4′-Epi-DNA: A DNA Mimic Containing 4′-hydroxymethyl-α-l-Xylo-Thymidine with Compact Backbone like RNA

References

• Bennet, C. F.; Swayze, E. E. RNA targeting therapeutics: molecular mechanisms of antisense oligonucleotides as a therapeutic platform. Annu. Rev. Pharmacol. Toxicol. 2010, 50, 259–293.
   PubMed Web of Science ®Google Scholar
• Kole, R.; Krainer, A. R.; Altman, S. RNA therapeutics: beyond RNA interference and antisense oligonucleotides. Nat. Rev. Drug Discov. 2012, 11, 125–140.
   PubMed Web of Science ®Google Scholar
• Levin, A. A. A review of the issues in the pharmacokinetics and toxicology of phosphorothioate antisense oligonucleotides. Biochim. Biophys. Acta 1999, 1489, 69–84.
   PubMed Web of Science ®Google Scholar
• Kurreck, J. Antisense technologies. Improvement through novel chemical modifications. Eur. J. Biochem. 2003, 270, 1628–1644.
   PubMedGoogle Scholar
• Shukla, S.; Sumaria, C. S.; Pradeepkumar, P. I. Exploring chemical modifications for siRNA therapeutics: A structural and functional outlook. Chem. Med. Chem. 2010, 5, 328–349.
   Web of Science ®Google Scholar
• Micklefield, J. Backbone modification of nucleic acids: Synthesis, structure and therapeutic applications. Curr. Med. Chem. 2001, 8, 1157–1179.
   PubMed Web of Science ®Google Scholar
• Lesnik, E. A.; Guinosso, C. J.; Kawasaki, A. M.; Sasmor, H.; Zounes, M.; Cummins, L. L.; Ecker, D. J.; Cook, P. D.; Freier, S. M. Oligodeoxynucleotides containing 2′-O-modified adenosine: Synthesis and effects on stability of DNA:RNA duplexes. Biochemistry 1993, 32, 7832–7838.
   PubMed Web of Science ®Google Scholar
• Manoharan, M. 2′-carbohydrate modifications in antisense oligonucleotide therapy:Importance of conformation, configuration and conjugation. Biochim. Biophys. Acta 1999, 1489, 117–130.
   PubMed Web of Science ®Google Scholar
• Martin, P. EinneuerZugangzu 2-O-Alkylribonucleosiden und Eigenchaftenderen Oligonucleotide. Helv. Chim. Acta 1995, 78, 486–504.
   Web of Science ®Google Scholar
• Koshkin, A. A.; Singh, S. K.; Nielsen, P.; Rajwanshi, V. K., Kumar, R.; Meldgaard, M.; Olsen, C. E.; Wengel, J. LNA(Locked Nucleic Acids): Synthesis of the adenine, cytosine, guanine, 5-methylcytosine, thymine and uracil bicyclonucleoside monomers, oligomerisation, and unprecedented nucleic acid recognition. Tetrahedron 1998, 54, 3607–3630.
   Web of Science ®Google Scholar
• Kurreck, J.; Wyszko, E.; Gillen, C.; ErdmannV. A. Design of antisense oligonucleotides stabilized by locked nucleic acids. Nucleic Acids Res. 2002, 30, 1911–1918.
   PubMed Web of Science ®Google Scholar
• Deleavey, G. F.; Watts, J. K.; Alain, T.; Robert, F.; Kalota, A.; Aishwarya, V.; Pelletier, J.; Gewirtz, A. M.; Sonenberg, N.; DamhaM. J. Synergistic effects between analogs of DNA and RNA improve the potency of siRNA-mediated gene silencing. Nucleic Acids Res. 2010, 38, 4547–4557.
   PubMed Web of Science ®Google Scholar
• Kawasaki, A. M.; Casper, M. D.; Freier, S. M.; Lesnik, E. A.; Zounes, M. C.; Cummins, L. L.; Gonzalez, C.; Cook, P.D. Uniformly modified 2′-deoxy-2′-fluoro phosphorothioate oligonucleotides as nuclease-resistant antisense compounds with high affinity and specificity for RNA targets. J. Med. Chem. 1993, 36, 831–841.
   PubMed Web of Science ®Google Scholar
• Frieden, M.; Christensen, S. M.; Mikkelsen, N. D.; Rosenbohm, C.; Thrue,C. A.; Westergaard, M.; Hansen, H. F.; Ørum, H.; Koch, T. Expanding the design horizon of antisense oligonucleotides with alpha-L-LNA. Nucleic Acids Res. 2003, 31, 6365–6372.
