A computational approach to modeling nucleic acid hairpin structures

Biophysical Journal

Volumn 72, Issue 2 I, 1997, Pages 876-885

  Tung, Chang Shung ^a,b  

^a LOS ALAMOS NATIONAL LABORATORY   (United States)

^b LOS ALAMOS NATIONAL LABORATORY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ALGORITHM; ARTICLE; DNA CONFORMATION; HYDROGEN BOND; MATHEMATICAL MODEL; MOLECULAR DYNAMICS; NUCLEOTIDE SEQUENCE; RNA CONFORMATION; SEQUENCE ANALYSIS; SYSTEM ANALYSIS;

EID: 0031021456     PISSN: 00063495     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0006-3495(97)78722-8     Document Type: Article

References (51)

1. Altona, C., and M. Sundaralingam. 1972. Conformational analysis of the sugar ring in nucleosides and nucleotides. A new description using the concept of pseudorotation. J. Am. Chem. Soc. 94:8205-8212.
2. Barton, H. A., R. S. Eisenstein, A. Bomford, and H. N. Munro. 1990. Determinants of the interaction between the iron-responsive element-binding protein and its binding site in rat L-ferritin mRNA. J. Biol. Chem. 265:7000-7008.
3. Bernstein, F. C., T. F. Koetzle, G. J. B. Williams, E. F. Meyer, Jr., M. D. Brice, J. R. Rodgers, O. Kennard, T. Shimanouchi, and M. Tasumi. 1977. The Protein Data Bank: a computer-based archival file for macromolecular structures. J. Mol. Biol. 112:535-542.
4. Blatt, N. B., S. E. Osborne, R. J. Cain, and G. D. Glick. 1993. Conformational studies of hairp in sequences from the ColE1 cruciform. Biochimie. 75:433-441.
5. Boulard, Y., J. Gabarro-Arpa, J. A. Cognet, M. Le Bret, A. Guy, R. Teoule, W. Guschlbauer, and G. V. Fazakerley. 1991. The solution structure of a DNA hairpin containing a loop of three thymidines determined by nuclear magnetic resonance and molecular mechanics. Nucleic Acids Res. 19:5159-5167.
6. Cain, R. J., E. R. Zuiderweg, and G. D. Glick. 1995. Solution structure of a DNA hairpin and its disulfide cross-linked analog. Nucleic Acids Res. 23:2153-2160.
7. Chattopadhyaya, R., S. Ikuta, K. Grzeskowiak, and R. E. Dickerson. 1988. X-ray structure of a DNA hairpin molecule. Nature. 334:175-179.
8. Cheong, C., G. Varani, and I. Tinoco, Jr. 1990. Solution structure of an unusually stable RNA hairpin. 5′GGAC(UUCG)GUCC. Nature. 346: 680-682.
9. Climie, S. C., and J. D. Friesen. 1987. Feedback regulation of the rplJL-rpoBC ribosomal protein operon of Escherichia coli requires a region of mRNA secondary structure. J. Mol. Biol. 198:371-381.
10. Cremer, D., and J. A. Pople. 1975. A general definition of ring puckering coordinates. J. Am. Chem. Soc. 97:1354-1358.
11. Davis, P. W., W. Thurmes, and I. Tinoco, Jr. 1993. Structure of a small RNA hairpin. Nucleic Acids Res. 21:537-545.
12. Dickerson, R. E., M. Bansal, C. R. Calladine, S. Diekmann, W. N. Hunter, O. Kennard, R. Lavery, H. C. Nelson, W. K. Olson, W. Saenger, Z. Shakked, H. Sklenar, D. M. Soumpasis, C. S. Tung, E. von Kitzing, A. H. C. Wang, and V. B. Zhurkin. 1989. Definitions and nomenclature of nucleic acid structure parameters. EMBO J. 8:1-4.
13. Endo, Y., Y. L. Chan, A. Lin, K. Tsurugi, and I. G. Wool. 1988. The cytotoxins alpha-sarcin and ricin retain their specificity when tested on a synthetic oligoribonucleotide (35-mer) that mimics a region of 28 S ribosomal ribonucleic acid. J. Biol. Chem. 263:7917-7920.
14. Erie, D. A., K. J. Breslauer, and W. K. Olson. 1993a. A Monte Carlo method for generating structures of short single-stranded DNA sequences. Biopolymers. 33:75-105.
