammer DH, Goldberg IH et al (1962) Polynucleotides. XIV. Specific synthesis of the C3′-C5′ internucleotide linkage. Synthesis of uridylyl(3′→5′)-uridine and uridylyl-(3′→5′)-adenosine. J Am Chem Soc 84:430–440
Schulhof JC, Molko DS, Teoule R (1987) 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 15:397–416
Sinha ND, Davis P, Usman N et al (1993) Labile exocyclic amino protection of nucleosides in DNA, RNA and oligonucleotide analog synthesis facilitating N-deacylation, minimizing depruination and chain degradation. Biochimie 75:13–23
Welz R, Müller S (2002) 5-(Benzylmercapto)-1H-tetrazole as activator for 2′-O-TBDMS phosphoramidite building blocks in RNA synthesis. Tetrahedron Lett 43:795–797
Sproat B, Colonna F, Mullah B et al (1995) An efficient method for the isolation and purification of ligoribonucleotides. Nucleosides Nucleotides 14:255–273
Vargeese C, Carter J, Yegge J et al (1998) Efficient activation of nucleoside phosphoramidites with 4,5-dicyanoimidazole during oligonucleotide synthesis. Nucleic Acids Res 26:1046–1050
Leuck M, Wolter A, Stumpe A (2008) U.S. Pat. Appl. Publ., US 20080064867 A1 20080313. Activator 42 is commercially available from Proligo Co. Ltd. For its recent use see: Utagawa E, Ohkubo A, Sekine M et al (2007) Synthesis of branched oligonucleotides with three different sequences using an oxidatively removable tritylthio group. J Org Chem 72:8259–8266
Hayakawa Y, Kataoka M, Noyori R (1996) Benzimidazolium triflate as an efficient promoter for nucleotide synthesis via the phosphoramidite method. J Org Chem 61:7996–7997
Hakimelahi H, Proba ZA, Ogilvie KK (1982) New catalyst and procedures for the dimethoxytritylation and selective silylation of ribonucleosides. Can J Chem 60:1106–1113
Ogilvie KK, Damha MJ, Usman N et al (1987) Developments in the chemical synthesis of naturally occurring DNA and RNA sequences with normal and unusual linkages. Pure Appl Chem 59:325–330
Usman N, Ogilvie KK, Jiang MY et al (1987) The automated chemical synthesis of long oligoribuncleotides using 2′-O-silylated ribonucleoside 3′-O-phosphoramidites on a controlled-pore glass support: synthesis of a 43-nucleotide sequence similar to the 3′-half molecule of an Escherichia coli formylmethionine tRNA. J Am Chem Soc 109:7845–7854
Ogilvie KK, Usman N, Nicoghosian K (1988) Total chemical synthesis of a 77-nucleotide-long RNA sequence having methionine-acceptance activity. Proc Natl Acad Sci U S A 85:5764–5768
Corey EJ, Venkateswarlu A (1972) Protection of hydroxyl groups as tert-butyldimethylsilyl derivatives. J Am Chem Soc 94:6190–6191
Nagai H, Fujiwara T, Fujii M et al (1989) Reinvestigation of deoxyribonucleoside phosphorothioites–synthesis and properties of deoxyribonucleoside-3′-dimethyl phosphites. Nucleic Acids Res 17:8581–8593
Tanimura H, Maeda M, Fukazawa T et al (1989) Chemical synthesis of the 24 RNA fragments corresponding to hop stunt viroid. Nucleic Acids Res 17:8135–8147
Tanimura H, Fukazawa T, Sekine M et al (1988) The practical synthesisof RNA fragments in the solid phase approach. Tetrahedron Lett 29:577–578
Iwai S, Ohtsuka E (1988) Synthesis of oligoribonucleotifes by the phosphoramidite approach using 5′-levullinyl and 2′-tetrahydrofuranyl protection. Tetrahedron Lett 29:5383–5386
Iwai S, Ohtsuka E (1988) 5′-Levulinyl and 2′-tetrahydrofurany protection for the synthesis of oligoribonucleotides by the phosphoramidite approach. Nucleic Acids Res 16:9443–9456
Van der Marel GA, Wille G, van Boom JH (1982) Solid-phase synthesis of the RNA fragment: rAAGAAGAAGAAGA. Recueil Trav Chim Pays-Bas 101:241–246