   PubMed Web of Science ®Google Scholar
• Noronha, A. M.; Wilds, C. J.; Lok, C. N.; Viazovkina, K., Arion, D., Parniak, M. A.; Damha, M. J. Synthesis and biophysical properties of arabinonucleic acids (ANA): Circular dichroic spectra, melting temperatures, and ribonuclease H susceptibility of ANA.RNA hybrid duplexes. Biochemistry 2000, 39, 7050–7062.
   PubMed Web of Science ®Google Scholar
• Lima, W. F.; Nichols, J. G.; Wu, H.; Prakash, T. P.; Migawa, M. T.; Wyrzykiewicz, T. K.; Bhat, B.; Crooke, S. T. Structural requirements at the catalytic site of the heteroduplex substrate for human RNase H1 catalysis. J. Biol. Chem. 2004, 279, 36317–36326.
   PubMed Web of Science ®Google Scholar
• Minasov, G.; Teplova, M.; Nielsen, P.; Wengel, J.; Egli,M. Structural basis of cleavage by RNase H of hybrids of arabinonucleic acids and RNA. Biochemistry 2000, 39, 3525–3532.
   PubMed Web of Science ®Google Scholar
• Damha, M. J.; Wilds, C. J.; Noronha, A.; Brukner, I.; Borkow, G.; Arion, D.; Parniak, M. A. Hybrids of RNA and Arabinonucleic Acids (ANA and 2‘F-ANA) are substrates of ribonuclease H. J. Am. Chem. Soc. 1998, 120, 12976–12977.
   Web of Science ®Google Scholar
• Denisov, A. Y.; Noronha, A. M.; Wilds, C. J.; Trempe, J.-F.; Pon, R. T.; Gehring, K.; Damha, M. J. Solution structure of an arabinonucleic acid (ANA)/RNA duplex in a chimeric hairpin: comparison with 2′-fluoro-ANA/RNA and DNA/RNA hybrids. Nucleic Acids Res. 2001, 29, 4284–4293.
   PubMed Web of Science ®Google Scholar
• Nielsen, K. M.; Petersen, M.; Håkansson, A. E.; Wengel, J.; Jacobsen, J. P. Alpha-L-LNA (alpha-L-ribo configured locked nucleic acid) recognition of DNA: an NMR spectroscopic study. Chemistry. 2002, 8, 3001–3009.
   PubMed Web of Science ®Google Scholar
• Nielsen, J. T.; Stein, P. C.; Petersen, M. NMR structure of an alpha-L-LNA:RNA hybrid: Structural implications for RNase H recognition. Nucleic Acids Res. 2003, 31, 5858–5867.
   PubMed Web of Science ®Google Scholar
• Wang, J.; Verbeure, B.; Luyten, I.; Lescrinier, E.; Froeyen, M.; HendrixC.; Rosemeyer, H.; Seela, F.; Van Aerschot, A.; Herdewijn, P. Cyclohexene Nucleic Acids (CeNA):  Serum Stable Oligonucleotides that Activate RNase H and Increase Duplex Stability with Complementary RNA. J. Am. Chem. Soc. 2000, 122, 8595–8602.
   Web of Science ®Google Scholar
• Nowotny, M.; Gaidamakov, S. A.; Crouch, R. J.; Yang, W. Crystal structures of RNase H bound to an RNA/DNA hybrid: Substrate specificity and metal-dependent catalysis. Cell 2005, 121, 1005–1016.
   PubMed Web of Science ®Google Scholar
• Wang, G.; Middleton, P. J.; Lin, C.; Pietrzkowski, Z. Biophysical and biochemical properties of oligodeoxy-nucleotides containing 4′-C- and 5′-C-substituted thymidines. Bioorg. Med. Chem. Lett. 1999, 9, 885–890.
   PubMed Web of Science ®Google Scholar
• Kanazaki, M.; Ueno, Y.; Shuto, S.; Matsuda, A. Highly Nuclease-resistant phosphodiester-type oligodeoxynucleotides containing 4‘α-C-aminoalkylthymidines form thermally stable duplexes with DNA and RNA. A candidate for potent antisense molecules. J. Am. Chem. Soc. 2000, 122, 2422–2432.
