Hydrogen bond formation between the naturally modified nucleobase and phosphate backbone

Nucleic Acids Research

Volumn 40, Issue 16, 2012, Pages 8111-8118

  Sheng, Jia ^a   Zhang, Wen ^a   Hassan, Abdalla E A ^a   Gan, Jianhua ^a   Soares, Alexei S ^b   Geng, Song ^c   Ren, Yi ^c   Huang, Zhen ^a  

^a GEORGIA STATE UNIVERSITY   (United States)

^b BROOKHAVEN NATIONAL LABORATORY   (United States)

^c SICHUAN UNIVERSITY   (China)

Author keywords

[No Author keywords available]

Indexed keywords

5' PHOSPHATE; OLIGONUCLEOTIDE; OXYGEN; PHOSPHATE; SELENIUM; SULFUR; UNCLASSIFIED DRUG; URACIL;

ARTICLE; CHEMICAL MODIFICATION; CONFORMATIONAL TRANSITION; CONTROLLED STUDY; CRYSTAL STRUCTURE; HYDROGEN BOND; MATHEMATICAL ANALYSIS; NUCLEIC ACID STRUCTURE; PRIORITY JOURNAL; RNA PROCESSING; X RAY CRYSTALLOGRAPHY;

CRYSTALLOGRAPHY, X-RAY; DNA, A-FORM; HYDROGEN BONDING; MODELS, MOLECULAR; OLIGODEOXYRIBONUCLEOTIDES; PHOSPHATES; SELENIUM; SULFUR; URACIL; URIDINE;

EID: 84870479727     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gks426     Document Type: Article

References (34)

