3DNA: A software package for the analysis, rebuilding and visualization of three-dimensional nucleic acid structures

Nucleic Acids Research

Volumn 31, Issue 17, 2003, Pages 5108-5121

  Lu, Xiang Jun ^a,b   Olson, Wilma K ^a  

^a RUTGERS UNIVERSITY   (United States)

^b SAIC FREDERICK INC   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

DNA; NUCLEIC ACID; NUCLEIC ACID BASE; PHOSPHATE; RNA; SUGAR;

ARTICLE; BASE PAIRING; CALCULATION; COMPUTER PROGRAM; CONFORMATION; CONTROLLED STUDY; DNA STRUCTURE; NUCLEIC ACID ANALYSIS; NUCLEIC ACID STRUCTURE; PRIORITY JOURNAL; PROTEIN DATABASE; RNA STRUCTURE; STANDARDIZATION; STRUCTURE ANALYSIS; X RAY DIFFRACTION;

BASE PAIRING; DNA; HYDROGEN BONDING; MODELS, MOLECULAR; NUCLEIC ACID CONFORMATION; SOFTWARE;

EID: 0242396923     PISSN: 03051048     EISSN: None     Source Type: Journal    
DOI: 10.1093/nar/gkg680     Document Type: Article

References (92)

1. Watson, J.D. and Crick, F.H.C. (1953) Genetical implications of the structure of deoxyribonucleic acid. Nature, 171, 964-967.
2. Saenger, W. (1984) Principles of Nucleic Acid Structure. Springer-Verlag, New York, NY, Ch. 6.
3. Klein, D.J., Schmeing, T.M., Moore, P.B. and Steitz, T.A. (2001) The kink-turn: a new RNA secondary structure motif. EMBO J., 20, 4214-4221.
4. Kang, C.H., Zhang, X., Ratliff, R., Moyzis, R. and Rich, A. (1992) Crystal structure of four-stranded Oxytricha telomeric DNA. Nature, 356, 126-131.
5. Smith, F.W. and Feigon, J. (1992) Quadruplex structure of Oxytricha telomeric DNA oligonucleotides. Nature, 356, 164-168.
6. Nelson, H.C.M., Finch, J.T., Luisi, B.F. and Klug, A. (1987) The structure of an oligo(dA)-oligo(dT) tract and its biological implications. Nature, 330, 221-226.
7. n tracts by B-DNA crystal structures. Nature, 354, 167-170.
8. Kim, S.H., Suddath, F.L., Quigley, G.J., McPherson, A., Sussman, J.L., Wang, A.H., Seeman, N.C. and Rich, A. (1974) Three-dimensional tertiary structure of yeast phenylalanine transfer RNA. Science, 185, 435-440.
9. Chattopadhyaya, R., Grzeskowiak, K. and Dickerson, R.E. (1990) Structure of a T4 hairpin loop on a Z-DNA stem and comparison with A-RNA and B-DNA loops. J. Mol. Biol., 211, 189-210.
10. Kim, Y., Geiger, J.H., Hahn, S. and Sigler, P.B. (1993) Crystal structure of a yeast TBP/TATA-box complex. Nature, 365, 512-520.
11. Kabsch, W., Sander, S. and Trifonov, E.N. (1982) The ten helical twist angles of B-DNA. Nucleic Acids Res., 10, 1097-1104.
12. Gorin, A.A., Zhurkin, V.B. and Olson, W.K. (1995) B-DNA twisting correlates with base pair morphology. J. Mol. Biol., 247, 34-48.
13. Franklin, R.E. and Gosling, R.G. (1953) Molecular configuration in sodium thymonucleate. Nature, 171, 740-741.
14. Marvin, D.A., Spencer, M., Wilkins, M.H.F. and Hamilton, L.D. (1958) A new configuration of deoxyribonucleic acid. Nature, 182, 387-388.
15. Pohl, F.M. and Jovin, T.M. (1972) Salt-induced co-operative conformational change of a synthetic DNA: equilibrium and kinetic studies with poly(dG-dC). J. Mol. Biol., 67, 375-396.
16. Ivanov, V.I., Minchenkova, L.E., Minyat, E.E., Frank-Kamenetskii, M.D. and Schyolkina, A.K. (1974) The B to A transition of DNA in solution. J. Mol. Biol., 87, 817-833.
17. Olson, W.K., Gorin, A.A., Lu, X-J., Hock, L.M. and Zhurkin, V.B. (1998) DNA sequence-dependent deformability deduced from protein-DNA crystal complexes. Proc. Natl Acad. Sci. USA, 95, 11163-11168.
