Promiscuous Watson-Crick cross-pairing within the family of pentopyranosyl (4′→2′) oligonucleotides

Organic Letters

Volumn 1, Issue 10, 1999, Pages 1527-1530

  Jungmann, Oliver ^a   Wippo, Harald ^a   Stanek, Michael ^a   Huynh, Hoan K ^a   Krishnamurthy, Ramanarayanan ^a   Eschenmoser, Albert ^a  

^a NONE

Author keywords

[No Author keywords available]

Indexed keywords

OLIGONUCLEOTIDE;

ARTICLE; BASE PAIRING; CHEMISTRY; CONFORMATION;

BASE PAIRING; NUCLEIC ACID CONFORMATION; OLIGONUCLEOTIDES;

EID: 0033581763     PISSN: 15237060     EISSN: None     Source Type: Journal    
DOI: 10.1021/ol990183y     Document Type: Article

References (21)

1. Chemistry of α-Aminonitriles. 26. Part 24: ref 2. Part 25: ref 4.
2. Micura, R.; Kudick, R.; Pitsch, S.; Eschenmoser, A. Angew. Chem., Int. Ed. 1999, 38, 680.
3. Eschenmoser, A. Verh. Ges. Dtsch. Naturforsch. Aerzte 1990, 116, 135. Eschenmoser, A.; Löwenthal, E. Chem. Soc. Rev. 1992, 21, 1.
4. Eschenmoser, A. Verh. Ges. Dtsch. Naturforsch. Aerzte 1990, 116, 135. Eschenmoser, A.; Löwenthal, E. Chem. Soc. Rev. 1992, 21, 1.
5. Beier, M.; Reck, F.; Wagner, T.; Krishnamurthy, R.; Eschenmoser, A. Science 1999, 283, 699. See also references on the chemistry of pyranosyl-RNA cited therein.
6. For probably the strongest oligonucleotide base-pairing system known ("LNA") see: Koshkin, A. A.; Nielsen, P.; Meldgaard, M.; Rajwanshi, V. K.; Singh, S. K.; Wengel, J. J. Am. Chem. Soc. 1998, 120, 13252.
7. A summary on the synthesis of pentopyranosyl (4′→2′) oligonucleotides was given in ref 4 and in: Pitsch, S.; Wendeborn, S.; Jaun, B.; Eschenmoser, A. Helv. Chim. Acta 1993, 76, 2161. A full account, to be published in Helv. Chim. Acta, is in preparation.
8. A summary on the synthesis of pentopyranosyl (4′→2′) oligonucleotides was given in ref 4 and in: Pitsch, S.; Wendeborn, S.; Jaun, B.; Eschenmoser, A. Helv. Chim. Acta 1993, 76, 2161. A full account, to be published in Helv. Chim. Acta, is in preparation.
9. Marky, L. A.; Breslauer, K. J. Biopolymers 1987, 26, 1601.
10. Cantor, C. R.; Schimmel, P. R. Biophysical Chemistry; Freeman: San Francisco, CA, 1980; Part III (The Behavior of Biological Macromolecules), pp 1135-1139.
11. Schlönvogt, I.; Pitsch, S.; Lesueur, C.; Eschenmoser, A.; Jaun, B.; Wolf, R. M. Helv. Chim. Acta 1996, 79, 2316.
12. Changing the nucleosidic torsion angle χ from the (idealized) value of -120° (Cl′-H in plane with nucleobase in anti configuration) toward -60° (Cl′-C2′ in plane with nucleobase) induces a corresponding reorientation of the base-pair axes at the cost of increasing steric repulsion between C2′(H) and the nucleobase, an interaction thought to be more repulsive than when χ changes from -120° toward -180°. On the other hand, matters are complicated because a repulsion between the nucleobase and the C5′ methylene group of the neighboring downstream sugar is to be expected when χ values change toward -180°. provided the 4′-phosphodiester conformation is equatorial, but not when it is axial.
13. Saenger, W. Principles of Nucleic Acid Structure; Springer-Verlag: New York, 1984; pp 69-78.
14. 20 strands (Neidlein, U.; Leumann, C. Tetrahedron Lett. 1992, 33, 8057 and references cited therein). For an interpretation of the weakness of purine-purine self-pairing in the pentopyranosyl series see ref 6.
15. 7
16. 4
17. See also the recent investigations on RNA-PNA chimeras: Koppitz, M.; Nielsen, P. E.; Orgel, L. E. J. Am. Chem. Soc. 1998, 120, 4563.
18. Eschenmoser, A.; Dobler, M. Helv. Chim. Acta 1992, 75, 218. Hunziker, J.; Roth, H.-J.; Böhringer, M.; Giger, A.; Diederichsen, U.; Göbel, M.; Krishnan, R.; Jaun, B.; Leumann, C.; Eschenmoser, A. Helv. Chim. Acta 1993, 76, 259. Groebke, K.; Hunziker, J.; Fraser, W.; Peng, L.; Diederichsen, U.; Zimmermann, K.; Holzner, A.; Leumann, C.; Eschenmoser, A. Helv. Chim. Acta 1998, 81, 375.
19. Eschenmoser, A.; Dobler, M. Helv. Chim. Acta 1992, 75, 218. Hunziker, J.; Roth, H.-J.; Böhringer, M.; Giger, A.; Diederichsen, U.; Göbel, M.; Krishnan, R.; Jaun, B.; Leumann, C.; Eschenmoser, A. Helv. Chim. Acta 1993, 76, 259. Groebke, K.; Hunziker, J.; Fraser, W.; Peng, L.; Diederichsen, U.; Zimmermann, K.; Holzner, A.; Leumann, C.; Eschenmoser, A. Helv. Chim. Acta 1998, 81, 375.
20. Eschenmoser, A.; Dobler, M. Helv. Chim. Acta 1992, 75, 218. Hunziker, J.; Roth, H.-J.; Böhringer, M.; Giger, A.; Diederichsen, U.; Göbel, M.; Krishnan, R.; Jaun, B.; Leumann, C.; Eschenmoser, A. Helv. Chim. Acta 1993, 76, 259. Groebke, K.; Hunziker, J.; Fraser, W.; Peng, L.; Diederichsen, U.; Zimmermann, K.; Holzner, A.; Leumann, C.; Eschenmoser, A. Helv. Chim. Acta 1998, 81, 375.
21. See e.g.: Seeman, N. C. Angew. Chem., Int. Ed. Engl. 1998, 37, 3220.