Basics of nucleic acid structure

Computational Studies of RNA and DNA

Volumn , Issue , 2006, Pages 1-44

  Schneider, Bohdan ^a   Berman, Helen M ^b  

^a INSTITUTE OF ORGANIC CHEMISTRY AND BIOCHEMISTRY   (Czech Republic)

^b RUTGERS UNIVERSITY   (United States)

Author keywords

3D; DNA; NDB; NMR; nucleic acid; Nucleic Acid Database; PDB; Protein Data Bank; RNA; structure; X ray crystallography

Indexed keywords

EID: 84887876951     PISSN: None     EISSN: None     Source Type: Book    
DOI: 10.1007/978-1-4020-4851-3_1     Document Type: Chapter

References (193)

1. Avery, O.T., MacLeod, C.M. & McCarthy, M. (1944). Studies on the chemical nature of the substance inducing transformation of pneumococcal types: Induction of transformation by a desoxyribonucleic acid fraction isolated from Pneumococcus Type III J.Exp.Med. 79, 137-158.
2. Hershey, A. & Chase, M. (1952). Cold Spring Harbor Symp. Quant. Biol. 16, 445-456.
3. Wilkins, M.H.F., Stokes, A.R. & Wilson, H.R. (1953). Molecular structure of deoxypentose nucleic acids. Nature 171, 738-740.
4. Franklin, R.E. & Gosling, R.G. (1953). Molecular configuration in sodium thymonucleate. Nature 171, 740-741.
5. Watson, J.D. & Crick, F H.C. (1953). A structure for deoxyribose nucleic acid. Nature 171, 737-738.
6. Saenger, W. (1984). Principles of nucleic acid structure. Springer Advanced Texts in Chemistry (Cantor, C.R., Ed.), Springer-Verlag.
7. Neidle, S. (2002). Nucleic Acid Structure and Recognition, Oxford University, Oxford.
8. Calladine, C.R. & Drew, H.R. (1997). Understanding DNA. The Molecule & How It Works, second edition, Academic, London
9. Neidle, S., Ed. (1999). Oxford handbook of nucleic acid structure. Oxford University, Oxford.
10. Branden, C. & Tooze, J. (1999). Introduction to Protein Structure, second edition, Garland, New York.
11. Zamenhof, S., Brawermann, G. & Chargaff, E. (1952). On the Desoxypentose Nucleic Acids from Several Microorganisms. Biochim.Biophys.Acta 9, 402-405.
12. Arai, S., Chatake, T., Ohhara, T., Kurihara, K., Tanaka, I., Suzuki, N., Fujimoto, Z., Mizuno, H. & Niimura, N. (2005). Complicated water orientations in the minor groove of the B-DNA dodecamer d(CCATTAATGG)2 observed by neutron diffraction measurement. Nucleic Acid Res. 33, 3017-3024.
13. Altona, C. & Sundaralingam, M. (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.
14. Murray-Rust, P. & Motherwell, S. (1978). Computer retrieval and analysis of molecular geometry. III Geometry of the β-1'-aminofuranoside fragment. Acta Cryst. B34, 2534-2546.
15. Dunitz, J.D. (1972). Approximate relationships between conformational parameters in 5-and 6-membered rings. Tetrahedron 28, 5459-5467.
16. Gelbin, A., Schneider, B., Clowney, L., Hsieh, S.-H., Olson, W.K. & Berman, H.M. (1996). Geometric parameters in nucleic acids: Sugar and phosphate constituents. J.Am.Chem.Soc. 118, 519-528.
17. Dong, F. & Miller, R.E. (2002). Vibrational transition moment angles in isolated biomolecules: A structural tool. Science 298, 1227-1230.
18. Luisi, B.F., Orozco, M., Šponer, J., Luque, F.J. & Shakked, Z. (1998). On the potential role of the amino nitrogen atom as a hydrogen acceptor in macromolecules. J.Mol.Biol. 279, 1123-1136.
19. Baur, W.H. (1974). The Geometry of Polyhedral Distortions. Predictive Relationships for the Phosphate Group. Acta Cryst. B30, 1195-1215.
20. Schneider, B., Kabelac, M. & Hobza, P. (1996). Geometry of the Phosphate Group and Its Interactions with Metal Cations in Crystals and ab initio calculations. J.Am.Chem.Soc. 118, 12207-12217.
21. Lemieux, R.U. (1971). Effects of unshared pairs of electrons and their solvation on conformational equilibria. Pure Appl.Chem. 25.
22. Wolfe, S. (1972). The gauche effect. Some stereochemical consequences of adjacent electron pairs and polar bonds. Acc.Chem.Res. 5, 102-111.
23. Schneider, B., Neidle, S. & Berman, H.M. (1997). Conformations of the sugar-phosphate backbone in helical DNA crystal structures. Biopolymers 42, 113-124.
24. Murray, L.J., Arendall, W.B., 3rd, Richardson, D.C. & Richardson, J.S. (2003). RNA backbone is rotameric. Proc.Natl.Acad.Sci.USA 100, 13904-13909.
25. Schneider, B., Moravek, Z. & Berman, H.M. (2004). RNA conformational classes. Nucleic Acids Res. 32, 1666-1677.
26. Allen, F.H., Bellard, S., Brice, M.D., Cartright, B.A., Doubleday, A., Higgs, H., Hummelink, T., Hummelink-Peters, B.G., Kennard, O., Motherwell, W.D.S., Rodgers, J.R. & Watson, D.G. (1979). The Cambridge Crystallographic Data Centre: Computer-based search, retrieval, analysis and display of information. Acta Cryst. B35, 2331-2339.
