Abstract
Bridge modifications between the 2′- and 4′-positions of a nucleoside have attracted much attention for improving properties of nucleic acid drugs, and many classes of 2′,4′-bridged nucleic acids have been developed to date. Evaluation of oligonucleotides containing 2′,4′-bridged nucleic acids suggests that, in addition to the bridge size, the number, type, and position of atoms composing the bridge unit affect (i) the binding affinity to target nucleic acid, (ii) resistance against nuclease degradation, and other factors. The addition of plural heteroatoms is an attractive bridge modification because interaction of the heteroatom with water can affect the properties of the oligonucleotides. In this chapter, focusing on 2′,4′-bridged nucleic acids containing plural heteroatoms in the bridge moiety, we mainly describe the design concept and synthesis. In addition, properties of 2′,4′-bridged nucleic acids are briefly explained.
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References
Singh SK, Koshkin AA, Wengel J, Nielsen P (1998) LNA (locked nucleic acids): synthesis and high-affinity nucleic acid recognition. Chem Commun: 455–456
Koshkin AA, Singh SK, Nielsen P, Rajwanshi VK, Kumar R, Meldgaard M, Olsen CE, Wengel J (1998) LNA (locked nucleic acids): synthesis of the adenine, cytosine, guanine, 5-methylcytosine, thymine and uracil bicyclonucleoside monomers, oligomerisation, and unprecedented nucleic acid recognition. Tetrahedron 54:3607–3630
Obika S, Nanbu D, Hari Y, Morio K, In Y, Ishida T, Imanishi T (1997) Synthesis of 2′-Ο,4′-C-methyleneuridine and – cytidine. Novel bicyclic nucleosides having a fixed C3′-endo sugar puckering. Tetrahedron Lett 38:8735–8738
Obika S, Nanbu D, Hari Y, Ando J, Morio K, Doi T, Imanishi T (1998) Stability and structural features of the duplexes containing nucleoside analogues with a fixed N-type conformation, 2′-O,4′-C-methyleneribonucleosides. Tetrahedron Lett 39:5401–5404
Petersen M, Wengel J (2003) LNA: a versatile tool for therapeutics and genomics. Trends Biotech 21:74–81
Koch T (2003) Locked nucleic acids: a family of high affinity nucleic acid probes. J Phys Condens Matter 15:S1861–S1871
Vester B, Wengel J (2004) LNA (locked nucleic acid): high-affinity targeting of complementary RNA and DNA. Biochemistry 43:13233–13241
Jepsen JS, Sørensen MD, Wengel J (2004) Locked nucleic acid: a potent nucleic acid analog in therapeutics and biotechnology. Oligonucleotides 14:130–146
Kaur H, Babu R, Maiti S (2007) Perspectives on chemistry and therapeutic applications of locked nucleic acid (LNA). Chem Rev 107:4672–4697
Veedu RN, Wengel J (2009) Locked nucleic acid as a novel class of therapeutic agents. RNA Biol 6:321–323
Campbell MA, Wengel J (2011) Locked vs. unlocked nucleic acids (LNA vs. UNA): contrasting structures work towards common therapeutic goals. Chem Soc Rev 40:5680–5689
Zhou C, Chattopadhyaya J (2009) The synthesis of therapeutic locked nucleos(t)ides. Curr Opin Drug Discov Dev 12:876–898
Rahman SMA, Imanishi T, Obika S (2009) Synthesis of several types of bridged nucleic acids. Chem Lett 38:512–517
Obika S, Rahman SMA, Fujisaka A, Kawada Y, Baba T, Imanishi T (2010) Bridged nucleic acids: development, synthesis and properties. Heterocycles 81:1347–1392
