Dynamics and energetics of the base flipping conformation studied with base pair-mimic nucleosides

Biochemistry

Volumn 48, Issue 47, 2009, Pages 11304-11311

  Nakano, Shu Ichi ^a   Oka, Hirohito ^a   Uotani, Yuuki ^a   Uenishi, Kazuya ^b   Fujii, Masayuki ^b   Sugimoto, Naoki ^a  

^a KONAN UNIVERSITY   (Japan)

^b KINKI UNIVERSITY   (Japan)

Author keywords

[No Author keywords available]

Indexed keywords

BASE CATALYSIS; BASE FLIPPING; BASE PAIR INTERACTIONS; BASE PAIRING; BASE PAIRS; BIOLOGICAL PROCESS; DEOXYADENOSINE; DNA REPAIR; DNA STRANDS; DOUBLE HELIX; HYDROLYSIS RATE; INOSINE; NAPHTHYL GROUPS; RIBONUCLEOTIDES; SITE-SPECIFIC; THERMAL STABILITY; UNUSUAL CONFORMATIONS;

BIOMOLECULES; DNA; FLUORINE CONTAINING POLYMERS; GENES; HYDROLYSIS; PROTEINS; RNA; THERMODYNAMIC STABILITY;

NUCLEIC ACIDS;

COMPLEMENTARY RNA; DEOXYADENOSINE; DEOXYCYTIDINE; DNA; NUCLEOSIDE DERIVATIVE; POLYDEOXYRIBONUCLEOTIDE SYNTHASE;

ARTICLE; BASE PAIRING; CATALYSIS; DNA HELIX; DNA RNA HYBRIDIZATION; ENERGY TRANSFER; MOLECULAR DYNAMICS; PRIORITY JOURNAL; THERMOSTABILITY;

BASE PAIRING; BASE SEQUENCE; BINDING SITES; COMPUTER SIMULATION; DEOXYADENOSINES; DEOXYCYTIDINE; DNA; DNA REPAIR; HYDROLYSIS; MOLECULAR MIMICRY; NUCLEIC ACID CONFORMATION; NUCLEOSIDES; RNA; THERMODYNAMICS;

EID: 72749109095     PISSN: 00062960     EISSN: None     Source Type: Journal    
DOI: 10.1021/bi901496q     Document Type: Article

References (33)