27. Berman, H.M., Olson, W.K., Beveridge, D.L., Westbrook, J., Gelbin, A., Demeny, T., Hsieh, S.-H., Srinivasan, A.R. & Schneider, B. (1992). The Nucleic Acid Database-A Comprehensive Relational Database of Three-Dimensional Structures of Nucleic Acids. Biophys.J. 63, 751-759.
28. Taylor, R. & Kennard, O. (1982). The molecular structures of nucleosides and nucleotides part I. J.Mol.Struct. 78, 1-28.
29. Clowney, L., Jain, S.C., Srinivasan, A.R., Westbrook, J., Olson, W.K. & Berman, H.M. (1996). Geometric Parameters In Nucleic Acids: Nitrogenous Bases. J.Am.Chem.Soc. 118, 509-518.
30. Parkinson, G., Vojtechovsky, J., Clowney, L., Brunger, A.T. & Berman, H.M. (1996). New parameters for the refinement of nucleic acid containing structures. Acta Cryst. D52, 57-64.
31. Brünger, A.T. (1992). X-PLOR, version 3.1, a system for X-ray crystallography and NMR 3.1 edit. Yale University Press, New Haven, CT.
32. Weiner, P. & Kollman, P. (1981). AMBER. J.Comput.Chem. 2, 287-303.
33. Brooks, B.R., Bruccoleri, R.E., Olafson, B.D., States, D.J., Swaminathan, S. & Karplus, M. (1983). CHARMM: A program for macromolecular energy, minimization, and dynamics calculations. J.Comput.Chem. 4, 187-217.
34. Leontis, N.B. & Westhof, E. (2001). Geometric nomenclature and classification of RNA base pairs. RNA 7, 499-512.
35. Šponer, J., Jurecka, P. & Hobza, P. (2004). Accurate interaction energies of hydrogen-bonded nucleic acid base pairs. J.Am.Chem.Soc. 126, 10142-10151.
36. 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., Saenger, W., Shakked, Z., Sklenar, H., Soumpasis, D.M., Tung, C.-S., Wang, A.H.-J. & Zhurkin, V.B. (1989). Definitions and nomenclature of nucleic acid structure parameters. EMBO J. 8, 1-4.
37. Lu, X.-J., El Hassan, M.A. & Hunter, C.A. (1997). Structure and conformation of helical nucleic acids: Analysis program (SCHNAaP). J.Mol.Biol. 273, 668-680.
38. El Hassan, M.A. & Calladine, C.R. (1995). The assessment of the geometry of dinucleotide steps in double-helical DNA: A new local calculation scheme with an appendix. J.Mol.Biol. 251, 648-664.
39. Gorin, A.A., Zhurkin, V.B. & Olson, W.K. (1995). B-DNA twisting correlates with base-pair morphology. J.Mol.Biol. 247, 34-48.
40. Kosikov, K.M., Gorin, A.A., Zhurkin, V.B. & Olson, W.K. (1999). DNA stretching and compression: Simulations of double helical structures. J.Mol.Biol. 289, 1301-1326.
41. Lavery, R. & Sklenar, H. (1989). Defining the structure of irregular nucleic acids: Conventions and principles. J.Biomol.Struct.Dyn. 6, 655-667.
42. Dickerson, R.E. (1998). DNA bending: The prevalence of kinkiness and the virtues of normality. Nucleic Acids Res. 26, 1906-1926.
43. Tung, C.-S., Soumpasis, D.M. & Hummer, G. (1994). An extension of the rigorous base-unit oriented description of nucleic acid structures. J.Biomol.Struct.Dyn. 11, 1327-1344.
44. Soumpasis, D.M. & Tung, C.S. (1988). A rigorous base pair oriented description of DNA structures. J.Biomol.Struct.Dyn. 6, 397-420.
45. Bansal, M., Bhattacharyya, D. & Ravi, B. (1995). NUPARM and NUCGEN: Software for analysis of sequence dependent nucleic acid structures. CABIOS 11, 281-287.
46. Bhattacharyya, A. & Lilley, D.M. (1989). The contrasting structures of mismatched DNA sequences containing looped-out bases (bulges) and multiple mismatches (bubbles). Nucleic Acids Res. 17, 6821-6840.
47. Babcock, M.S., Pednault, E.P.D. & 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.
48. 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., Sklenar, H., Suzuki, M., Tung, C.-S., Westhof, E., Wolberger, C. & Berman, H.M. (2001). A standard reference frame for the description of nucleic acid base-pair geometry. J.Mol.Biol. 313, 229-237.
49. Drew, H.R., Wing, R.M., Takano, T., Broka, C., Tanaka, S., Itakura, K. & Dickerson, R.E. (1981). Structure of a B-DNA dodecamer: Conformation and dynamics. Proc.Natl.Acad.Sci.USA 78, 2179-2183.
50. McCall, M., Brown, T. & Kennard, O. (1985). The crystal structure of d(G-G-G-G-C-C-C-C). A model for poly(dG)•poly(dC). J.Mol.Biol. 183, 385-396.