   Web of Science ®Google Scholar
• Fensholdt, J.; Thrane, H.; Wengel, J. Synthesis of oligodeoxynucleotides containing 4′-C-(Hydroxymethyl)thymidine: Novel promising antisense molecules. Tetrahedron Lett. 1995, 36, 2535–2538.
   Web of Science ®Google Scholar
• Nielsen, K. D.; Kirpekar, F.; Roepstorff, P.; Wengel, J. Oligonucleotide analogues containing 4′-C-(Hydroxymethyl)uridine:Synthesis, evaluation and mass spectrometric analysis. Bio. Med. Chem. 1995, 3, 1493–1502.
   PubMed Web of Science ®Google Scholar
• Gaubert, G.; Babu, B. R.; Vogel, S.; Bryld, T.; Vester, B.; Wengel, J. Synthesis and RNA-selective hybridization of α-l-ribo- and β-d-lyxo-configured oligonucleotides. Tetrahedron 2006, 62, 2278–2294.
   Web of Science ®Google Scholar
• Rosemeyer, H.; Seela, F. 1-(2′-Deoxy-β-D-xylofuranosyl)thymine building blocks for solid-phase synthesis and properties of Oligo(2′-Deoxyxylonucleotides). Helv. Chim. Acta 1991, 74, 748–760.
   Web of Science ®Google Scholar
• Maiti, M.; Maiti, M.; Knies, C.; Dumbre, S.; Lescrinier, E.; Rosemeyer, H.; Ceulemans, A.; Herdewijn, P. Xylonucleic acid: synthesis, structure, and orthogonal pairing properties. Nucleic Acids Res. 2015, 43, 7189–7200.
   PubMed Web of Science ®Google Scholar
• Guangyu, W.; Seifert, W. E. Synthesis and evaluation of oligodeoxynucleotides containing 4′-C-substituted thymidines. Tetrahedron Lett. 1996, 37, 6515–6518.
   Web of Science ®Google Scholar
• More, J. D.; Finney, N. S. A simple and advantageous protocol for the oxidation of alcohols with o-Iodoxybenzoic Acid (IBX). Org. Lett. 2002, 4, 3001–3003.
   PubMed Web of Science ®Google Scholar
• Omura, K.; Swern, D. Oxidation of alcohols by “activated” dimethyl sulfoxide. a preparative, steric and mechanistic study. Tetrahedron 1978, 34, 1651–1660.
   Web of Science ®Google Scholar
• Mancuso, A. J.; Swern, D. Activated dimethyl sulfoxide: Useful reagents for synthesis. Synthesis 1981, 165–185.
   Google Scholar
• PfitznerK. E.; Moffatt, J. G. Sulfoxide-Carbodiimide Reactions. I. A Facile Oxidation of Alcohols. J. Am. Chem. Soc. 1965, 87, 5661–5670.
   Web of Science ®Google Scholar
• Jones, G. H.; Taniguchi, M.; Tegg, D.; Moffatt, J. G. 4′-Substituted nucleosides. 5. Hydroxymethylation of nucleoside 5′-aldehydes. J. Org. Chem. 1979, 44, 1309–1317.
   Web of Science ®Google Scholar
• Obika, S.; Nanbu, D.; Hari, Y.; MorioK.-I.; In, Y.; Ishida, T.; Imanishi, T. Synthesis of 2′-O,4′-C-methyleneuridine and -cytidine. Novel bicyclic nucleosides having a fixed C3′-endo sugar puckering. Tetrahedron Lett. 1997, 38, 8735–8738.
   Web of Science ®Google Scholar
• Altona, C.; Sundaralingam, M. Conformational analysis of the sugar ring in nucleosides and nucleotides. New description using the concept of pseudorotation. J. Am. Chem. Soc. 1972, 94, 8205–8212.
   PubMed Web of Science ®Google Scholar
• Abes, S.; Turner, J. J.; Ivanova, G. D.; Owen, D.; Williams, D.; Arzumanov, A.; Clair, P.; Gait, M. J.; Lebleu, B. Efficient splicing correction by PNA conjugation to an R6-Penetratin delivery peptide. Nucleic Acids Res. 2007, 13, 4495–4502.
   Web of Science ®Google Scholar
• Gait, M. J. Oligonucleotide Synthesis: A Practical Approach. IRL Press Oxford, 1984.
   Google Scholar
• Agrawal, S. Methods in Molecular Biology. Vol.20, ed.N.J. Totowa, Humana Press, Inc.
   Google Scholar