Synthesis and hybridization of 2′-O-methyl-RNAs incorporating 2′-O-carbamoyluridine and unique participation of the carbamoyl group in U-G base pair

Bioorganic and Medicinal Chemistry

Volumn 17, Issue 20, 2009, Pages 7275-7280

  Seio, Kohji ^a   Tawarada, Ryuya ^a   Sasami, Takeshi ^a   Serizawa, Masashi ^a   Ise, Misako ^a   Ohkubo, Akihiro ^a   Sekine, Mitsuo ^a  

^a TOKYO INSTITUTE OF TECHNOLOGY   (Japan)

Author keywords

2 O Modified RNA; Mismatched base pair

Indexed keywords

2' O CARBAMOYLURIDINE; RNA DERIVATIVE; UNCLASSIFIED DRUG; URIDINE DERIVATIVE;

ARTICLE; BASE MISPAIRING; BASE PAIRING; HYDROGEN BOND; MOLECULAR DYNAMICS; RNA HYBRIDIZATION; RNA SYNTHESIS; SIMULATION; THERMOSTABILITY;

BASE PAIR MISMATCH; BASE PAIRING; CIRCULAR DICHROISM; MAGNETIC RESONANCE SPECTROSCOPY; MASS SPECTROMETRY; MODELS, MOLECULAR; MOLECULAR CONFORMATION; NUCLEIC ACID HYBRIDIZATION; RNA; URIDINE;

EID: 71749087533     PISSN: 09680896     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.bmc.2009.08.053     Document Type: Article

References (39)