Lloyd W, Reese C, Song Q et al (2000) Some observations relating to the use of 1-aryl-4-alkoxypiperidin-4-yl groups for the protection of the 2′-hydroxy functions in the chemical synthesis of oligoribonucleotides. J Chem Soc Perkin Trans I:165–176
Reese C, Thompson EA (1988) A new synthesis of 1-arylpiperidin-4-ols. J Chem Soc Perkin Trans I:2881–2885
Capaldi DC, Reese CB (1994) Use of the 1-(2-fluorophenyl)-4-methoxypiperidin-4-yl (Fpmp) and related protecting groups in oligoribonucleotide synthesis: stability of internucleotide linkages to aqueous acid. Nucleic Acids Res 22:2209–2216
Scaringe SA, Wincott FE, Caruthers MH (1998) Novel RNA synthesis method using 5′-O-silyl-2′-O-orthoester protecting groups. J Am Chem Soc 120:11820–11821
Dahl BJ, Bjergarde K, Henriksen L et al (1990) A highly reactive, odorless substitute for thiophenol triethylamine as a deprotection reagent in the synthesis of oligonucleotides and their analogs. Acta Chem Scand 44:639–641
Schwartz WE, Breaker RR, Asteriadis GT et al (1992) Rapid synthesis of oligoribonucleotides using 2′-O-(ortho-nitrobenzyloxymethyl)-protected monomers. Bioorg Med Chem Lett 2:1019–1024
Miller TJ, Schwartz ME, Gough GR (2000) 2′-Hydroxyl-protecting groups that are either photochemically labile or sensitive to fluoride ions. In: Beaucage SL, Bergstrom DE, Glick GD et al (eds) Current protocols in nucleic acid chemistry. Wiley, New York, pp 2.5.1–2.5.36
Miller TJ, Schwartz ME, Gough GR (2000) Synthesis of oligoribonucleotides using the 2-nitrobenzyloxymethyl group for 2′-hydroxyl protection. In: Beaucage SL, Bergstrom DE, Glick GD et al (eds) Current protocols in nucleic acid chemistry. Wiley, New York, pp 3.7.1–3.7.8
DeBear JS, Hayes JA, Koleck MP et al (1987) A universal glass support for oligonucleotide synthesis. Nucleoside Nucleotides 6:821–830
Pitsch S (1997) An efficient synthesis of enantiomeric ribonucleic acids from D-glucose. Helv Chim Acta 80:2286–2314
Pitsch S, Weiss PA, Wu X et al (1999) Fast and reliable automated synthesis of RNA and partially 2′-O-protected precursors (‘caged RNA’) based on two novel, orthogonal 2′-O-protecting groups. Helv Chim Acta 82:1753–1761
Wincott FE, Usman N (1994) 2′-(Trimethylsilyl)ethoxymethyl protection of the 2′-hydroxyl group in oligoribonucleotide synthesis. Tetrahedron Lett 35:6827–6830
Pitsch S, Weiss PA, Jenny L et al (2001) Reliable chemical synthesis of oligoribonucleotides (RNA) with 2′-O-[(triisopropylsilyl)oxy]methyl(2′-O-tom)-protected phosphoramidites. Helv Chim Acta 84:3773–3794
Pitsch S, Weiss PA (2001) Chemical synthesis of RNA sequences with 2′-O-[(triisopropylsilyl)oxy]methyl-protected ribonucleoside phosphoramidites. In: Beaucage SL, Bergstrom DE, Glick GD et al (eds) Current protocols in nucleic acid chemistry. Wiley, New York, pp 3.8.1–3.8.15
Wu X, Pitsch S (1999) Functionalization of the sugar moiety of oligoribonucleotides on solid support. Bioconjug Chem 10:921–924
Wu X, Pitsch S (1998) Synthesis and pairring properties of oligoribonucleotide analogues containing a metal-binding site attached to β-D-allofuranosyl cytosine. Nucleic Acids Res 26:4315–4323
Wu X, Pitsch S (2000) Synthesis of 5′-C- and 2′-O-(bromoalkyl)-substituted ribonucleoside phosphoramidites for the post-synthetic functionalization of oligonucleotides on solid support. Helv Chim Acta 83:1127–1144
Stutz A, Höbartner C, Pitsch S (2000) Novel fluoride-labile mucleobase-protecting groups for the synthesis of 3′(2′)-O-aminoacylated RNA sequences. Helv Chim Acta 83:2477–2483
Wenter P, Pitsch S (2003) Synthesis of selectively 15N-labeled 2′-O-[[triisopropylsilyl]oxy]methyl] (=tom)-protected ribonucleoside phosphoramidites and their incorporation into a bistable 32 mer RNA sequence. 86:3955–3974