15. Erie, D. A., A. K. Suri, K. J. Breslauer, R. A. Jones, and W. K. Olson. 1993b. Theoretical predictions of DNA hairpin loop conformations: correlations with thermodynamic and spectroscopic data. Biochemistry. 32:436-454.
16. Feng, S., and E. C. Holland. 1988. HIV-1 tat trans-activation requires the loop sequence within tar. Nature. 334:165-167.
17. Freedman, L. P., J. M. Zengel, R. H. Archer, and L. Lindahl. 1987. Autogenous control of the S10 ribosomal protein operon of Escherichia coli: genetic dissection of transcriptional and posttranscriptional regulation. Proc. Natl. Acad. Sci. USA. 84:6516-6520.
18. Goldstein, H. 1959. Classical Mechanics. Addison-Wesley, Reading, MA.
19. Gupta, G., A. E. Garcia, P. Catasti, R. Ratliff, E. M. Bradbury, R. K. Moyzis. 1994. Stem-loop structures of the repetitive DNA sequences located at human centromeres. In Proceedings of the Eighth Conversation. R. H. Sarma and M. H. Sarma, editors. Adenine Press, New York. 137-154.
20. Hirao, I., G. Kawai, S. Yoshizawa, Y. Nishimura, Y. Ishido, K. Watanabe, and K. Miura. 1994. Most compact hairpin-turn structure exerted by a short DNA fragment, d(GCGAAGC) in solution: an extraordinarily stable structure resistant to nucleases and heat. Nucleic Acids Res. 22:576-582.
21. Hummer, G., and D. M. Soumpasis. 1993. Correlations and free energies in restricted primitive model descriptions of electrolytes. J. Chem. Phys. 98:581-591.
22. Jack, A., J. E. Ladner, and A. Klug. 1976. Crustallographic refinement of yeast phenylalanine transfer RNA at 2.5 angstrom resolution. J. Mol. Biol. 108:619-649.
23. Kajava, A., and H. Ruterjans. 1993. Molecular modelling of the 3-D structure of RNA tetraloops with different nucleotide sequences. Nucleic Acids Res. 21:4556-4562.
24. Leibold, E. A., A. Laudano, and Y. Yu. 1990. Structural requirements of iron-responsive elements for binding of the protein involved in both transferrin receptor and ferritin mRNA post-transcriptional regulation. Nucleic Acids Res. 18:1819-1824.
25. Metropolis, N., A. W. Rosenbluth, M. N. Rosenbluth, A. H. Teller, and E. Teller. 1953. Equation of state calculations by fast computing machines. J. Chem. Phys. 21:1087-1092.
26. Miller, K. J. 1979. Interactions of molecules with nucleic acids. I. An algorithm to generate nucleic acid structures with an application to the B-DNA structure and a counterclockwise helix. Biopolymers. 18: 959-980.
27. Moyzis, R. K., J. M. Buckingham, L. S. Cram, M. Dani, L. L. Deaven, M. D. Jones, J. Meyne, R. L. Ratliff, and J. R. Wu. 1988. A highly conserved repetitive DNA sequence, (TTAGGG)n, present at the telomeres of human chromosomes. Proc. Natl. Acad. Sci. USA. 85: 6622-6626.
28. Olson, W. K., and P. J. Flory. 1972. Spatial configuration of polynucleotide chains. I. Steric interactions in polyribonucleotides: a virtual bond model. Biopolymers. 11:1-23.
29. Orita, M., F. Nishikawa, T. Shimayama, K. Taira, Y. Endo, and S. Nishikawa. 1993. High-resolution NMR study of a synthetic oligoribonucleotide with a tetranucleotide GAGA loop that is a substrate for the cytotoxic protein, ricin. Nucleic Acids Res. 21:5670-5678.
30. Philippe, C., C. Portier, M. Mougel, M. Grunberg-Manago, J. P. Ebel, B. Ehresmann, and C. Ehresmann. 1990. Target site of Escherichia coli ribosomal protein S15 on its messenger RNA. Conformation and interaction with the protein. J. Mol. Biol. 211:415-426.
31. Puglisi, J. D., R. Tan, B. J. Calnan, A. D. Frankel, and J. R. Williamson. 1992. Conformation of the TAR RNA-arginine complex by NMR spectroscopy. Science. 257:76-80.