51. Holbrook, S.R., Cheong, C., Tinoco Jr., I. & Kim, S.-H. (1991). Crystal structure of an RNA double helix incorporating a track of non-Watson-Crick base pairs. Nature 353, 579-581.
52. Gessner, R.V., Frederick, C.A., Quigley, G.J., Rich, A. & Wang, A.H.-J. (1989). The molecular structure of the left-handed Z-DNA double helix at 1.0-Å atomic resolution. J.Biol.Chem. 264, 7921-7935.
53. Haider, S., Parkinson, G.N. & Neidle, S. (2002). Crystal structure of the potassium form of an Oxytricha nova G-quadruplex. J.Mol.Biol. 320, 189-200.
54. Chen, L., Cai, L., Zhang, X. & Rich, A. (1994). Crystal Structure of a Four-Stranded Intercalated DNA: D(C4). Biochemistry 33, 13540-13546.
55. Sussman, J.L., Holbrook, S.R., Warrant, R.W. & Kim, S.-H. (1978). Crystal structure of yeast phenylalanine transfer RNA. I. Crystallographic refinement. J.Mol.Biol. 123, 607-630.
56. Pley, H.W., Flaherty, K.M. & McKay, D.B. (1994). Three-dimensional structure of a hammerhead ribozyme. Nature 372, 68-74.
57. Cate, J.H., Gooding, A.R., Podell, E., Zhou, K.H., Golden, B.L., Kundrot, C.E., Cech, T.R. & Doudna, J.A. (1996). Crystal structure of a group I ribozyme domain: Principles of RNA packing. Science 273, 1678-1685.
58. Dickerson, R.E., Drew, H.R., Conner, B.N., Wing, R.M., Fratini, A.V. & Kopka, M.L. (1982). The Anatomy of A-, B-, and Z-DNA. Science 216, 475-485.
59. Chandrasekaran, R. & Arnott, S. (1989). Landolt-Börnstein Numerical Data and Functional Relationships in Science and Technology, Group VII/1b, Nucleic Acids (Saenger, W., Ed.), Springer-Verlag, Berlin.
60. Olson, W.K., Gorin, A.A., Lu, X.-J., Hock, L.M. & Zhurkin, V.B. (1998). DNA sequence-dependent deformability deduced from protein-DNA crystal complexes. Proc.Natl.Acad.Sci.USA 95, 11163-11168.
61. Berman, H.M. (1997). Crystal studies of B-DNA: The answers and the questions. Biopolymers 44, 23-44.
62. Dickerson, R.E., Goodsell, D. & Kopka, M.L. (1996). MPD and DNA bending in crystals and in solution. J.Mol.Biol. 256, 108-125.
63. Heinemann, U., Alings, C. & Hahn, M. (1994). Crystallographic studies of DNA helix structure. Biophys.Chem. 50, 157-167.
64. Gorin, A. & Zhurkin, V.B. (1995). DNA structure and flexibility in DNA-protein complexes. A comparative study based on X-ray data. Mathematical Approaches to DNA.
65. Quintana, J.R., Grzeskowiak, K., Yanagi, K. & Dickerson, R.E. (1992). Structure of a B-DNA decamer with a central T-A step: C-G-A-T-T-A-A-T-C-G. J.Mol.Biol. 225, 379-395.
66. Yanagi, K., Prive, G.G. & Dickerson, R.E. (1991). Analysis of local helix geometry in three B-DNA decamers and eight dodecamers. J.Mol.Biol. 217, 201-214.
67. Young, M.A., Ravishanker, G., Beveridge, D.L. & Berman, H.M. (1995). Analysis of local helix bending in crystal structures of DNA oligonucleotides and DNA-Protein complexes. Biophys.J. 68, 2454-2468.
68. Lipanov, A., Kopka, M.L., Kaczor-Grzeskowiak, M., Quintana, J. & Dickerson, R.E. (1993). The Structure of the B-DNA Decamer C-C-A-A-C-I-T-T-G-G in Two Different Space Groups: Conformational Flexibility of B-DNA. Biochemistry 32, 1373-1380.
69. Privé, G.G., Yanagi, K. & Dickerson, R.E. (1992). Structure of the B-DNA decamer C-C-A-A-C-G-T-T-G-G and comparison with isomorphous decamers C-C-A-A-G-A-T-T-G-G and C-C-A-G-G-C-G-T-G-G. J.Mol.Biol. 217, 177-199.
70. Davey, C.A., Sargent, D.F., Luger, K., Maeder, A.W. & Richmond, T.J. (2002). Solvent mediated interactions in the structure of the nucleosome core particle at 1.9 a resolution. J.Mol.Biol. 319, 1097-1113.
71. Kim, Y., Geiger, J.H., Hahn, S. & Sigler, P.B. (1993). Crystal structure of a yeast TBP/TATA-box complex. Nature 365, 512-520.
72. Kim, J.L., Nikolov, D.B. & Burley, S.K. (1993). Co-crystal structure of TBP recognizing the minor groove of a TATA element. Nature 365, 520-527.
73. Guzikevich-Guerstein, G. & Shakked, Z. (1996). A novel form of the DNA double helix imposed on the TATA-box by the TATA-binding protein. Nat.Struct.Biol. 3, 32-37.
74. Leontis, N., Stombaugh, J. & Westhof, E. (2002). The non-Watson-Crick base pairs and their associated isostericity matrices. Nucleic Acids Res. 30, 3497-3531.