1. Agris, P.F. (2008) Bringing order to translation: the contributions of transfer RNA anticodon-domain modifications. EMBO Rep., 9, 629-635.
2. Agris, P.F., Vendeix, F.A. and Graham, W.D. (2007) tRNA's wobble decoding of the genome: 40 years of modification. J. Mol. Biol., 366, 1-13.
3. Gustilo, E.M., Vendeix, F.A. and Agris, P.F. (2008) tRNA's modifications bring order to gene expression. Curr. Opin. Microbiol., 11, 134-140.
4. Cantara, W.A., Crain, P.F., Rozenski, J., McCloskey, J.A., Harris, K.A., Zhang, X., Vendeix, F.A., Fabris, D. and Agris, P.F. (2011) The RNA modification database, RNAMDB: 2011 update. Nucleic Acids Res., 39, D195-D201.
5. Nishimura, S. (1972) Minor components in transfer RNA: their characterization, location and function. Prog. Nucleic Acid Res. Mol. Biol., 12, 49-85.
6. Albani, M., Schmidt, W., Kersten, H., Geibel, K. and Luderwald, I. (1976) 5-methoxyuridine, a new modified constituent in tRNAs of Bacillaceae. FEBS Lett., 70, 37-42.
7. Murao, K., Ishikura, H., Albani, M. and Kersten, H. (1978) On the biosynthesis of 5-methoxyuridine and uridine-5-oxyacetic acid in specific procaryotic transfer RNAs. Nucleic Acids Res., 5, 1273-1281.
8. Takai, K., Okumura, S., Hosono, K., Yokoyama, S. and Takaku, H. (1999) A single uridine modification at the wobble position of an artificial tRNA enhances wobbling in an Escherichia coli cell-free translation system. FEBS Lett., 447, 1-4.
9. Takai, K. and Yokoyama, S. (2003) Roles of 5-substituents of tRNA wobble uridines in the recognition of purine-ending codons. Nucleic Acids Res., 31, 6383-6391.
10. Egert, E., Lindner, H.J., Hillen, W. and Buhm, M.C. (1980) Influence of substituents at the 5-position on the structure of uridine. J. Am. Chem. Soc., 102, 3707-3713.
11. Egert, E. and Lindner, H. (1979) Crystal structure and conformation of 2-thio-5-methylaminomethyluridine dihydrate. Acta. Crystallogr. B, 35, 122-125.
12. Egert, E. and Lindner, H. (1978) Crystal structure and conformation of 5-aminouridine. Acta. Crystallogr. B, 34, 2204-2208.
13. Sheng, J., Jiang, J., Salon, J. and Huang, Z. (2007) Synthesis of a 20-Se-thymidine phosphoramidite and its incorporation into oligonucleotides for crystal structure study. Org. Lett., 9, 749-752.
14. Jiang, J., Sheng, J., Carrasco, N. and Huang, Z. (2007) Selenium derivatization of nucleic acids for crystallography. Nucleic Acids Res., 35, 477-485.
15. Otwinowski, Z. and Minor, W. (1997) Processing of X-ray diffraction data collected in oscillation mode. Methods Enzymol., 276, 307-326.
16. McCoy, A.J., Grosse-Kunstleve, R.W., Adams, P.D., Winn, M.D., Storoni, L.C. and Read, R.J. (2007) Phaser crystallographic software. J. Appl. Crystallogr., 40, 658-674.
17. Murshudov, G.N., Vagin, A.A. and Dodson, E.J. (1997) Refinement of macromolecular structures by the maximum-likelihood method. Acta. Crystallogr. D Biol. Crystallogr., 53, 240-255.
18. Parkinson, G., Vojtechovsky, J., Clowney, L., Brunger, A.T. and Berman, H.M. (1996) New parameters for the refinement of nucleic acid-containing structures. Acta. Crystallogr. D Biol. Crystallogr., 52, 57-64.
19. Brunger, A.T. (1992) Free R value: a novel statistical quantity for assessing the accuracy of crystal structures. Nature, 355, 472-475.
20. Read, R.J. (1986) Improved fourier coefficients for maps using phases from partial structures with errors. Acta. Crystallogr. A, 42, 140-149.
21. Lee, C., Yang, W. and Parr, R.G. (1988) Development of the Colle-Salvetti correlation-energy formula into a functional of the electron density. Phys. Rev. B Condens. Matter, 37, 785-789.
22. Becke, A. (1993) Density functional thermochemistry. III. The role of exact exchange. J. Chem. Phys., 98, 5648-5652.
23. Salon, J., Sheng, J., Gan, J. and Huang, Z. (2010) Synthesis and crystal structure of 20-Se-modified guanosine containing DNA. J. Org. Chem., 75, 637-641.
24. Hassan, A.E., Sheng, J., Zhang, W. and Huang, Z. (2010) High fidelity of base pairing by 2-selenothymidine in DNA. J. Am. Chem. Soc., 132, 2120-2121.
25. Salon, J., Sheng, J., Jiang, J., Chen, G., Caton-Williams, J. and Huang, Z. (2007) Oxygen replacement with selenium at the thymidine 4-position for the Se base pairing and crystal structure studies. J. Am. Chem. Soc., 129, 4862-4863.
26. Sheng, J. and Huang, Z. (2010) Selenium derivatization of nucleic acids for X-ray crystal-structure and function studies. Chem. Biodivers., 7, 753-785.
27. Sheng, J., Salon, J., Gan, J. and Huang, Z. (2010) Synthesis and crystal structure study of 20-Se-adenosine-derivatized DNA. Sci. China Chem., 53, 78-85.
28. Zhang, W., Sheng, J., Hassan, A.E. and Huang, Z. (2012) Synthesis of 20-Deoxy-5-(methylselenyl)cytidine and Se-DNAs for structural and functional studies. Chem. Asian J., 7, 476-479.
29. Hassan, A.E., Sheng, J., Jiang, J., Zhang, W. and Huang, Z. (2009) Synthesis and crystallographic analysis of 5-Se-thymidine DNAs. Org. Lett., 11, 2503-2506.
30. Stout, M.G. and Robins, R.K. (1972) The synthesis of some 5-methoxypyrimidine nucleosides. J. Heterocycl. Chem., 9, 545-549.
31. Lin, L., Sheng, J. and Huang, Z. (2011) Nucleic acid X-ray crystallography via direct Selenium derivatization. Chem. Soc. Rev., 40, 4591-4602.
32. Jiang, L. and Lai, L. (2002) CHO hydrogen bonds at protein-protein interfaces. J. Biol. Chem., 277, 37732-37740.
33. Castellano, R.K. (2004) Progress toward understanding the nature and function of C-HO interactions. Curr. Org. Chem., 8, 845-865.
34. Emsley, J. (1980) Very strong hydrogen bonding. Chem. Soc. Rev., 9, 91-124.