Analysis of a theoretical model based on similarity for studying RNA base pairings

Journal of Theoretical Biology

Volumn 181, Issue 4, 1996, Pages 359-371

  Di Gennaro, Patrizia ^a   Sello, Guido ^a   Termini, Manuela ^a  

^a UNIVERSITY OF MILAN   (Italy)

Author keywords

[No Author keywords available]

Indexed keywords

NUCLEIC ACID BASE; RNA;

ARTICLE; BASE PAIRING; GENETIC CODE; MODEL; PRIORITY JOURNAL; RNA STRUCTURE;

EID: 0030596737     PISSN: 00225193     EISSN: None     Source Type: Journal    
DOI: 10.1006/jtbi.1996.0137     Document Type: Article

References (28)

1. BADER, R. F. W. & LEGARE, D. A. (1992). Properties of atoms in molecules: structures and reactivities of boranes and carboranes. Can. J. Chem., 70, 657-676.
2. BAUMER, L. & SELLO, G. (1992). A new method for the calculation of natural bond polarity using molecular electronic energy. J. Chem. Info. Comput. Sci. 32, 125-130.
3. BOWIE, J. W., REIDHAAR-OLSON, J. F., LIM W. A. & SAUER, R. T. (1990). Deciphering the message in protein sequences: tolerance to amino acid substitution. Science 247, 1306-1310.
4. CHIU, S. K., RAO, B. J., STORY, R. M. & RADDING, C. M. (1993). Interactions of three strands in joints made by RecA protein. Biochemistry 32, 13146-13155.
5. GORDY, W. A. (1946). A new method of determining electronegativity from other atomic properties. Phys. Rev. 69, 604-607.
6. GORDY, W. A. & THOMAS, W. J. P. (1956). Electronegativities of the element. J. Chem. Phys., 24, 439-444.
7. JOCHUM, C., HICKS, M. G. & SUNKEL, J. (1992). The Belstein workshop on similarity in organic chemistry. J. Chem. Info. Comput. Sci. 32, 577-748.
8. JOHNSON, M. A. (1989). A review and examination of the mathematical spaces underlying molecular similarity analysis. J. Math. Chem. 3, 117-145.
9. JOHNSON, M. A. & MAGGIORA, G. M. (1990). Concepts and Applications of Molecular Similarity. New York: J. Wiley & Sons, Inc.
10. KLEINA, L. G. & MILLER, J. H. (1990). Genetic studies of the lac repressor XIII. Extensive amino acid replacement generated by the use of natural and synthetic nonsense suppressors. J. Mol. Biol. 212, 295-318.
11. LACKS, S. (1966). Integration efficiency and genetic recombination in pneumococcal transformation. Genetics 53, 207-235.
12. LEONI, B. & SELLO, G. (1995). A proposal toward the identification of substructure electronic similarity. In: Molecular Similarity and Reactivity: from Quantum Chemical to Phenomenological Approaches (Carbo' R., ed.), pp. 267-289. Dordrecht: Kluwer Academic Publishers.
13. MATTHEWS, B. W. (1993). Structural and genetic analysis of protein folding and stability. Curr. Opin. Struct. Biol. 3, 589-593.
14. OSAWA, S., JUKES, T. H., WATANABE, K. & MUTO, A. (1992). Recent evidence for evolution of the genetic code. Microbiol. Rev. 56, 229-264.
15. PAULING, L. (1960). The Nature of the Chemical Bond. 3rd edn. Ithaca: Cornell University Press.
16. POTEETE, A. R., RENNELL, D. & BOUVIER, S. E. (1992). Functional significance of conserved amino acid residues. Proteins 13, 38-40.
17. PRITCHARD, H. O. & SKINNER, H. A. (1955). The Concept of Electronegativity. Chem. Rev. 55, 745-786.
18. RAO, B. J., CHIU, S. J. & RADDING, C. M. (1993). Homologous recognition and triplex formation promoted by RecA protein between duplex oligonucleotides and single-stranded DNA. J. Mol. Biol. 229, 328-343.
19. RAO, B. J. & RADDING, C. M. (1993). Homologous recognition promoted by RecA protein via non-Watson-Crick bonds between identical DNA strands. Proc. Natn. Acad. Sci. U.S.A. 90, 6646-6650.
20. RAO, B. J. & RADDING, C. M. (1995). RecA protein mediates homologous recognition via non-Watson-Crick bonds in base triplets. Phil. Trans. R. Soc. Lond. B 347, 5-12.
21. RENNELL, D., BOUVIER, S. E., HARDY L. W. & POTEETE, A. R. (1991). Systematic mutation of bacteriophage T5 lysozyme. J. Mol. Biol. 222, 67-87.
22. ROUVRAY, D. H. (1990). The evolution of the concept of molecular similarity. In: Concepts and Applications of Molecular Similarity (Johnson, M. A. & Maggiora, G. M., eds), pp. 15-42. New York: J. Wiley & Sons, Inc.
23. ROUVRAY, D. H. (1992). Definition and role of similarity concepts in the chemical and physical sciences. J. Chem. Info. Comput. Sci. 32, 580-586.
24. SELLO, G. (1992). A new definition of functional groups and a general procedure for their identification in organic structures. J. Am. Chem. Soc. 114, 3306-3311.
25. SELLO, G. & TERMINI, M. (1995). Analysis of the transferability of similarity calculations from substructures to complex compounds. Unpublished results.
26. UMLAUF, S. W., COX, M. M. & INMAN, R. B. (1990). Triple helical pairing intermediates formed by RecA protein. Science 259, 1892-1896.
27. WATSON, J. D. & CRICK, F. H. C. (1953). Molecular structure of nucleic acids. Nature 171, 738-740.
28. ZHURKIN, V. B., RAGHUNATHAN, G., ULYANOV, N. B., CAMERINI-OTERO, R. D. & JERNIGAN, R. L. (1994). A parallel DNA triplex as a model for the intermediate in homologous recombination. J. Mol. Biol. 239, 181-200.