1. Czauderna F., Fechtner M., Dames S., Aygun H., Klippel A., Pronk G.J., Giese K., and Kaufmann J. Nucleic Acid Res. 31 (2003) 2705
2. Chiu Y., and Rana T.M. RNA 9 (2003) 1034
3. Jackson A., Burchard J., Leake D., Reynold A., Schelter J., Guo J., Johnson J.M., Lim L., Karpilow J., Nichols K., Marshall W., Khvorova A., and Linsley P.S. RNA 12 (2006) 1197
4. Bryan A., Kraynack B.A., and Baker A.F. RNA 12 (2006) 163
5. Beuvink I., Kolb F.A., Budach W., Granier A., Lange J., Natt F., Dengler U., Hall J., Filipowicz W., and Weiler J. Nucleic Acids Res. 35 (2007) e52
6. Freier S.M., and Altmann K.-H. Nucleic Acids Res. 25 (1997) 4429
7. Inoue H., Hayase Y., Imura A., Iwai S., Miura K., and Ohtsuka E. Nucleic Acids Res. 15 (1987) 6131
8. Martin P. Helv. Chim. Acta 78 (1995) 486
9. Martin P. Helv. Chim. Acta 79 (1996) 1930
10. Martin P. Helv. Chim. Acta 86 (2003) 204
11. Baker B.F., Lot S.S., Condon T.P., Cheng-Flournoy S., Lesnik E.A., Sasmor H.M., and Bennett C.F. J. Biol. Chem. 272 (1997) 11994
12. Teplova M., Minasov G., Tereshko V., Inamati G.B., Cook P.D., Manoharan M., and Egli M. Nat. Strut. Biol. 6 (1997) 535
13. Maier M.A., Guzaev A.P., and Manoharan M. Org. Lett. 2 (2000) 1819-1822
14. Rajeev K.G., Prakash T.P., and Manoharan M. Org. Lett. 5 (2003) 3005
15. Yu R.Z., Geary R.S., Monteith D.K., Matson J., Truong L., Fitchett J., and Levin A.A. J. Pharm. Sci. 93 (2004) 48
16. Grotli M., Douglas M., Eritja R., and Sproat B.S. Tetrahedron 54 (1998) 5899
17. Griffey R.H., Monia B.P., Cummins L.L., Freier S., Greig M.J., Guinosso C.J., Lesnik E., Manalili S.M., Mohan V., Owens S., Ross B.R., Sasmor H., Wancewicz E., Weiler K., Wheeler P.D., and Cook P.D. J. Med. Chem. 39 (1995) 5100-5109
18. Prakash T.P., Manoharan M., Fraser A.S., Kawasaki A.M., Lesnik E.A., and Owens S.R. Tetrahedron Lett. 41 (2000) 4855
19. Prakash T.P., Kawasaki A.M., Lesnik E.A., Owens S.R., and Manoharan M. Org. Lett. 5 (2003) 403
20. Pattanayek R., Sethaphong L., Pan C., Prhavc M., Prakash T.P., Manoharan M., and Egli M. J. Am. Chem. Soc. 126 (2004) 15006
21. Saneyoshi H., Seio K., and Sekine M. J. Org. Chem. 70 (2005) 10453
22. Sundaralingam M., and Pan B. Biophys. Chem. 95 (2002) 273
23. Auffinger P., and Westhof E. Angew. Chem., Int. Ed. 40 (2001) 4648
24. Auffinger P., and Westhof E. J. Mol. Biol. 300 (2000) 1113
25. Banerjee R., Maji S.K., and Banerjee A. Acta Crystallogr., Sect. C 56 (2000) 1120
26. Semetey V., Hemmerlin C., Didierjean C., Schaffner A.P., Giner A.G., Aubry A., Briand J.P., Marraud M., and Guichard G. Org. Lett. 3 (2001) 3843-3846
27. Miyata K., Kobori A., Tamamushi R., Ohkubo A., Taguchi H., Seio K., and Sekine M. Eur. J. Org. Chem. (2006) 3626-3637
28. Markiewicz W.T., Biala E., and Kierzek R. Bull. Pol. Acad. Sci., Chem. 32 (1984) 433
29. Westman E., and Stromberg R. Nucleic Acids Res. 22 (1994) 2430
30. Hayakawa Y., and Kataoka M. J. Am. Chem. Soc. 120 (1998) 12395
31. Altona C. Recl. Trav. Chim. Pays-Bas 101 (1982) 413
32. Prhavc M., Lesnik E.A., Mohan V., and Manoharan M. Tetrahedron Lett. 42 (2001) 8777
33. Lesnik E.A., Guinosso C.J., Kawasaki A.M., Sasmor H., Zounes M., Cummins L.L., Ecker D.J., Cook P.D., and Freier S.M. Biochemistry 32 (1993) 7832
34. Cornell W.D., Cieplak P., Bayly C.I., Gould I.R., Merz Jr. K.M., Ferguson D.M., Spellmeyer D.C., Fox T., Caldwell J.W., and Kollman P.A. J. Am. Chem. Soc. 117 (1995) 5179
35. Biswas R., and Sundaralingam M. J. Mol. Biol. 270 (1997) 511
36. Biswas R., Wahl M.C., Ban C., and Sundaralingam M. J. Mol. Biol. 267 (1997) 1149
37. Shi K., Wahl M., and Sundaralingam M. Nucleic Acids Res. 27 (1999) 2196
38. Frisch, M. J.; Trucks, G. W.; Schlegel, H. B.; Scuseria, G. E.; Robb, M. A.; Cheeseman, J. R.; Montgomery, J. A.; Jr.; Vreven, T.; Kudin, K. N.; Burant, J. C.; Millam, J. M.; Iyengar, S. S.; Tomasi, J.; Barone, V.; Mennucci, B.; Cossi, M.; Scalmani, G.; Rega, N.; Petersson, G. A.; Nakatsuji, H.; Hada, M.; Ehara, M.; Toyota, K.; Fukuda, R.; Hasegawa, J.; Ishida, M.; Nakajima, T.; Honda, Y.; Kitao, O.; Nakai, H.; Klene, M.; Li, X.; Knox, J. E.; Hratchian, H. P.; Cross, J. B.; Bakken, V.; Adamo, C.; Jaramillo, J.; Gomperts, R.; Stratmann, R. E.; Yazyev, O.; Austin, A. J.; Cammi, R.; Pomelli, C.; Ochterski, J. W.; Ayala, P. Y.; Morokuma, K.; Voth, G. A.; Salvador, P.; Dannenberg, J. J.; Zakrzewski, V. G.; Dapprich, S.; Daniels, A. D.; Strain, M. C.; Farkas, O.; Malick, D. K.; Rabuck, A. D.; Raghavachari, K.; Foresman, J. B.; Ortiz, J. V.; Cui, Q.; Baboul, A. G.; Clifford, S.; Cioslowski, J.; Stefanov, B. B.; Liu, G.; Liashenko, A.; Piskorz, P.; Komaromi, I.; Martin, R. L.; Fox, D. J.; Keith, T.; Al-Laham, M. A.; Peng, C. Y.; Nanayakkara, A.; Challacombe, M.; Gill, P. M. W.; Johnson, B.; Chen, W.; Wong, M. W.; Gonzalez, C.; Pople, J. A. Gaussian 03, Revision C.02, 2004.
39. Case, A.; Darden, T. A.; Cheatham, T. E., III, Simmerling, C. L.; Wang, J.; Duke, R. E.; Luo, R.; Merz, K. M.; Pearlman, D. A.; Crowley, M.; Walker, R. C.; Zhang, W.; Wang, B.; Hayik, S.; Roitberg, A.; Seabra, G.; Wong, K. F.; Paesani, F.; Wu, X.; Brozell, S.; Tsui, V.; Gohlke, H.; Yang, L.; Tan, C.; Mongan, J.; Hornak, V.; Cui, G.; Beroza, P.; Mathews, D. H.; Schafmeister, C.; Ross, W. S. and Kollman, P. A. AMBER 9.0.