1. Turner, D. H., Sugimoto, N., Kierzek, R., and Dreiker, S. D. (1987) Free energy increments for hydrogen bonds in nucleic acid base pairs. J. Am. Chem. Soc. 109, 3793-13784
2. Bommarito, S., Peyret, N., and SantaLucia, J., Jr. (2000) Thermodynamic parameters for DNA sequences with dangling ends. Nucleic Acids Res. 28, 1929-1934.
3. Ohmichi, T., Nakano, S., Miyoshi, D., and Sugimoto,N. (2002) Long RNA dangling end has large energetic contribution to duplex stability. J. Am. Chem. Soc. 124, 10367-10372.
4. Moody, E. M., and Bevilacqua, P. C. (2003) Thermodynamic coupling of the loop and stem in unusually stableDNAhairpins closed by CG base pairs. J. Am. Chem. Soc. 125, 2032-2033.
5. Roberts, R. J., and Cheng, X. (1998) Base flipping. Annu. Rev. Biochem. 67, 181-198.
6. Yi-Brunozzi, H. Y., Stephens, O. M., and Beal, P. A. (2001) Conformational changes that occur during an RNA-editing adenosine deamination reaction. J. Biol. Chem. 276, 37827-37833.
7. Sankpal, U. T., and Rao, D. N. (2002) Structure, function, and mechanism of HhaI DNA methyltransferases. Crit. Rev. Biochem. Mol. Biol. 37, 167-197.
8. Gelfand, C. A., Plum, G. E., Grollman, A. P., Johnson, F., and Breslauer, K. J. (1998) Thermodynamic consequences of an abasic lesion in duplex DNA are strongly dependent on base sequence. Biochemistry 37, 7321-7327. (Pubitemid 28235215)
9. Sagi, J., Guliaev, A. B., and Singer, B. (2001) 15-mer DNA duplexes containing an abasic site are thermodynamically more stable with adjacent purines than with pyrimidines. Biochemistry 40, 3859-3868. (Pubitemid 32280422)
10. Hazel, R. D., Tian, K., and de Los Santos, C. (2008) NMR solution structures of bistranded abasic site lesions in DNA. Biochemistry 47, 11909-11919.
11. Krosky, D. J., Schwarz, F. P., and Stivers, J. T. (2004) Linear free energy correlations for enzymatic base flipping: How do damaged base pairs facilitate specific recognition? Biochemistry 43, 4188-4195.
12. Lipscomb, L. A., Zhou, F. X., Presnell, S. R., Woo, R. J., Peek, M. E., Plaskon, R. R., and Williams, L. D. (1996) Structure of DNAporphyrin complex. Biochemistry 35, 2818-2823.
13. Morales-Rojas, H., and Kool, E. T. (2002) A porphyrin C-nucleoside incorporated into DNA. Org. Lett. 4, 4377-4380.
14. Smirnov, S., Matray, T. J., Kool, E. T., and de los Santos, C. (2002) Integrity of duplex structures without hydrogen bonding: DNA with pyrene paired at abasic sites. Nucleic Acids Res. 30, 5561-5569.
15. Tuma, J., Connors, W. H., Stitelman, D. H., and Richert, C. (2002) On the effect of covalently appended quinolones on termini of DNA duplexes. J. Am. Chem. Soc. 124, 4236-4246.
16. David, A., Bleimling, N., Beuck, C., Lehn, J. M., Weinhold, E., and Teulade-Fichou, M. P. (2003) DNA mismatch-specific base flipping by a bisacridine macrocycle. ChemBioChem 4, 1326-1331. (Pubitemid 38036414)
17. Nakano, S., Uotani, Y., Uenishi, K., Fujii, M., and Sugimoto, N. (2005) DNA base flipping by a base pair-mimic nucleoside. Nucleic Acids Res. 33, 7111-7119. (Pubitemid 43125079)
18. Nakano, S., Uotani, Y., Uenishi, K., Fujii, M., and Sugimoto, N. (2005) Site-selective RNA cleavage by DNA bearing a base pairmimic nucleoside. J. Am. Chem. Soc. 127, 518-519.
19. Richard, R. G. (1975) in Handbook of Biochemistry and Molecular Biology: Nucleic Acids (Fasman, G. D., Ed.) 3rd ed., Vol.1, p 597, CRC Press, Cleveland, OH.
20. Puglisi, J. D., and Tinoco, I., Jr. (1989) Absorbance melting curves of RNA. Methods Enzymol. 180, 304-325.
21. Sugimoto, N., Nakano, M., and Nakano, S. (2000) Thermodynamicsstructure relationship of single mismatches in RNA/DNA duplexes. Biochemistry 39, 11270-11281.
22. Jencks, W. P. (1969) Catalysis in Chemistry and Enzymology , pp 163-242, John Wiley & Sons, Inc., New York.
23. Li, Y., and Breaker, R. R. (1999) Kinetics of RNA degradation by specific base catalysis of transesterification invoving 20-hydrolyl group. J. Am. Chem. Soc. 121, 5364-5372.
24. Zhou, D. M., and Taira, K. (1998) The hydrolysis of RNA: From theoretical calculations to the hammerhead ribozyme-mediated cleavage of RNA. Chem. Rev. 98, 991-1026.
25. Soukup, G. A., and Breaker, R. R. (1999) Relationship between internucleotide linkage geometry and the stability of RNA. RNA 5, 1308-1325.
26. Tereshko, V., Wallace, S. T., Usman, N., Wincott, F. E., and Egli, M. (2001) X-ray crystallographic observation of "in-line" and "adjacent" conformations in a bulged self-cleaving RNA/DNA hybrid. RNA 7, 405-420.
27. Winkler, W. C., Cohen-Chalamish, S., and Breaker, R. R. (2002) An mRNA structure that controls gene expression by binding FMN. Proc. Natl. Acad. Sci. U.S.A. 99, 15908-15913.
28. Gopinath, S. C.,Matsugami, A.,Katahira,M., andKumar, P. K. (2005) Human vault-associated non-coding RNAs bind to mitoxantrone, a chemotherapeutic compound. Nucleic Acids Res. 33, 4874-4881.
29. Espinoza, C. A., Goodrich, J. A., and Kugel, J. F. (2007) Characterization of the structure, function, and mechanism of B2 RNA, an ncRNA repressor of RNA polymerase II transcription. RNA 13, 583-596.
30. Miyata, K., Tamamushi, R., Ohkubo, A., Taguchi, H., Seio, K., and Sekine, M. (2004) Synthesis and hybridization affinity of oligodeoxyribonucleotides incorporating 4-N-(N-arylcarbamoly)deoxycytidine derivatives. Tetrahedron Lett. 45, 9365-9368. (Pubitemid 39539209)
31. Andersen, A. A., and Collins, R. A. (2000) Rearrangement of a stable RNA secondary structure during VS ribozyme catalysis. Mol. Cell 5, 469-478.
32. Reiter, N. J., Blad, H., Abildgaard, F., and Butcher, S. E. (2004) Dynamics in the U6 RNA intramolecular stem-loop: A base flipping conformational change. Biochemistry 43, 13739-13747. (Pubitemid 39431057)
33. Barthel, A., and Zacharias, M. (2006) Conformational transitions in RNA single uridine and adenosine bulge structures: A molecular dynamics free energy simulation study. Biophys. J. 90, 2450-2462.