18. Lu, X-J., Shakked, Z. and Olson, W.K. (2000) A-form conformational motifs in ligand-bound DNA structures. J. Mol. Biol., 300, 819-840.
19. Dickerson, R.E., Bansal, M., Calladine, C.R., Diekmann, S., Hunter, W.N., Kennard, O., von Kitzing, E., Lavery, R., Nelson, H.C.M., Olson, W.K. et al. (1989) Definitions and nomenclature of nucleic acid structure parameters. J. Mol. Biol., 208, 787-791.
20. Olson, W.K., Bansal, M., Burley, S.K., Dickerson, R.E., Gerstein, M., Harvey, S.C., Heinemann, U., Lu, X.-J., Neidle, S., Shakked, Z. et al. (2001) A standard reference frame for the description of nucleic acid base-pair geometry. J. Mol. Biol., 313, 229-237.
21. Leontis, N.B. and Westhof, E. (2001) Geometric nomenclature and classification of RNA base pairs. RNA, 7, 499-512.
22. Duarte, C.M. and Pyle, A.M. (1998) Stepping through an RNA structure: a novel approach to conformational analysis. J. Mol. Biol., 284, 1465-1478.
23. Gendron, P., Lemieux, S. and Major, F. (2001) Quantitative analysis of nucleic acid three-dimensional structures. J. Mol. Biol., 308, 919-936.
24. Klosterman, P.S., Tamura, M., Holbrook, S.R. and Brenner, S.E. (2002) SCOR: a structural classification of RNA database. Nucleic Acids Res., 30, 392-394.
25. Lemieux, S. and Major, F. (2002) RNA canonical and non-canonical base pairing types: a recognition method and complete repertoire. Nucleic Acids Res., 30, 4250-4263.
26. Leontis, N.B., Stombaugh, J. and Westhof, E. (2002) The non-Watson-Crick base pairs and their associated isostericity matrices. Nucleic Acids Res., 30, 3497-3531.
27. Takasu, A., Watanabe, K. and Kawai, G. (2002) Classification of RNA structures based on hydrogen bond and base-base stacking patterns: application for NMR structures. J. Biochem. (Tokyo), 132, 211-215.
28. Lavery, R. and Sklenar, H. (1989) Defining the structure of irregular nucleic acids: conventions and principles. J. Biomol. Struct. Dyn., 6, 655-667.
29. Babcock, M.S., Pednault, E.P.D. and Olson, W.K. (1994) Nucleic acid structure analysis. Mathematics for local Cartesian and helical structure parameters that are truly comparable between structures. J. Mol. Biol., 237, 125-156.
30. Tung, C.S., Soumpasis, D.M. and Hummer, G. (1994) An extension of the rigorous base-unit oriented description of nucleic-acid structures. J. Biomol. Struct. Dyn., 11, 1327-1344.
31. Bansal, M., Bhattacharyya, D. and Ravi, B. (1995) NUPARM and NUCGEN: software for analysis and generation of sequence dependent nucleic acid structures. Comput. Appl. Biosci., 11, 281-287.
32. El Hassan, M.A. and Calladine, C.R. (1995) The assessment of the geometry of dinucleotide steps in double-helical DNA: a new local calculation scheme. J. Mol. Biol., 251, 648-664.
33. Mazur, J. and Jernigan, R.L. (1995) Comparison of rotation models for describing DNA conformations: application to static and polymorphic forms. Biophys. J., 68, 1472-1489.
34. Lu, X-J., El Hassan, M.A. and Hunter, C.A. (1997) Structure and conformation of helical nucleic acids: analysis program (SCHNAaP). J. Mol. Biol., 273, 668-680.
35. Dickerson, R.E. (1998) DNA bending: the prevalence of kinkiness and the virtues of normality. Nucleic Acids Res., 26, 1906-1926.