Porcher S, Pitsch S (2005) Synthesis of 2′-O-[(triisopropylsilyl)oxy]methyl (=tom)-protected ribonucleoside phosphoramidites containing various nucleobase analogues. Helv Chim Acta 88:2683–2703
Umemoto T, Wada T (2004) Oligoribonucleotide synthesis by the use of 1-(2-cyanoethoxy)ethyl (CEE) as a 2′-hydroxy protecting group. Tetrahedron Lett 45:9529–9531
Matysiak S, Fitznar HP, Schnell R et al (1998) Nucleosides – part LXIII – acetals as new 2′-O-protecting functions for the synthesis of oligoribonucleotides: synthesis of uridine building blocks and evaluation of their relative acid stability. Helv Chim Acta 81:1545–1566
Ohgi T, Masutomi Y, Ishiyama K (2005) A new RNA synthetic Method with a 2′-O-(2-cyanoethoxyemthyl) protecting group. Org Lett 7:3477–3480
Zhou C, Honcharenko D, Chattopadhyaya J (2007) 2-(4-Tolylsulfonyl)ethoxymethyl (TEM)–a new 2′-OH protecting group for solid-supported RNA synthesis. Org Biomol Chem 5:333–343
Zhou C, Pathmasire W, Honchararenko D et al (2007) High-quality oligo-RNA synthesis using the new 2′-O-TEM protecting group by selectively quenching the addition of p-tolyl vinyl sulphone to exocyclic amino functions. Can J Chem 85:293–301
Semenyuk A, Foldesi A, Johansson T et al (2006) Synthesis of RNA using 2′-O-DTM protection. J Am Chem Soc 128:12356–12357
Sekine M, Nakanishi T (1991) Oligoribonucleotide synthesis by use of [[2-(methylthio)phenyl]thio]methyl (MPTM) group as the 2′-hydroxyl protecting groups. Chem Lett:121–124
Sekine M, Nakanishi T (1989) [[2-(Methylthil)phenyl]thio]methyl (MPTM): a new protecting group of hydroxyl groups caable of conversion to a methyl group. J Org Chem 54:5998–6000
Sekine M, Hata T (1999) Chemical synthesis of oligonucleotides by use of phenylthio group. Curr Org Chem 3:25–66
Cieslak J, Kauffman JS, Kolodziejski MJ et al (2007) Assessment of 4-nitrogenated benzyloxymethyl groups for 2′-hydroxyl protection in solid-phase RNA synthesis. Org Lett 9:671–674
Lackey JG, Mitra D, Somoza MM et al (2009) Acetal levulinyl ester (ALE) groups for 2′-hydroxyl protection of ribonucleosides in the synthesis of oligoribonucleotides on glass and microarrays. J Am Chem Soc 131:8496–8502
Gough GR, Miller TJ, Mantick NA (1996) p-Nitrobenzyloxymethyl: a new fluoride-removable protecting group for ribboneoside 2′-hydroxyls. Tetrahedron Lett 37:981–982
Pon RT, Yu S (1997) Hydroquinone-O,O′-diacetic acid (‘Q-linker’) as a replacement for succinyl and oxalyl linker arms in solid phase oligonucleotide synthesis. Nucleic Acids Res 25:3629–3635
Saneyoshi H, Seio K, Sekine M (2005) A general method for the synthesis of 2′-O-cyanoethylated oligoribonucleotides having promising hybridization affinity for DNA and RNA and enhanced nuclease resistance. J Org Chem 70:10453–10460
Saneyoshi H, Ando K, Seio K et al (2007) Chemical synthesis of RNA via 2′-O-cyanoethylated intermediates. Tetrahedron 63:11195–11203
Velikyan I, Acharya S, Trifonova A et al (2001) The pK(a)’s of 2′-hydroxyl group in nucleosides and nucleotides. J Am Chem Soc 123:2893–2894
Markiewicz W T, Tos-Marciniak A et al WO2014148928 A1
Kataoka M. (2014) JP WO2014/017615 A
Matsuno Y, Takao S, Kim S, Chiba K (2016) Synthetic method for oligonucleotide block by using alkyl-chain-soluble support. Org Lett 18:800–803
Aoki E, Suzuki H, Itoh A. (2013) WO/2013/027843
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Sekine, M. (2018). Recent Development of Chemical Synthesis of RNA. In: Obika, S., Sekine, M. (eds) Synthesis of Therapeutic Oligonucleotides. Springer, Singapore. https://doi.org/10.1007/978-981-13-1912-9_3
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DOI: https://doi.org/10.1007/978-981-13-1912-9_3
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