Yamamoto T, Nakatani M, Narukawa K, Obika S (2011) Antisense drug discovery and development. Fut Med Chem 3:339–365
Zhou C, Chattopadhyaya J (2012) Intramolecular free-radical cyclization reactions on pentose sugars for the synthesis of carba-LNA and carba-ENA and the application of their modified oligonucleotides as potential RNA targeted therapeutics. Chem Rev 112:3808–3832
Astakhova IK, Wengel J (2014) Scaffolding along nucleic acid duplexes using 2′-amino-locked nucleic acids. Acc Chem Res 47:1768–1777
Morita K, Hasegawa C, Kaneko M, Tsutsumi S, Sone J, Ishikawa T, Imanishi T, Koizumi M (2002) 2′-O,4′-C-Ethylene-bridged nucleic acids (ENA): high-nuclease-resistant and thermodynamically stable oligonucleotides for antisense drug. Bioorg Med Chem Lett 12:73–76
Morita K, Takagi M, Hasegawa C, Kaneko M, Tsutsumi S, Sone J, Ishikawa T, Imanishi T, Koizumi M (2003) Synthesis and properties of 2′-O,4′-C-ethylene-bridged nucleic acids (ENA) as effective antisense oligonucleotides. Bioorg Med Chem 11:2211–2226
Wang G, Gunic E, Girardet J-L, Stoisavljevic V (1999) Conformationally locked nucleosides. Synthesis and hybridization properties of oligodeoxynucleotides containing 2′,4′-C-bridged 2′-deoxynucleosides. Bioorg Med Chem Lett 9:1147–1150
Wang G, Girardet J-L, Gunic E (1999) Conformationally locked nucleosides. Synthesis and stereochemical assignments of 2′-C,4′-C-bridged bicyclonucleosides. Tetrahedron 55:7707–7724
Singh SK, Kumar R, Wengel J (1998) Synthesis of novel bicycle[2.2.1] ribonucleosides: 2′-amino- and 2′-thio-LNA monomeric nucleosides. J Org Chem 63:6078–6079
Singh SK, Kumar R, Wengel J (1998) Synthesis of 2′-amino-LNA: a novel conformationally restricted high-affinity oligonucleotide analogue with a handle. J Org Chem 63:10035–10039
Kumar R, Singh SK, Koshkin AA, Rajwanshi VK, Meldgaard M, Wengel J (1998) The first analogues of LNA (locked nucleic acids): phosphorothioate-LNA and 2′-thio-LNA. Bioorg Med Chem Lett 8:2219–2222
Morihiro K, Kodama T, Kentefu, Moai Y, Veedu RN, Obika S (2013) Selenomethylene locked nucleic acid enables reversible hybridization in response to redox changes. Angew Chem Int Ed 52:5074–5078
Xu J, Liu Y, Dupouy C, Chattopadhyaya J (2009) Synthesis of conformationally locked carba-LNAs through intramolecular free-radical addition to C=N. Electrostatic and steric implication of the carba-LNA substituents in the modified oligos for nuclease and thermodynamic stabilities. J Org Chem 74:6534–6554
Sørensen MD, Petersen M, Wengel J (2003) Functionalized LNA (locked nucleic acid): high-affinity hybridization of oligonucleotides containing N-acylated and N-alkylated 2′-amino-LNA monomers. Chem Commun: 2130–2131
Varghese OP, Barman J, Pathmasiri W, Plashkevych O, Honcharenko D, Chattopadhyaya J (2006) Conformationally constrained 2′-N,4′-C-ethylene-bridged thymidine (aza-ENA-T): Synthesis, structure, physical, and biochemical studies of aza-ENA-T-modified oligonucleotides. J Am Chem Soc 128:15173–15187
Albæk N, Petersen M, Nielsen P (2006) Analogues of a locked nucleic acid with three-carbon 2′,4′-linkages: synthesis by ring-closing metathesis and influence on nucleic acid duplex stability and structure. J Org Chem 71:7731–7740