36. Schneider, B., Cohen, D.M., Schleifer, L., Srinivasan, A.R., Olson, W.K. and Berman, H.M. (1993) A systematic method for studying the spatial distribution of water molecules around nucleic acid bases. Biophys. J., 65, 2291-2303.
37. Luscombe, N.M., Laskowski, R.A. and Thornton, J.M. (1997) NUCPLOT: a program to generate schematic diagrams of protein-nucleic acid interactions. Nucleic Acids Res., 25, 4940-4945.
38. Kono, H. and Sarai, A. (1999) Structure-based prediction of DNA target sites by regulatory proteins. Protein Struct. Funct. Genet., 35, 114-131.
39. Pabo, C.O. and Nekludova, L. (2000) Geometric analysis and comparison of protein-DNA interfaces: why is there no simple code for recognition? J. Mol. Biol., 301, 597-624.
40. Berman, H.M., Olson, W.K., Beveridge, D.L., Westbrook, J., Gelbin, A., Demeny, T., Hsieh, S.-H., Srinivasan, A.R. and Schneider, B. (1992) The Nucleic Acid Database: a comprehensive relational database of three-dimensional structures of nucleic acids. Biophys. J., 63, 751-759.
41. Bernstein, F.C., Koetzle, T.F., Williams, G.J., Meyer, E.E., Jr, Brice, M.D., Rodgers, J.R., Kennard, O., Shimanouchi, J. and Tasumi, M. (1977) The Protein Data Bank: a computer-based archival file for macromolecular structures. J. Mol. Biol., 112, 535-542.
42. Calladine, C.R. and Drew, H.R. (1997) Understanding DNA: The Molecule and How It Works. Academic Press, San Diego, CA, Ch. 3.
43. Chandrasekaran, R. and Arnott, S. (1989) The structures of DNA and RNA helices in oriented fibers. In Saenger, W. (ed.), Landolt-Börnstein Numerical Data and Functional Relationships in Science and Technology, Group VII/1b, Nucleic Acids. Springer-Verlag, Berlin, Germany, pp. 31-170.
44. Arnott, S. (1999) Polynucleotide secondary structures: an historical perspective. In Neidle,S. (ed.), Oxford Handbook of Nucleic Acid Structure. Oxford University Press, Oxford, UK, pp. 1-38.
45. Alexeev, D.G., Lipanov, A.A. and Skuratovskii, I.Y. (1987) The structure of poly(dA)·poly(dT) as revealed by an X-ray fibre diffraction. J. Biomol. Struct. Dyn., 4, 989-1011.
46. van Dam, L. and Levitt, M.H. (2000) BII nucleotides in the B and C forms of natural-sequence polymeric DNA: a new model for the C form of DNA with 40° helical twist. J. Mol. Biol., 304, 541-561.
47. Premilat, S. and Albiser, G. (1983) Conformations of A-DNA and B-DNA in agreement with fiber X-ray and infrared dichroism. Nucleic Acids Res., 11, 1897-1908.
48. Premilat, S. and Albiser, G. (1984) Conformations of C-DNA in agreement with fiber X-ray and infrared dichroism. J. Biomol. Struct. Dyn., 2, 607-613.
49. Premilat, S. and Albiser, G. (1986) DNA models for A, B, C and D conformations related to fiber X-ray, infrared and NMR measurements. J. Biomol. Struct. Dyn., 3, 1033-1043.
50. Premilat, S. and Albiser, G. (1997) X-ray fibre diffraction study of an elevated temperature structure of poly(dA)·poly(dT). J. Mol. Biol., 274, 64-71.
51. Premilat, S. and Albiser, G. (1999) Helix-helix transitions in DNA: fibre X-ray study of the particular cases poly(dG-dC) and poly(dA) 2poly(dT). Eur. Biophys. J., 28, 574-582.
52. Premilat, S. and Albiser, G. (2001) A new D-DNA form of poly(dA-dT)-poly(dA-dT): an A-DNA type structure with reversed Hoogsteen pairing. Eur. Biophys. J., 30, 404-410.
53. Rose, I.A., Hanson, K.R., Wilkinson, K.D. and Wimmer, M.J. (1980) A suggestion for naming faces of ring compounds. Proc. Natl Acad. Sci. USA, 77, 2439-2441.