75. Varani, G. & McClain, W.H. (2000). The G x U wobble base pair. A fundamental building block of RNA structure crucial to RNA function in diverse biological systems. EMBO Rep. 1, 18-23.
76. Baeyens, K.J., DeBondt, H.L., Pardi, A. & Holbrook, S.R. (1996). A curved RNA helix incorporating an internal loop with G center dot A and A center dot A non-Watson-Crick base pairing. Proc.Natl.Acad.Sci.USA 93, 12851-12855.
77. Wang, A.H.-J., Quigley, G.J., Kolpak, F.J., Crawford, J.L., van Boom, J.H., van der Marel, G.A. & Rich, A. (1979). Molecular structure of a left-handed double helical DNA fragment at atomic resolution. Nature 282, 680-686.
78. Wang, A.H.-J., Quigley, G.J., Kolpak, F.J., van der Marel, G.A., van Boom, J.H. & Rich, A. (1981). Left-handed double helical DNA: Variations in the backbone conformation. Science 211, 171-176.
79. Schwartz, T., Behlke, J., Lowenhaupt, K., Heinemann, U. & Rich, A. (2001). Structure of the DLM-1-Z-DNA complex reveals a conserved family of Z-DNA-binding proteins. Nat.Struct.Biol 8, 761-765.
80. Westhof, E. (1988). Water: An integral part of nucleic acid structure. Ann.Rev.Biophys.Chem. 17, 125-144.
81. Chalikian, T.V. & Breslauer, K.J. (1998). Thermodynamic analysis of biomolecules: A volumetric approach. Curr.Opin.Struct.Biol. 8, 657-664.
82. Leikin, S., Parsegian, V.A. & Rau, D.C. (1993). Hydration forces. Annu.Rev.Phys.Chem. 44, 369-395.
83. Rau, D.C. & Parsegian, V.A. (1992). Direct measurement of the intermolecular forces between counterion-condensed DNA double helices. Biophys.J. 61, 246-259.
84. Neidle, S., Achari, A., Taylor, G.L., Berman, H.M., Carrell, H.L., Glusker, J.P. & Stallings, W. (1977). The structure of a proflavine: Dinucleoside phosphate complex - A model for nucleic acid drug interaction. Nature 269, 304-307.
85. Schneider, B., Ginell, S.L. & Berman, H.M. (1992). Low temperature structures of dCpG-proflavine: Conformational and hydration effects. Biophys.J. 63, 1572-1578.
86. Drew, H.R. & Dickerson, R.E. (1981). Structure of a B-DNA Dodecamer III Geometry of Hydration. J.Mol.Biol. 151, 535-556.
87. Kennard, O., Cruse, W.B.T., Nachman, J., Prange, T., Shakked, Z. & Rabinovich, D. (1986). Ordered water structure in an A-DNA octamer at 1.7A resolution. J.Biomol.Struct.Dyn. 3, 623-647.
88. Saenger, W., Hunter, W.N. & Kennard, O. (1986). DNA conformation is determined by economics in the hydration of phosphate groups. Nature 324, 385-388.
89. Eisenstein, M. & Shakked, Z. (1995). Hydration patterns and intermolecular interactions in A-DNA crystal structures. Implications for DNA recognition. J.Mol.Biol. 248, 662-678.
90. Egli, M., Portmann, S. & Usman, N. (1996). RNA hydration: A detailed look. Biochemistry 35, 8489-8494.
91. Schneider, B., Cohen, D.M., Schleifer, L., Srinivasan, A.R., Olson, W.K. & Berman, H.M. (1993). A systematic method for studying the spatial distribution of water molecules around nucleic acid bases. Biophys.J. 65, 2291-2303.
92. Schneider, B. & Berman, H.M. (1995). Hydration of the DNA bases is local. Biophys.J. 69, 2661-2669.
93. Schneider, B., Patel, K. & Berman, H.M. (1998). Hydration of the phosphate group in double helical DNA. Biophys.J. 75, 2422-2434.
94. Moravek, Z., Neidle, S. & Schneider, B. (2002). Protein and drug interactions in the minor groove of DNA. Nucleic Acids Res. 30, 1182-1191.
95. Woda, J., Schneider, B., Patel, K., Mistry, K. & Berman, H.M. (1998). An analysis of the relationship between hydration and protein-DNA interactions. Biophys.J. 75, 2170-2177.
96. Schneider, B. & Kabelac, M. (1998). Stereochemistry of binding of metal cations and water to a phosphate group. J.Am.Chem.Soc. 120, 161-165.
97. Schultze, P., Smith, F.W. & Feigon, J. (1994). Refined solution structure of the dimeric quadruplex formed from the Oxytricha telomeric oligonucleotide d(GGGGTTTTGGGG). Structure 2, 221-233.
98. Vargason, J.M. & Ho, P.S. (2002). The effect of cytosine methylation on the structure and geometry of the Holliday junction-The structure of d(CCGGTACm(5)CGG) at 1.5 A resolution. J.Biol.Chem. 277, 21041-21049.
99. Thorpe, J.H., Gale, B.C., Teixeira, S.C. & Cardin, C.J. (2003). Conformational and hydration effects of site-selective sodium, calcium and strontium ion binding to the DNA Holliday junction structure d(TCGGTACCGA)(4). J.Mol.Biol. 327, 97-109.
100. Gopaul, D.N., Guo, F. & Van Duyne, G.D. (1998). Structure of the Holliday junction intermediate in Cre-loxP site-specific recombination. EMBO J. 17, 4175-4187.