Srivastava P, Barman J, Pathmasiri W, Plashkevych O, Wenska M, Chattopadhyaya J (2007) Five- and six-membered conformationally locked 2′,4′-carbocyclic ribo-thymidines: synthesis, structure, and biochemical studies. J Am Chem Soc 129:8362–8379
Zhou C, Liu Y, Andaloussi M, Badgujar N, Plashkevych O, Chattopadhyaya J (2009) Fine tuning of electrostatics around the internucleotidic phosphate through incorporation of modified 2′,4′-carbocyclic-LNAs and – ENAs leads to significant modulation of antisense properties. J Org Chem 74:118–134
Zhou C, Plashkevych O, Chattopadhyaya J (2009) Double sugar and phosphate backbone-constrained nucleotides: synthesis, structure, stability, and their incorporation into oligodeoxynucleotides. J Org Chem 74:3248–3265
Kumar S, Hansen MH, Albæk N, Steffansen SI, Petersen M, Nielsen P (2009) Synthesis of functionalized carbocyclic locked nucleic acid analogues by ring-closing diene and enyne metathesis and their influence on nucleic acid stability and structure. J Org Chem 74:6756–6769
Seth PP, Vasquez G, Allerson CA, Berdeja A, Gaus H, Kinberger GA, Prakash TP, Migawa MT, Bhat B, Swayze EE (2010) Synthesis and biophysical evaluation of 2′,4′-constrained 2′O-methoxyethyl and 2′,4′-constrained 2′O-ethyl nucleic acid analogues. J Org Chem 75:1569–1581
Liu Y, Xu J, Karimiahmadabadi M, Zhou C, Chattopadhyaya J (2010) Synthesis of 2′,4′-propylene-bridged (carba-ENA) thymidine and its analogues: the engineering of electrostatic and steric effects at the bottom of the minor groove for nucleobase and thermodynamic stabilities and elicitation of RNase H. J Org Chem 75:7112–7128
Johannsen MW, Crispino L, Wamberg MC, Kalra N, Wengel J (2011) Amino acids attached to 2′-amino-LNA: synthesis and excellent duplex stability. Org Biomol Chem 9:243–252
Seth PP, Allerson CA, Berdeja A, Siwkowski A, Pallan PS, Gaus H, Prakash TP, Watt AT, Egli M, Swayze EE (2010) An exocyclic methylene group acts as a bioisostere of the 2′-oxygen atom in LNA. J Am Chem Soc 132:14942–14950
Upadhayaya RS, Deshpande SG, Li Q, Kardile RA, Sayyed AY, Kshirsagar EK, Salunke RV, Dixit SS, Zhou C, Földesi A, Chattopadhyaya J (2011) Carba-LNA-5MeC/A/G/T modified oligos show nucleobase-specific modulation of 3′-exonuclease activity, thermodynamic stability, RNA selectivity, and RNase H elicitation: synthesis and biochemistry. J Org Chem 76:4408–4431
Yamaguchi T, Horiba M, Obika S (2015) Synthesis and properties of 2′-O,4′-C-spirocyclopropylene bridged nucleic acid (scpBNA), an analogue of 2′,4′-BNA/LNA bearing a cyclopropane ring. Chem Commun 51:9737–9740
Yahara A, Shrestha AR, Yamamoto T, Hari Y, Osawa T, Yamaguchi M, Nishida M, Kodama T, Obika S (2012) Amido-bridged nucleic acids (AmNAs): synthesis, duplex stability, nuclease resistance, and in vitro antisense potency. ChemBioChem 13:2513–2516
Yamamoto T, Yahara A, Waki R, Yasuhara H, Wada F, Harada-Shiba M, Obika S (2015) Amido-bridged nucleic acids with small hydrophobic residues enhance hepatic tropism of antisense oligonucleotides in vivo. Org Biomol Chem 13:3757–3765
Martin P (1995) Ein neuer zugang zu 2′-O-alkylribonucleosiden und eigenschaften deren oligonucleotide. Helv Chim Acta 78:486–504