54. Lavery, R., Zakrzewska, K., Sun, J.S. and Harvey, S.C. (1992) A comprehensive classification of nucleic-acid structural families based on strand direction and base-pairing. Nucleic Acids Res., 20, 5011-5016.
55. Burkard, M.E., Turner, D.H. and Tinoco, I., Jr (1999) Structures of base pairs involving at least two hydrogen bonds. In Gesteland, R.F., Cech, T.R. and Atkins, J.F. (eds), The RNA World. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY, pp. 675-680.
56. Zhurkin, V.B., Lysov, Y.P, and Ivanov, V.I. (1979) Anisotropic flexibility of DNA and the nucleosomal structure. Nucleic Acids Res., 6, 1081-1096.
57. Trikha, J., Ilman, D.J. and Hogle, J.M. (1999) Crystal structure of a 14 bp RNA duplex with non-symmetrical tandem G·U wobble base pairs. Nucleic Acids Res., 27, 1728-1739.
58. Masquida, B. and Westhof, E. (2000) On the wobble G·U and related pairs. RNA, 6, 9-15.
59. Varani, G. and McClain, W.H. (2000) The G·U wobble base pair. EMBO Rep., 1, 18-23.
60. Masquida, B., Sauter, C. and Westhof, E. (1999) A sulfate pocket formed by three G·U pairs in the 0.97 Å resolution X-ray structure of a nonameric RNA. RNA, 5, 1384-1395.
61. Babcock, M.S. and Olson, W.K. (1994) The effect of mathematics and coordinate system on comparability and "dependencies" of nucleic acid structure parameters. J. Mol. Biol., 237, 98-124.
62. Nissen, P., Hansen, J., Ban, N., Moore, P.B. and Steitz, T.A. (2000) The structural basis of ribosome activity in peptide bond synthesis. Science, 289, 920-930.
63. Brodersen, D.E., Clemons., W.M., Jr, Carter, A.P., Morgan-Warren, R.J., Wimberly, B.T. and Ramakrishnan, V. (2000) The structural basis for the action of the antibiotics tetracycline, pactamycin and hygromycin B on the 30S ribosomal subunit. Cell, 103, 1143-1154.
64. Pioletti, M., Schluenzen, F., Harms, J., Zarivach, R., Gluehmann, M., Avila, H., Bashan, A., Bartels, H., Auerbach, T., Jacobi, C. et al. (2001) Crystal structures of complexes of the small ribosomal subunit with tetracycline, edeine and IF3. EMBO J., 20, 1829-1839.
65. Wimberly, B.T., Brodersen, D.E., Clemons, W.M., Jr, Morgan-Warren, R.J., Carter, A.P., Vonrhein, C., Hartsch, T. and Ramakrishnan, V. (2000) Structure of the 30S ribosomal subunit. Nature, 407, 327-339.
66. Cys-EF-Tu-GDPNP reveals general and specific features in the ternary complex and in tRNA. Struct. Fold. Des., 7, 143-156.
67. Kosikov, K.M., Gorin, A.A., Zhurkin, V.B. and Olson, W.K. (1999) DNA stretching and compression: large-scale simulations of double helical structures. J. Mol. Biol., 289, 1301-1326.
68. Kosikov, K.M., Gorin, A.A., Lu, X.-J., Olson, W.K. and Manning, G.S. (2002) Bending of DNA by asymmetric charge neutralization: all-atom energy simulations. J. Am. Chem. Soc., 124, 4838-4847.
69. Dickerson, R.E. and Ng, H.L. (2001) DNA structure from A to B. Proc. Natl Acad. Sci. USA, 98, 6986-6988.
70. Dickerson, R.E. (1992) DNA structure from A to Z. Methods Enzymol., 211, 67-111.
71. Wang, A.H.-J., Quigley, G.J., Kolpak, F.J., Crawford, J.L., van Boom, J.H., van der Marel, G. and Rich, A. (1979) Molecular structure of a left-handed double helical DNA fragment at atomic resolution. Nature, 282, 680-686.
72. Srinivasan, A.R. and Olson, W.K. (1987) Nucleic acid model building. The multiple backbone solutions associated with a given base morphology. J. Biomol. Struct. Dyn., 4, 895-938.