101. Shepard, W., Cruse, W.B.T., Fourme, R., de la Fortelle, E. & Prangé, T. (1998). A zipper-like duplex in DNA: The crystal structure of d(GCGAAAGCT) at 2.1A resolution. Structure 6, 849-861.
102. 6- methylguanine. Biochemistry 33, 3487-3493.
103. Park, H., Zhang, K., Ren, Y., Nadji, S., Sinha, N., Taylor, J.-S. & Kang, C. (2002). Crystal Structure of a DNA Decamer Containing a Thymine-dimer. Proc.Natl.Acad.Sci.USA 99, 15965-15970.
104. Egli, M., Tereshko, V., Teplova, M., Minasov, G., Joachimiak, A., Sanishvili, R., Weeks, C.M., Miller, R., Maier, M.A., An, H., Cook, P.D. & Manoharan, M. (1998). X-ray crystallographic analysis of the hydration of A-and B-Form DNA at atomic resolution. Biopolymers 48, 234-252.
105. Minasov, G., Teplova, M., Nielsen, P., Wengel, J. & Egli, M. (2000). Structural basis of cleavage by RNase H of hybrids of arabinonucleic acids and RNA. Biochemistry 39, 3525-3532.
106. Declercq, R., Van Aerschot, A., Read, R.J., Herdewijn, P. & Van Meervelt, L. (2002). Crystal structure of double helical hexitol nucleic acids. J.Am.Chem.Soc. 124, 928-933.
107. Cruse, W.B.T., Salisbury, S.A., Brown, T., Cosstick, R., Eckstein, F. & Kennard, O. (1986). Chiral Phosphorothioate Analogues of B-DNA. The Crystal Structure of Rp-d(Gp(S)CpGp(S)CpGp(S)C). J.Mol.Biol. 192, 891-905.
108. Heinemann, U., Rudolph, L.-N., Alings, C., Morr, M., Heikens, W., Frank, R. & Bloecker, H. (1991). Effect of a single 3'-methylene phosphonate linkage on the conformation of an A-DNA octamer double helix. Nucleic Acids Res. 19, 427-433.
109. Tereshko, V., Gryaznov, S. & Egli, M. (1998). Consequences of replacing the DNA 3'-oxygen by an amino group: High-resolution crystal structure of a fully modified N3'-P5' phosphoramidate DNA dodecamer duplex. J.Am.Chem.Soc. 120, 269-283.
110. Rasmussen, H. & Sandholm, J. (1997). Crystal structure of a peptide nucleic acid (PNA) duplex at 1.7 Å resolution. Nat.Struct.Biol. 4, 98-101.
111. Betts, L., Josey, J.A., Veal, J.M. & Jordan, S.R. (1995). A Nucleic-Acid Triple-Helix Formed by a Peptide Nucleic-Acid DNA Complex. Science 270, 1838-1841.
112. Nissen, P., Ippolito, J.A., Ban, N., Moore, P.B. & Steitz, T.A. (2001). RNA tertiary interactions in the large ribosomal subunit: The A-minor motif. Proc.Natl.Acad.Sci.USA 98, 4899-4903.
113. Battle, D.J. & Doudna, J.A. (2002). Specificity of RNA-RNA helix recognition. Proc.Natl.Acad.Sci.USA 99, 11676-11681.
114. Klein, D.J., Schmeing, T.M., Moore, P.B. & Steitz, T.A. (2001). The Kink-Turn: A new RNA secondary structure motif. EMBO J. 20, 4214-4221.
115. Strobel, S.A., Adams, P.L., Stahley, M.R. & Wang, J. (2004). RNA kink turns to the left and to the right. RNA 10, 1852-1854.
116. Adams, P.L., Stahley, M.R., Kosek, A.B., Wang, J. & Strobel, S.A. (2004). Crystal structure of a self-splicing group I intron with both exons. Nature 430, 45-50.
117. Robertus, J.D., Ladner, J.E., Finch, J.T., Rhodes, D., Brown, R.S., Clark, B.F.C. & Klug, A. (1974). Structure of yeast phenylalanine tRNA at 3 A resolution. Nature 250, 546-551.
118. Kim, S.-H., Suddath, F.L., Quigley, G.J., McPherson, A., Sussman, J.L., Wang, A.H.-J., Seeman, N.C. & Rich, A. (1974). Three-dimensional tertiary structure of yeast phenylalanine transfer RNA. Science 185, 435-440.
119. Cech, T., Zaug, A. & Grabowski, P. (1981). In vitro splicing of the ribosomal RNA precursor of Tetrahymena: Involvement of a guanosine nucleotide in the excision of the intervening sequence. Cell 27, 487-496.
120. Gilbert, W. (1986). Origin of Life-the RNA World. Nature 319, 618-618.
121. Gesteland, R.F., Cech, T.R. & Atkins, J.F. (1999). The RNA World, second edition. Cold Spring Harbor monograph series, 37, Cold Spring Harbor Laboratory Press, Cold Spring Harbor.
122. Zhang, L. & Doudna, J.A. (2002). Structural insights into group II Intron catalysis and branch-site selection. Science 295, 2084-2088.
123. Krasilnikov, A.S., Yang, X., Pan, T. & Mondragon, A. (2003). Crystal structure of the specificity domain of ribonuclease P. Nature 421, 760-764.
