The First Example of a Hoogsteen Basepaired DNA Duplex in Dynamic Equilibrium with a Watson-Crick Basepaired Duplex—A Structural (NMR), Kinetic and Thermodynamic Study

References and Footnotes

• Altmann , K-H. , Kesselring , R. and Pieles , U. 1996 . Tetrahedron , 52 : 12699 (a) (b) Portmann, S., Altmann, K-H., Reynes, N. and Egli, M. (1997) J. Am. Chem. Soc. 119, 2396
   Web of Science ®Google Scholar
• Knorre , D. G. , Vlassov , V. V. , Zarytova , V. F. , Lebedev , A. V. and Fedorova , O. S. 1994 . Design and Targeted Reactions of Oligonucleotide Derivates. Boca Raton , FL : CRC Press . (a) (b) Puri, N. and Chattopadhyaya, J. (1999) Nucleosides & Nucleotides 18, 2785, (c) Damah, M. J., Wilds, C. J., Noronha, A., Brukner, I., Borkow, G., Arion,D. and Parniak, M. A. (1998) J. Am. Chem. Soc. 120, 12976
   Google Scholar
• Patel , D. J. 1992 . Cur. Opin. Struct. Biol. , 2 : 345 (a) (b) Brown, T. and Kennard, O. (1992) Cur. Opin. Struct. Biol. 2, 354, (c) Wang, A. H-J. (1992) Cur. Opin. Struct. Biol. 2, 361, (d) Cho, Y., Zhu, F. C., A., L. B. and Gorenstein, D. G. (1993) J. Biomol. Struct. Dynamics 11, 685 (e) Gorenstein, D. G. (1994) Chem. Rev. 94, 1315, (f) Mesmaeker, A. D.,Altmann, K- H., Waldner, A. and Wendeborn, S. (1995) Cur. Opin. Struct. Biol. 5, 343, (g) Krugh, T. R. (1994) Cur. Opin. Struct. Biol. 4, 351, (h) Schweitzer, B. I., Mikita, T., Kellogg, G. W., Gardner, K. H. and Beardsley, G. P. (1994) Biochemistry 33, 11460, (i) Gonzßlez, C., Stec, W., Reynolds, M. A. and James, T. L. (1995) Biochemistry 34, 4969
   Google Scholar
• Denisov , A. Y. , Zamaratski , E. V. , Maltseva , T. V. , Sandstr÷m , A. , Bekiroglu , S. , Altmann , K-H. , Egli , M. and Chattopadhyaya , J. 1998 . J. Biomol. Struct. Dyn. , 16 : 547 and references therein for references to other NMR and X-ray work on Dickerson's dodecamer
   PubMed Web of Science ®Google Scholar
• Marquez , V. E. and Lim , M-I. 1986 . Med. Res. Rev. , 6 : 1
   PubMed Web of Science ®Google Scholar
• Thibaudeau , C. and Chattopadhyaya , J. 1999 . Stereoelectronic Effects in Nucleosides and Nucleotides and their Structural Implications. Sweden : Uppsala University Press . (a) (b) Bekiroglu, S., Thibaudeau, C., Kumar, A., Matsuda, A., Marquez, V. and Chattopadhyaya, J. (1998) J. Org. Chem 63, 5447, (c) Ossipov, D., Zamaratski, E., and Chattopadhyaya, J. (1999) Helv. Chim. Acta, 82, 2186
   Google Scholar
• Koole , L. H. , Buck , H. M. , Nyilas , A. and Chattopadhyaya , J. 1987 . Can. J. Chem. , 65 : 2089 (a) (b) Plavec, J., Tong, W. and Chattopadhyaya, J. (1993) J. Am. Chem. Soc. 115, 9734, (c) Plavec, J., Thibaudeau, C., Viswanadham, G., Sund, C. and Chattopadhyaya, J. (1994) J. Chem. Soc. Chem. Commun. 781, (d) Thibaudeau, C., Plavec, J., Garg, N., Papchikhin, A. and Chattopadhyaya, J. (1994) J. Am. Chem. Soc. 116, 4038, (e) Plavec, J., Thibaudeau, C. and Chattopadhyaya, J. (1994) J. Am. Chem. Soc. 116, 6558, (f) Plavec, J., Thibaudeau, C., Viswamadham, G., Sund, C., Sandstr÷m, A. and Chattopadhyaya, J. (1995) Tetrahedron 51, 11775, (g) Thibaudeau, C., Plavec, J. and Chattopadhyaya, J. (1996) J. Org. Chem. 61, 266, (h) Plavec, J., Thibaudeau, C. and Chattopadhyaya, J. (1996) Pure Appl. Chem. 68, 2137, (i) Thibaudeau, C., F÷ldesi, A. and Chattopadhyaya, J. (1997) Tetrahedron 53, 14043, (j) Luyten, I., Thibaudeau, C. and Chattopadhyaya, J. (1997) J. Org. Chem. 62, 8800, (k) Luyten, I., Thibaudeau, C. and Chattopadhyaya, J. (1997) Tetrahedron 53, 6433, (l) Thibaudeau, C., Plavec, J. and Chattopadhyaya J. (1998) J. Org. Chem. 63, 4967