73. Vargason, J.M., Eichman, B.F. and Ho, P.S. (2000) The extended and eccentric E-DNA structure induced by cytosine methylation or bromination. Nature Struct. Biol., 7, 758-761.
74. Ng, H.L. and Dickerson, R.E. (2001) Mildly eccentric E-DNA. Nature Struct. Biol., 8, 107.
75. Ng, H.L., Kopka, M.L. and Dickerson, R.E. (2000) The structure of a stable intermediate in the A × B DNA helix transition. Proc. Natl Acad. Sci. USA, 97, 2035-2039.
76. Lu, X-J., Babcock, M.S. and Olson, W.K. (1999) Mathematical overview of nucleic acid analysis programs. J. Biomol. Struct. Dyn., 16, 833-843.
77. Heinemann, U., Lauble, H., Frank, R. and Bloecker, H. (1987) Crystal structure analysis of an A-DNA fragment at 1.8 Ångströms resolution. Nucleic Acids Res., 15, 9531-9550.
78. Vargason, J.M., Henderson, K. and Ho, P.S. (2001) A crystallographic map of the transition from B-DNA to A-DNA. Proc. Natl Acad. Sci. USA, 98, 7265-7270.
79. Kim, J.L., Nikolov, D.B. and Burley, S.K. (1993) Co-crystal structure of TBP recognizing the minor groove of a TATA element. Nature, 365, 520-527.
80. Guzikevich-Guerstein, G. and Shakked, Z. (1995) A novel form of the DNA double helix imposed on the TATA-box by the TATA-binding protein. Nature Struct. Biol., 3, 32-37.
81. Patikoglou, G.A., Kim, J.L., Sun, L., Yang, S.-H., Kodadek, T. and Burley, S.K. (1999) TATA element recognition by the TATA box-binding protein has been conserved throughout evolution. Genes Dev., 13, 3217-3230.
82. Murphy, F.V., IV, Sweet, R.M. and Churchill, M.E.A. (1999) The structure of a chromosomal high mobility group protein-DNA complex reveals sequence-neutral mechanisms important for non-sequence-specific DNA recognition. EMBO J., 18, 6610-6618.
83. Merritt, E.A. and Bacon, D.J. (1997) Raster3D: photorealistic molecular graphics. Methods Enzymol., 277, 505-524.
84. Kraulis, P.J. (1991) MolScript: a program to produce both detailed and schematic plots of protein structures. J. Appl. Crystallogr., 24, 946-950.
85. Lu, X.-J., El Hassan, M.A. and Hunter, C.A. (1997) Structure and conformation of helical nucleic acids: rebuilding program (SCHNArP). J. Mol. Biol., 273, 681-691.
86. Shakked, Z., Guerstein-Guzikevich, G., Eisenstein, M., Frolow, F. and Rabinovich, D. (1989) The conformation of the DNA double helix in the crystal is dependent on its environment. Nature, 342, 456-459.
87. Shui, X., McFail-Isom, L., Hu, G.G. and Williams, L.D. (1998) The B-DNA dodecamer at high resolution reveals a spine of water on sodium. Biochemistry, 37, 8341-8355.
88. Luger, K., Mäder, A.W., Richmond, R.K., Sargent, D.F. and Richmond, T.J. (1997) Crystal structure of the nucleosome core particle at 2.8 Å resolution. Nature, 389, 251-260.
89. Clowney, L., Jain, S.C., Srinivasan, A.R., Westbrook, J., Olson, W.K. and Berman, H.M. (1996) Geometric parameters in nucleic acids: nitrogenous bases. J. Am. Chem. Soc., 118, 509-518.
90. Sayle, R.A. and Milnerwhite, E.J. (1995) RasMol: biomolecular graphics for all. Trends Biochem. Sci., 20, 374-376.
91. Rice, P.A., Yang, S.-W., Mizuuchi, K. and Nash, H.A. (1996) Crystal structure of an IHF-DNA complex: a protein-induced DNA U-turn. Cell, 87, 1295-1306.
92. Lu, X-J. and Olson, W.K. (1999) Resolving the discrepancies among nucleic acid conformational analyses. J. Mol. Biol., 285, 1563-1575.