124. Krasilnikov, A.S., Xiao, Y., Pan, T. & Mondragon, A. (2004). Basis for structural diversity in homologous RNAs. Science 306, 104-107.
125. Serganov, A., Keiper, S., Malinina, L., Tereshko, V., Skripkin, E., Hobartner, C., Polonskaia, A., Phan, A.T., Wombacher, R., Micura, R., Dauter, Z., Jaschke, A. & Patel, D.J. (2005). Structural basis for Diels-Alder ribozyme-catalyzed carbon-carbon bond formation. Nat.Struct.Mol.Biol. 12, 218-224.
126. Quintana, J.R., Lipanov, A.A. & Dickerson, R.E. (1991). Low-temperature crystallo-graphic analysis of the binding of the Hoechst-33258 to the double-helical DNA dodecamer C-G-C-G-A-A-T-T-C-G-C-G. Biochemistry 30, 10294-10306.
127. Moore, M. H., Hunter, W.N., Langlois d'Estaintot, B. & Kennard, O. (1989). DNA-Drug interactions. The crystal structure of d(CGATCG) complexed with daunomycin. J.Mol.Biol. 206, 693-705.
128. Takahara, P.M., Rosenzweig, A.C., Frederick, C.A. & Lippard, S.J. (1995). Crystal Structure of Double-Stranded DNA Containing the Major Adduct of the Anticancer Drug Cisplatin. Nature 377, 649-652.
129. Jain, S.C., Tsai, C.-C. & Sobell, H.M. (1977). Visualization of drug-nucleic acid interactions at atomic resolution. II. Structure of an ethidium/dinucleoside monophosphate crystalline complex, ethidium: 5-iodocytidylyl(3'-5')guanosine. J.Mol.Biol. 114, 317-331.
130. Kamitori, S. & Takusagawa, F. (1994). Multiple binding modes of anticancer drug actinomycin D: X-ray, molecular modeling, and spectroscopic studies of d(GAAGCTTC)2-actinomycine D complexes and its host DNA. J.Am.Chem.Soc. 116, 4154-4165.
131. Robinson, H., Gao, Y.G., Yang, X., Sanishvili, R., Joachimiak, A. & Wang, A.H.-J. (2001). Crystallographic analysis of a novel complex of actinomycin D bound to the DNA decamer CGATCGATCG. Biochemistry 40, 5587-5592.
132. Gao, Y.-G., Liaw, Y.-C., Robinson, H. & Wang, A.H.-J. (1990). Binding of the antitumor drug nogalamycin and its derivatives to DNA: Structural comparison. Biochemistry 29, 10307-10316.
133. Todd, A.K., Adams, A., Thorpe, J.H., Denny, W.A., Wakelin, L.P. & Cardin, C.J. (1999). Major groove binding and 'DNA-induced' fit in the intercalation of a derivative of the mixed topoisomerase I/II poison N-(2-(dimethylamino)ethyl)acridine-4-carboxamide (DACA) into DNA: X-ray structure complexed to d(CG(5-BrU)ACG)2 at 1.3-A resolution. J.Med.Chem. 42, 536-540.
134. Kopka, M.L., Yoon, C., Goodsell, D., Pjura, P. & Dickerson, R.E. (1985). Binding of an antitumor drug to DNA. Netropsin and C-G-C-G-A-A-T-T-BrC- G-C-G. J.Mol.Biol. 183, 553-563.
135. Tabernero, L., Bella, J. & Alemán, C. (1996). Hydrogen bond geometry in DNA-minor groove binding drug complexes. Nucleic Acids Res. 24, 3458-3466.
136. Coll, M., Frederick, C.A., Wang, A.H.-J. & Rich, A. (1987). A Bifurcated Hydrogen-Bonded Conformation in the d(A•T) Base Pairs of the DNA Dodecamer d(CGCGAAATTTGCG) and Its Complex With Distamycin. Proc.Natl.Acad.Sci.USA 84, 8385-8389.
137. Chen, X., Ramakrishnan, B., Rao, S.T. & Sundaralingam, M. (1994). Side by side binding of two distamycin a drugs in the minor groove of an alternating B-DNA duplex. Nat.Struct.Biol. 1, 169-175.
138. Dervan, P.B. & Buerli, R.W. (1999). Sequence-specific DNA recognition by polyamides. Curr.Opin.Chem.Biol.3, 688-693.
139. Kielkopf, C.L., White, S., Szewczyk, J.W., Turner, J.M., Baird, E.E., Dervan, P.B. & Rees, D.C. (1998). A structural basis for recognition of A.T and T.A base pairs in the minor groove of B-DNA. Science 282, 111-115.
140. Goodsell, D.S., Ng, H.L., Kopka, M.L., Lown, J.W. & Dickerson, R.E. (1995). Structure of a dicationic monoimidazole lexitropsin bound to DNA. Biochemistry 34, 16654-16661.
141. Dervan, P.B. & Edelson, B.S. (2003). Recognition of the DNA minor groove by pyrrole-imidazole polyamides. Curr.Opin.Struct.Biol. 13, 284-299.
142. Dervan, P.B. (2001). Molecular recognition of DNA by small molecules. Bioorg.Med.Chem. 9, 2215-2235.
143. Silverman, A.P., Bu, W.M., Cohen, S.M. & Lippard, S.J. (2002). 2.4-A crystal structure of the asymmetric platinum complex {Pt(ammine) (cyclohexylamine)}(2+) bound to a dodecamer DNA complex. J.Biol.Chem. 277, 49743-49749.
