Hydrophobic effects in duplexes with modified oligonucleotide backbones and RNA

Bioorganic and Medicinal Chemistry Letters

Volumn 6, Issue 19, 1996, Pages 2363-2366

  Waldner, Adrian ^a   De Mesmaeker, Alain ^a   Wendeborn, Sebastian ^a  

^a CIBA GEIGY LTD   (Switzerland)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; RNA STRUCTURE;

EID: 0030575609     PISSN: 0960894X     EISSN: None     Source Type: Journal    
DOI: 10.1016/0960-894X(96)00434-9     Document Type: Article

References (11)

1. 1. De Mesmaeker, A.; Waldner, A.; Lebreton, J.; Hoffmann, P.; Fritsch, V.; Wolff, R.M. and Freier, S.M. Angew. Chem. Int. Ed. Engl., 1994, 33, 226.
2. 2. Wolf, R.M.; Fritsch, V.; De Mesmaeker, A.; Lebreton, J. and Waldner, A. Molecular Mechanics and Dynamics Studies on Amide-Modified Backbones in Antisense Oligodeoxynucleotides. In Computer-Aided Molecular Design; Reynolds, C.H.; Holloway, M.K.; Cox, H.K. Eds.; ACS Symposium Series 589, American Chemical Society, Washington, DC 1994; pp 114-126.
3. 3. Blackburn, G.M. DNA and RNA Structure. In Nucleic Acids in Chemistry and Biology, Blackburn, G.M.; Gait, M.J. Eds.; IRL Press, Oxford, 1990; pp 17-70.
4. 4. "Amide-3" denotes that this modification was the third one synthesized in our labs.
5. 5. Itai, A.; Toriumi, Y.; Saito, S.; Kagechika, H. and Sudo, K. J. Amer. Chem. Soc., 1992, 114, 10649.
6. 6. De Mesmaeker, A.; Waldner, A.; Lebreton, J.; Fritsch, V. and Wolf, R.M. Novel Backbone Replacements for Oligonucleotides. In Carbohydrate Modifications in Antisense Research; Sanghvi, Y.S.; Cook, P.D. Eds.; ACS Symposium Series 580, American Chemical Society, Washington, DC 1994; pp 24-39.
7. 7. Mukayama, T.; Aikawa, Y. and Kobayashi, S. Chem. Lett., 1976, 13.
8. 8. Each oligonucleotide was prepared on an ABI 390 DNA synthesizer using standard phosphoramidite chemistry according to Gait, M.J, Oligonucleotides Synthesis: A Practical Approach, IRL Press, Oxford 1984, but with prolonged times (10 min.) for the coupling step. DMT Oligonucleotides were purified by reverse phase HPLC. The purity of the oligodeoxynucleotides were checked by capillary gel electrophoresis and their molecular weight was determined by mass spectrometry ( MALDI-TOF: Pieles, U.; Zürcher, W.; Schär, M.; Moser, H. Nucl. Acids Res., 1993, 21, 3191).
9. 8. Each oligonucleotide was prepared on an ABI 390 DNA synthesizer using standard phosphoramidite chemistry according to Gait, M.J, Oligonucleotides Synthesis: A Practical Approach, IRL Press, Oxford 1984, but with prolonged times (10 min.) for the coupling step. DMT Oligonucleotides were purified by reverse phase HPLC. The purity of the oligodeoxynucleotides were checked by capillary gel electrophoresis and their molecular weight was determined by mass spectrometry ( MALDI-TOF: Pieles, U.; Zürcher, W.; Schär, M.; Moser, H. Nucl. Acids Res., 1993, 21, 3191).
10. 9. Wendeborn, S.; Wolf, R.M.; De Mesmaeker, A. Tetrahedron Lett., 1995, 36, 6879.
11. +] (supplemented as NaCl), 0.1 mM EDTA. Tm's were obtained from fits of absorbance vs. temperature curves to a two state model with linear slope baselines (Freier, S.M.; Albergo, D.D.; Turner, D.H. Biopolymers, 1983, 22, 1107). All values are averages of at least three experiments.