   Web of Science ®Google Scholar
• Marquez , V. E. , Ezzitouni , A. , Russ , P. , Siddiqui , M. A. , Ford , H. J. , Feldman , R. J. , Mitsuya , H. , George , C. and Barchi , J. J. J. 1998 . J. Am. Chem. Soc. , 120 : 2780 (a) (b) Altmann, K-H., Kesselring, R., Francotte, E. and Rihs, G. (1994) Tetrahedron Lett. 35, 2331, (c) Marquez, V. E., Siddiqui, M. A., Ezzitouni, A., Russ, P., Wang, J., Wagner, R. W. and Metteuci, M. D. (1996) J. Med. Chem. 39, 3739
   Web of Science ®Google Scholar
• Isaksson , J. , Maltseva , T. , Agback , P. , Luo , X. , Kumar , A. , Zamratski , E. and Chattopadhyaya , J. 1999 . Nucleosides and Nucleotides , 18 ( 6&7 ) : 1593 – 1596 . Earlier, we reported the preliminary solution structures of these interconverting WC/Hoogsteen duplexes for this molecule on the basis of an incomplete NMR constraint data set in a congress abstract. This is now thoroughly revised, and the full methodology and results are presented herein, including the thermodynamics and kinetics of the inter conversion. At a higher temperature (>50°C), this interconverting WC/Hoogsteen duplex were earlier assumed to transform to a hairpinû type structure on the basis of insufficient evidence. Upon closer examination, this is found not to be true and is therefore rejected. In fact, the resonances that were attributed to the hairpin structure has its origin in the coalescence of the two sets of chemical shifts in the NMR-time scale due to the quick structural exchange of the interconverting WC/Hoogsteen duplex prior to melting (see Figures 10A-C)
   PubMedGoogle Scholar
• Saenger , W. 1988 . Principles of Nucleic Acid Structure. New York, Berlin, Heidelberg, Tokyo : Springer-Verlag . (a) (b) Arnott, S. and Hukins, D. W. L. (1972) Biochem. Biophys. Res. Comm. 47, 1504
   Google Scholar
• Sklenár , V. and Feigon , J. 1990 . Nature , 345 : 836
   PubMed Web of Science ®Google Scholar
• Maltseva , T. V. , Altmann , K-H. , Egli , M. and Chattopadhyaya , J. 1998 . J. Biomol. Struct. Dyn. , 16 : 569 (a) (b) Otting, G., Liepinsh, E., Farmer II, B. T. and Wthrich, K. (1991) J. Biomol. NMR 1, 209
   PubMed Web of Science ®Google Scholar
• Chary , K. V. R. , Rastogi , V. K. and Govil , G. 1993 . J. Magn. Reson. 102 B. 81
   Google Scholar
• Brnger , A. T. 1990 . X-PLOR 3.1, Manual. New Haven , CT : Yale University Press .
   Google Scholar
• Varani , G. , Aboul-ela , F. and Allain , F. H-T. 1996 . Prog. NMR Spectrosc. , 29 : 51
   Web of Science ®Google Scholar
• Omichinski , J. G. , Pedone , P. V. , Felsenfeld , G. , Gronenborn , A. M. and Clore , G. M. 1997 . Nature Struct. Biol. , 4 : 122
   PubMedGoogle Scholar
• Borgias , B. A. , Thomas , P. D. , Liu , H. , Kumar , A. and James , T. L. 1993 . Mardigras3.0/Corma5.0. Manual San Francisco , CA : University of California .