32. Raghunathan, G., R. L. Jernigan, H. T. Miles, and V. Sasisekharan. 1991. Conformational feasibility of a hairpin with two purines in the loop. 5′-d-GGTACIAGTACC-3′. Biochemistry. 30:782-788.
33. Romaniuk, P. J., P. Lowary, H. N. Wu, G. Stormo, and O. C. Uhlenbeck. 1987. RNA binding site of R17 coat protein. Biochemistry. 26: 1563-1568.
34. Seeman, N. C., J. M. Rosenberg, F. L. Suddath, J. J. Park Kim, and A. Rich. 1976. A simplified alphabetical nomenclature for dihedral angles in the polynucleotide backgone. J. Mol. Biol. 104:142-143.
35. Shen, L. X., Z. Cai, and I. Tinoco, Jr. 1995. RNA structure at high resolution. FASEB J. 9:1023-1033.
36. Soumpasis, D. M. 1984. Statistical mechanics of the B-Z transition of DNA: contribution of diffuse ionic interactions. Proc. Natl. Acad. Sci. USA. 81:5116-5120.
37. Soumpasis, D. M., and C. S. Tung. 1988. A rigorous basepair oriented description of DNA structures. J. Biomol. Struct. Dyn. 6:397-420.
38. Srinivasan, A. R., and W. K. Olson. 1987. Nucleic acid model building: the multiple backbone solutions associated with a given base morphology. J. Biomol. Struct. Dyn. 4:895-938.
39. Sussman, J. L., S. R. Holbrook, R. W. Warrant, and S.-H. Kim. 1978. Crystal structure of yeast phenylalanine tRNA. I. Crystallographic refinement. J. Mol. Biol. 123:607-630.
40. Tuerk, C., P. Gauss, C. Thermes, D. R. Groebe, M. Gayle, N. Guild, G. Stormo, Y. d'Aubenton-Carafa, O. C. Uhlenbeck, and I. Tinoco, Jr. 1988. CUUCGG hairpins: extraordinarily stable RNA secondary structures associated with various biochemical processes. Proc. Natl. Acad. Sci. USA. 85:1364-1368.
41. Tung, C. S. 1993. Computation of Biomolecular Structures: Achievements, Problems, and Perspectives. D. M. Soumpasis and T. M. Jovin, editors. Springer Verlag, New York. 87-97.
42. Tung, C. S., T. I. Oprea, G. Hummer, and A. E. Garcia. 1996. Three-dimensional model of a selective theophylline-binding RNA molecule. J. Mol. Recognit. (in press).
43. Tung, C. S., and D. M. Soumpasis. 1996. Structural prediction of A- and B-DNA duplexes based on coordinates of the phosphorus atoms. Biophys. J. 70:917-923.
44. Tung, C. S., D. M. Soumpasis, and G. Hummer. 1994. An extension of the rigorous base-unit oriented description of nucleic acid structures. J. Biomol. Struct. Dyn. 11:1327-1344.
45. Valegard, K., J. B. Murray, P. G. Stockley, N. J. Stonehouse, and L. Liljas. 1994. Crystal structure of an RNA bacteriophage coat protein-operator complex. Nature. 371:623-626.
46. Weiner, S. J., P. A. Kollman, D. A. Case, U. Chandra Singh, C. Ghio, G. Algona, S. Profeta, Jr., and P. Weiner. 1984. A new force field for molecular mechanical simulation of nucleic acids and proteins. J. Am. Chem. Soc. 106:765-784.
47. Weiner, S. J., P. A. Kollman, D. T. Nguyen, and D. A. Case. 1986. An all atom force field for simulations of proteins and nucleic acids. J. Comput. Chem. 7:230-252.
48. Witherell, G. W., J. M. Gott, and O. C. Uhlenbeck. 1991. Specific interaction between RNA phage coat proteins and RNA. Prog. Nucleic Acids Res. Mol. Biol. 40:185-220.
49. Witherell, G. W., and O. C. Uhlenbeck. 1989. Specific RNA binding by Q beta coat protein. Biochemistry. 28:71-76.
50. Zhou, N., and H. J. Vogel. 1993. Two-dimensional NMR and restrained molecular dynamics studies of the hairpin d(T8C4A8): detection of an extraloop cytosine. Biochemistry. 32:637-645.
51. Zhurkin, V. B., Y. P. Lysov, and V. I. Ivanov. 1978. Different families of double-stranded conformations of DNA as revealed by computer calculations. Biopolymers. 17:377-412.