Baker BF, Lot SS, Condon TP, Cheng-Flournoy S, Lesnik EA, Sasmor HM, Bennett (1997) 2′-O-(2-methoxy)ethyl-modified anti-intercellular adhesion molecule 1(ICAM-1) oligonucleotides selectively increase the ICAM-1 mRNA level and inhibit formation of the ICAM-1 translation initiation complex in human umbilical vein endothelial cells. J Biol Chem 272:11994–12000
Seth PP, Siwkowski A, Allerson CA, Vasquez G, Lee S, Prakash TP, Wancewicz EV, Witchell D, Swayze EE (2009) Short antisense oligonucleotides with novel 2′-4′ conformationally restricted nucleoside analogues show improved potency without increased toxicity in animals. J Med Chem 52:10–13
Prakash TP, Siwkowski A, Allerson CR, Migawa MT, Lee S, Gaus HJ, Black C, Seth PP, Swayze EE, Bhat B (2010) Antisense oligonucleotides containing conformationally constrained 2′,4′-(N-methoxy)aminomethylene and 2′,4′-aminooxymethylene and 2′-Ο,4′-C-aminomethylene bridged nucleoside analogues show improved potency in animal models. J Med Chem 53:1636–1650
Mori K, Kodama T, Baba T, Obika S (2011) Bridged nucleic acid conjugates at 6′-thiol: synthesis, hybridization properties and nuclease resistances. Org Biomol Chem 9:5272–5279
Baba T, Kodama T, Mori K, Imanishi T, Obika S (2010) A novel bridged nucleoside bearing a conformationally switchable sugar moiety in response to redox changes. Chem Commun 46:8058–8060
Barrón LB, Waterman KC, Filipiak P, Hug GL, Nauser T, Schöneich C (2004) Mechanism and kinetics of photoisomerization of a cyclic disulfide, trans-4,5-dihydroxy-1,2-dithiacyclohexane. J Phys Chem A 108:2247–2255
Barrón LB, Waterman KC, Offerdahl TJ, Munson E, Schöneich C (2005) Reactions of aliphatic thiyl radicals in the solid state: photoisomerization of trans-4,5-dihydroxy-1,2-dithiacyclohexane and oxidation of dithiothreitol. J Phys Chem A 109:9241–9248
Shrestha AR, Kotobuki Y, Hari Y, Obika S (2014) Guanidine bridged nucleic acid (GuNA): an effect of a cationic bridged nucleic acid on DNA binding affinity. Chem Commun 50:575–577
Rahman SMA, Seki S, Obika S, Yoshikawa H, Miyashita K, Imanishi T (2008) Design, synthesis, and properties of 2′,4′-BNANC: a bridged nucleic acid analogue. J Am Chem Soc 130:4886–4896
Miyashita K, Rahman SMA, Seki S, Obika S, Imanishi T (2007) N-methyl substituted 2′,4′-BNANC: a highly nuclease-resistant nucleic acid analogue with high-affinity RNA selective hybridization. Chem Commun: 3765–3767
Rahman SMA, Seki S, Obika S, Haitani S, Miyashita K, Imanishi T (2007) Highly stable pyrimidine-motif triplex formation at physiological pH values by a bridged nucleic acid analogue. Angew Chem Int Ed 46:4306–4309
Yamamoto T, Yasuhara H, Wada F, Harada-Shiba M, Imanishi T, Obika S (2012) Superior silencing by 2′,4′-BNANC-based short antisense oligonucleotides compared to 2′,4′-BNA/LNA-based apolipoprotein B antisense inhibitors. J Nucleic Acids 2012:707323
Yamamoto T, Harada-Shiba M, Nakatani M, Wada S, Yasuhara H, Narukawa K, Sasaki K, Shibata M, Torigoe H, Yamaoka T, Imanishi T, Obika S (2012) Cholesterol-lowering action of BNA-based antisense oligonucleotides targeting PCSK9 in atherogenic diet-induced hypercholesterolemic mice. Mol Ther Nucleic Acids 1:e22
Kondo J, Nomura Y, Kitahara Y, Obika S, Torigoe H (2016) The crystal structure of 2′,4′-BNANC[N-Me]-modified antisense gapmer in complex with the target RNA. Chem Commun 52:2354–2357