   Google Scholar
• Babcock , M. S. , Pednault , E. P. D. and Olson , W. K. 1993 . J. Biomol. Struct. Dyn. , 11 : 597
   PubMed Web of Science ®Google Scholar
• Van De Ven . 1997 . Multidimensional NMR in Liquids. 78 – 82 . Wiley
   Google Scholar
• Aurelia V2.1.3 Bruker Analytik GmbH .
   Google Scholar
• Overmars , F. 1997 . Conformational Aspects of Branched DNA. Ridderkerk : Ridderprint B.V. . Dissertation
   Google Scholar
• Davis , T. M. , McFail-Isom , L. , Keane , E. and Williams , L. D. 1998 . Biochemistry , 37 : 6975 (a) (b) Ivanov, V. I., Minchenkova, L.E., Schyolkina, A. K. and Poletayev, A. I. (1973) Biopolymers 12, 89, (c) Alen, F. S., Gray, D. M., Roberts, G. P. and Tonoko Jr. I. (1972) Biopolymers 11, 853, (d) Summers, M. F., Byrd, R. A., Gallo, K. A., Samson, C. J., Zon, G. and Egan, W. (1985) Nucl. Acids Res. 13, 6375
   PubMed Web of Science ®Google Scholar
• Blommers , M. J. J. , Van deVen , F. J. M. , Van derMarel , G. A. , VanBoom , J. H. and Hilbers , C. W. 1991 . Eur. J. Biochem. , 201 : 33 (a) (b) Jaeger, J. A. and Tinoco Jr. I. (1993) Biochemistry 32, 12523
   PubMedGoogle Scholar
• Hosour , R. V. , Govil , G. and Miles , H. T. 1988 . Magn. Reson. Chem. , 26 : 927 (a) (b) Gronenborn, A. M. and Clore, G. M. (1985) Prog. NMR Spectrosc. 17, 1–31, (c) Van de Ven, F. J. M. and Hilbers, C. W. (1998) Eur. J. Biochem. 178, 1
   Google Scholar
• Nerdal , W. , Hare , D. R. and Reid , B. R. 1989 . Biochemistry , 28 : 10008 (a) (b) Yamakage, S-I, Maltseva, T. V., Nilson, F. P., F÷ldesi, A. and Chattopadhyaya, J. (1993) Nucl. Acids Research 21, 5005
   PubMed Web of Science ®Google Scholar
• Conte , M. R. , Bauer , C. J. and Lane , A. N. 1996 . J. Biomol. NMR , 7 : 190
   PubMedGoogle Scholar
• Rinkel , L. J. and Altona , C. 1987 . J. Biomol. Struct. Dyn. , 4 : 621
   PubMed Web of Science ®Google Scholar
• Chou , S-H. , Zhu , L. , Gao , Z. , Cheng , J-W. and Reid , B. R. 1996 . J. Mol. Biol. , 264 : 981
   PubMed Web of Science ®Google Scholar
• Kim , S-G. , Lin , L-J. and Reid , B. R. 1992 . Biochemistry , 31 : 3564
   PubMed Web of Science ®Google Scholar
• Rongata , V. K. , Jones , C. R. and Gorenstein , D. G. 1990 . Biochemistry , 29 : 5245 (a) (b) Chary, K. V. R., Rastogi, V. K. and Govil, G. (1993) J. Magn. Reson. 102 B, 81
   PubMedGoogle Scholar
• Gorenstein , D. G. 1984 . Phosphorous-31 NMR: Principles and applications. New York : Academic Press .
   Google Scholar
• 1995 . SYBYL 6.2 Tripos, Inc., St. Louis, Missouri
   Google Scholar
• Sasosekharan , V. 1972 . Jerus. Symp. Quant. Chem. Biochem. , 5 : 247 (a) 260 (b) Lugovskoi, A. A. and Dashevskii, V. G. (1972) Mol. Biol. (USSR) 6, 354
   Google Scholar
• Smirnov , S. , Johnson , F. , Marumoto , R. and de losSantos , C. 2000 . J. Biomol. Struct. Dyn. , 17 : 981
   PubMed Web of Science ®Google Scholar