144. Coste, F., Malinge, J.M., Serre, L., Shepard, W., Roth, M., Leng, M. & Zelwer, C. (1999). Crystal structure of a double-stranded DNA containing a cisplatin interstrand cross-link at 1.63 A resolution: Hydration at the platinated site. Nucleic Acids Res. 27, 1837-1846.
145. Kopka, M.L., Goodsell, D.S., Baikalov, I., Grzeskowiak, K., Cascio, D. & Dickerson, R.E. (1994). Crystal structure of a covalent DNA-drug adduct: Anthramycin bound to C-C-A-A-C-G-T-T-G-G and a molecular explanation of specificity. Biochemistry 33, 13593-13610.
146. Hermann, T. (2005). Drugs targeting the ribosome. Curr.Opin.Struct.Biol. 15, 355-366.
147. Brodersen, D.E., Clemons Jr., W.M., Carter, A.P., Morgan-Warren, R., Wimberly, B.T. & 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.
148. Carter, A.P., Clemons, W.M.J., Brodersen, D.E., Wimberly, B.T., Morgan-Warren, R. & Ramakrishnan, V. (2000). Functional insights from the structure of the 30S ribosomal subunit and its interactions with antibiotics. Nature 407, 340-348.
149. Fourmy, D., Recht, M.I., Blanchard, S.C. & Puglisi, J.D. (1996). Structure of the a Site of Escherichia Coli 16S Ribosomal RNA Complexed with an Aminoglycoside Antibiotic. Science 274, 1367-1371.
150. Vicens, Q. & Westhof, E. (2001). Crystal structure of paromomycin docked into the eubacterial ribosomal decoding A site. Structure 9, 647-658.
151. Harms, J.M., Bartels, H., Schlunzen, F. & Yonath, A. (2003). Antibiotics acting on the translational machinery. J.Cell.Sci. 116, 1391-1393.
152. Hansen, J.L., Ippolito, J.A., Ban, N., Nissen, P., Moore, P.B. & Steitz, T.A. (2002). The structures of four macrolide antibiotics bound to the large ribosomal subunit. Mol.Cell. 10, 117-128.
153. Schlunzen, F., Harms, J.M., Franceschi, F., Hansen, H.A., Bartels, H., Zarivach, R. & Yonath, A. (2003). Structural basis for the antibiotic activity of ketolides and azalides. Structure 11, 329-338.
154. 8K antibiotics bound to mutated large ribosomal subunits provide a structural explanation for resistance. Cell 121, 257-270.
155. Matthews, B.W. (1988). No code for recognition. Nature 335, 294-295.
156. Luscombe, N.M., Laskowski, R.A. & Thornton, J.M. (2001). Amino acid-base interactions: A three-dimensional analysis of protein-DNA interactions at an atomic level. Nucleic Acids Res. 29, 2860-2874.
157. Nadassy, K., Wodak, S.J. & Janin, J. (1999). Structural features of protein-nucleic acid recognition sites. Biochemistry 38, 1999-2017.
158. Jones, S., van Heyningen, P., Berman, H.M. & Thornton, J.M. (1999). Protein-DNA interactions: A structural analysis. J. Mol. Biol. 287, 877-896.
159. Schultz, S.C., Shields, G.C. & Steitz, T.A. (1991). Crystal structure of a CAP-DNA complex: The DNA is bent by 90°. Science 253, 1001-1007.
160. Kim, Y., Grable, J.C., Love, R., Greene, P.J. & Rosenberg, J.M. (1990). Refinement of Eco RI endonuclease crystal structure: A revised protein chain tracing. Science 249, 1307-1309.
161. Luger, K., Mader, A.W., Richmond, R.K., Sargent, D.F. & Richmond, T.J. (1997). Crystal structure of the nucleosome core particle at 2.8 A resolution. Nature 389, 251-260.
162. Hargreaves, D., Rice, D.W., Sedelnikova, S.E., Artymiuk, P.J., Lloyd, R.G. & Rafferty, J.B. (1998). Crystal structure of E.coli RuvA with bound DNA Holliday junction at 6 A resolution. Nat.Struct.Biol. 5, 441-446.
163. Harrison, S.C. (1991). A structural taxonomy of DNA-binding domains. Nature 353, 715-719.
164. Travers, A.A. (1992). DNA conformation and configuration in protein-DNA complexes. Curr.Opin.Struct.Biol. 2, 71-77.
165. Mo, Y., Vaessen, B., Johnston, K. & Marmorstein, R. (1998). Structures of SAP-1 bound to DNA targets from the E74 and c-fos promoters: Insights into DNA sequence discrimination by Ets proteins. Mol.Cell 2, 201-212.
166. Elrod-Erickson, M., Benson, T.E. & Pabo, C.O. (1998). High-resolution structures of variant Zif268-DNA complexes: Implications for understanding zinc finger-DNA recognition. Structure 6, 451-464.
167. Nair, S.K. & Burley, S.K. (2003). X-ray structures of Myc-Max and Mad-Max recognizing DNA. Molecular bases of regulation by proto-oncogenic transcription factors. Cell 112, 193-205.
168. Patikoglou, G.A., Kim, J.L., Sun, L., Yang, S.H., Kodadek, T. & Burley, S.K. (1999). TATA element recognition by the TATA box-binding protein has been conserved throughout evolution. Genes Dev. 13, 3217-3230.