Torigoe H, Rahman SM, Takuma H, Sato N, Imanishi T, Obika S, Sasaki K (2011) Interrupted 2′-O,4′-C-aminomethylene bridged nucleic acid modification enhances pyrimidine motif triplex-forming ability and nuclease resistance under physiological condition. Nucleosides Nucleotides Nucleic Acids 30:63–81
Shrestha AR, Hari Y, Yahara A, Osawa T, Obika S (2011) Synthesis and properties of a bridged nucleic acid with a perhydro-1,2-oxazin-3-one ring. J Org Chem 76:9891–9899
Hari Y, Osawa T, Kotobuki Y, Yahara A, Shrestha AR, Obika S (2013) Synthesis and properties of thymidines with six-membered amide bridge. Bioorg Med Chem 21:4405–4412
Mitsuoka Y, Fujimura Y, Waki R, Kugimiya A, Yamamoto T, Hari Y, Obika S (2014) Sulfonamide-bridged nucleic acid: synthesis, high RNA selective hybridization, and high nuclease resistance. Org Lett 16:5640–5643
Mitsuoka Y, Aoyama H, Kugimiya A, Fujimura Y, Yamamoto T, Waki R, Wada F, Tahara S, Sawamura M, Noda M, Hari Y, Obika S (2016) Effect of an N-substituent in sulfonamide-bridged nucleic acid (SuNA) on hybridization ability and duplex structure. Org Biomol Chem. https://doi.org/10.1039/c6ob01051b
Gryaznov SM, Letsinger RL (1992) Selective O-phophitilation with nucleoside phosphoramidite reagents. Nucleic Acids Res 20:1879–1882
Barman J, Gurav D, Oommen OP, Varghese OP (2015) 2′-N-Guanidino,4′-C-ethylene bridged thymidine (GENA-T) modified oligonucleotide exhibits triplex formation with excellent enzymatic stability. RSC Adv 5:12257–12260
Hari Y, Obika S, Ohnishi R, Eguchi K, Osaki T, Ohishi H, Imanishi T (2006) Synthesis and properties of 2′-O,4′-C-methyleneoxymethylene bridged nucleic acid. Bioorg Med Chem 14:1029–1038
Mitsuoka Y, Kodama T, Ohnishi R, Hari Y, Imanishi T, Obika S (2009) A bridged nucleic acid, 2′,4′-BNACOC: synthesis of fully modified oligonucleotides bearing thymine, 5-methylcytosine, adenine and guanine 2′,4′-BNACOC monomers and RNA-selective nucleic-acid recognition. Nucleic Acids Res 37:1225–1238
Morihiro K, Kodama T, Nishida M, Imanishi T, Obika S (2009) Synthesis of light-responsive bridged nucleic acid and changes in affinity with complementary ssRNA. ChemBioChem 10:1784–1788
Morihiro K, Kodama T, Obika S (2011) Benzylidene acetal type bridged nucleic acids: changes in properties upon cleavage of the bridge triggered by external stimuli. Chem Eur J 17:7918–7926
Kasahara Y, Kitadume S, Morihiro K, Kuwahara M, Ozaki H, Sawai H, Imanishi T, Obika S (2010) Effect of 3′-end capping of aptamer with various 2′,4′-bridged nucleotides: enzymatic post-modification toward a practical use of polyclonal aptamers. Bioorg Med Chem Lett 20:1626–1629
Nishida M, Baba T, Kodama T, Yahara A, Imanishi T, Obika S (2010) Synthesis, RNA selective hybridization and high nuclease resistance of an oligonucleotide containing novel bridged nucleic acid with cyclic urea structure. Chem Commun 46:5283–5285
Hari Y, Morikawa T, Osawa T, Obika S (2013) Synthesis and properties of 2′-O, 4′-C-ethyleneoxy bridged 5-methyluridine. Org Lett 15:3702–3705
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Hari, Y., Obika, S. (2018). 2′,4′-Bridged Nucleic Acids Containing Plural Heteroatoms in the Bridge Moiety. In: Obika, S., Sekine, M. (eds) Synthesis of Therapeutic Oligonucleotides. Springer, Singapore. https://doi.org/10.1007/978-981-13-1912-9_12
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