169. Brennan, R.G. (1992). DNA Recognition by the Helix-Turn-Helix Motif. Curr.Opin.Struct.Biol. 2, 100-108.
170. Littlewood, T.D. & Evan, G.I. (1995). Transcription factors 2: Helix-loop-helix. Protein Profile 2, 621-702.
171. Anderson, W.F., Ohlendorf, D.H., Takeda, Y. & Matthews, B.W. (1981). Structure of the cro repressor from bacteriophage a; and its interaction with DNA. Nature 290, 754-758.
172. Cho, Y., Gorina, S., Jeffrey, P.D. & Pavletich, N.P. (1994). Crystal structure of a p53 tumor suppressor-DNA complex: Understanding tumorigenic mutations. Science 265, 346-355.
173. Schmiedeskamp, M. & Klevit, R.E. (1994). Zinc finger diversity. Curr.Opin.Struct.Biol. 4, 28-35.
174. Marmorstein, R., Carey, M., Ptashne, M. & Harrison, S.C. (1992). DNA recognition by GAL4: Structure of a protein-DNA complex. Nature 356, 408-414.
175. Pathak, D. & Sigler, P.B. (1992). Updating structure-function relationships in the bZip family of transcription factors. Curr.Opin.Struct. Biol. 2, 116-123.
176. Ellenberger, T.E., Brandl, C.J., Struhl, K. & Harrison, S.C. (1992). The GCN4 basic region leucine zipper binds DNA as a dimer of uninterrupted α helices-crystal structure of the protein-DNA complex. Cell 71, 1223-1237.
177. Phillips, S.E.V. (1994). The β-ribbon DNA recognition motif. Ann.Rev.Biophys. Biomol.Struct. 23, 671-701.
178. Somers, W.S. & Phillips, S.E.V. (1992). Crystal structure of the met repressor-operator complex at 2.8 Å resolution reveals DNA recognition by β-strands. Nature 359, 387-393.
179. Raumann, B.E., Rould, M.A., Pabo, C.O. & Sauer, R.T. (1994). DNA recognition by β-sheets in the arc repressor operator crystal structure. Nature 367, 754-757.
180. Jones, S., Daley, D.T.A., Luscombe, N.M., Berman, H.M. & Thornton, J.M. (2001). Protein-RNA interactions: A structural analysis. Nucleic Acids Res. 29, 934-954.
181. Draper, D. (1999). Themes in RNA-protein recognition. J.Mol.Biol. 293, 255-270.
182. Oubridge, C., Ito, H., Evans, P.R., Teo, C.H. & Nagai, K. (1994). Crystal structure at 1.92 Å resolution of the RNA-binding domain of the U1A spliceosomal protein complexed with an RNA hairpin. Nature 372, 432-438.
183. Schluenzen, F., Tocilj, A., Zarivach, R., Harms, J., Gluehmann, M., Janell, D., Bashan, A., Bartels, H., Agmon, I., Franceschi, F. & Yonath, A. (2000). Structure of functionally activated small ribosomal subunit at 3.3 A resolution. Cell 102, 615-623.
184. Wimberly, B.T., Brodersen, D.E., Clemons Jr., W.M., Morgan-Warren, R., Carter, A.P., Vonrhein, C., Hartsch, T. & Ramakrishnan, V. (2000). Structure of the 30S ribosomal subunit. Nature 407, 327-339.
185. Ban, N., Nissen, P., Hansen, J., Moore, P.B. & Steitz, T.A. (2000). The complete atomic structure of the large ribosomal subunit at 2.4 Å resolution. Science 289, 905-920.
186. Yusupova, G.Z., Yusupov, M.M., Cate, J.H.D. & Noller, H.F. (2001). The path of messenger RNA through the ribosome. Cell 106, 233-241.
187. Allen, F.H., Davies, J.E., Galloy, J.J., Johnson, O., Kennard, O., Macrae, C.F., Mitchell, E.M., Mitchell, G.F., Smith, J.M. & Watson, D.G. (1991). The development of versions 3 and 4 of the Cambridge Structural Database System. J.Chem.Inf.Comp.Sci. 31, 187-204.
188. Berman, H.M., Westbrook, J., Feng, Z., Gilliland, G., Bhat, T.N., Weissig, H., Shindyalov, I.N. & Bourne, P.E. (2000). The Protein Data Bank. Nucleic Acids Res. 28, 235-242.
189. Doreleijers, J.F., Mading, S., Maziuk, D., Sojourner, K., Yin, L., Zhu, J., Markley, J.L. & Ulrich, E.L. (2003). BioMagResBank database with sets of
190. Bourne, P., Berman, H.M., Watenpaugh, K., Westbrook, J.D. & Fitzgerald, P.M.D. (1997). The macromolecular Crystallographic Information File (mmCIF). Meth.Enzymol. 277, 571-590.
191. Rutgers University, New Brunswick, NJ. (1998). AutoDep Input Tool. Westbrook, J. NDB-406.
192. Rutgers University, New Brunswick, NJ. (1998). NUCheck. Feng, Z., Westbrook, J. & Berman, H.M. NDB-407.
193. Klosterman, P.S., Tamura, M., S.R., H. & Brenner, S.E. (2002). SCOR: A structural classification of RNA database. Nucleic Acids Res. 30, 392-394.