A Standard Reference Frame for the Description
of Nucleic Acid Base-pair Geometry
Supplementary Material

References of High Resolution A-DNA structures surveyed in this study

1. ADO002 [1.9Å] 5'-D(*GP*GP*GP*GP*CP*GP*CP*CP*CP*C)-3'
   G.Savitha & M. A. Viswamitra (1999) ``A-DNA Decamer with Two Independent Duplexes in the Asymmetric Unit.'' Acta Crystallogr., Sect. D, 55, 1136-1143.

2. ADO003 [1.1Å, 21.4%] 5'-d(ApGpGpGpGpCpCpCpCpT)-3'
   Y. -G. Gao, H. H. Robinson & A. H. -J. Wang (1999) ``High-resolution A-DNA Crystal Structures of d(AGGGGCCCCT): An A-DNA Model of poly(dG)·poly(dC).'' Eur. J. Biochem., 261, 413-420.

3. ADO004 [1.5Å, 23.6 %] 5'-d(ApGpGpGpGpCpCpCpCpT)-3'
   Y. -G. Gao, H. H. Robinson & A. H. -J. Wang (1999) ``High-resolution A-DNA Crystal Structures of d(AGGGGCCCCT): An A-DNA Model of poly(dG)·poly(dC).'' Eur. J. Biochem., 261, 413-420.

4. ADH008 [1.8Å, 17.1%] 5'-D(*GP*CP*CP*CP*GP*GP*GP*C)-3'
   U. Heinemann, H. Lauble, R. Frank & H. Bloecker (1987) ``Crystal Structure Analysis of an A-DNA Fragment at 1.8 Ångstroms Resolution: d(GCCCGGGC).'' Nucleic Acids Res., 15, 9531-9550.

5. ADH010 [1.8Å, 19.8%] 5'-D(*GP*GP*TP*AP*TP*AP*CP*C)-3'
   Z. Shakked, D. Rabinovich, O. Kennard, W. B. T. Cruse, S. A. Salisbury & M. A. Viswamitra (1983) ``Sequence-Dependent Conformation of an A-DNA Double Helix. The Crystal Structure of the Octamer d(G-G-T-A-T-A-C-C).'' J. Mol. Biol., 166, 183-201.

6. ADH0102 [1.6Å, 16.9%] 5'-D(P*CP*CP*CP*GP*CP*GP*GP*G)-3'
   L. G. Fernandez, J. A. Subirana, N. Verdaguer, D. Pyshnyi, L. Campos & L. Malinina (1997) ``Structural Variability of A-DNA in Crystals of the Octamer d(pCpCpCpGpCpGpGpG).'' J. Biomol. Struct. Dyn., 15, 151-163.

7. ADH0103 [1.9Å, 17.2%] 5'-D(P*CP*CP*CP*GP*CP*GP*GP*G)-3'
   L. G. Fernandez, J. A. Subirana, N. Verdaguer, D. Pyshnyi, L. Campos & L. Malinina (1997) ``Structural Variability of A-DNA in Crystals of the Octamer d(pCpCpCpGpCpGpGpG).'' J. Biomol. Struct. Dyn., 15, 151-163.

8. ADH0104 [1.6Å, 18.1%] 5'-D(P*CP*CP*CP*GP*CP*GP*GP*G)-3'
   L. G. Fernandez, J. A. Subirana, N. Verdaguer, D. Pyshnyi, L. Campos & L. Malinina (1997) ``Structural Variability of A-DNA in Crystals of the Octamer d(pCpCpCpGpCpGpGpG).'' J. Biomol. Struct. Dyn., 15, 151-163.

9. ADH0105 [1.9Å, 19.0%] 5'-D(P*CP*CP*CP*GP*CP*GP*GP*G)-3'
   L. G. Fernandez, J. A. Subirana, N. Verdaguer, D. Pyshnyi, L. Campos & L. Malinina (1997) ``Structural Variability of A-DNA in Crystals of the Octamer d(pCpCpCpGpCpGpGpG).'' J. Biomol. Struct. Dyn., 15, 151-163.

10. ADH014 [2.0Å, 11.5%] 5'-D(*GP*TP*GP*TP*AP*CP*AP*C)-3', Spermine
    S. C. Jain, G. Zon & M. Sundaralingam (1989) ``Base Only Binding of Spermine in the Deep Groove of the A-DNA Octamer d(GTGTACAC).'' Biochemistry, 28, 2360-2364.

11. ADH026 [1.7Å, 16.2%] 5'-D(*GP*GP*GP*CP*GP*CP*CP*C)-3', Tetragonal, 293K
    D. Rabinovich, T. Haran, M. Eisenstein & Z. Shakked (1988) ``Structures of the Mismatched Duplex d(GGGTGCCC) and One of Its Watson-Crick Analogues d(GGGCGCCC).'' J. Mol. Biol., 200, 151-161.

12. ADH027 [2.0Å, 21.0%] 5'-D(*GP*GP*GP*CP*GP*CP*CP*C)-3', Tetragonal, 115K
    M. Eisenstein, H. Hope, T. E. Haran, F. Frolow, Z. Shakked & D. Rabinovich (1988) ``Low-Temperature Study of the A-DNA Fragment d(GGGCGCCC).'' Acta Crystallogr., Sect. B, 44, 625-628.

13. ADH029 [1.9Å, 16.0%] 5'-D(*GP*GP*GP*CP*GP*CP*CP*C)-3', Hexagonal, 100K
    Z. Shakked, G. Guerstein-Guzikevich, M. Eisenstein, F. Frolow & D. Rabinovich (1989) ``The Conformation of the DNA Double Helix in the Crystal Is Dependent on Its Environment.'' Nature, 342, 456-460.

14. ADH033 [1.5Å, 17.7%] 5'-D(*AP*TP*GP*CP*GP*CP*AP*T)-3', W/O Spermine
    G. R. Clark, D. G. Brown, M. R. Sanderson, T. Chwalinski, S. Neidle, J. M. Veal, R. L. Jones, W. D. Wilson, G. Zon, E. Garman & D. I. Stuart (1990) ``Crystal and Solution Structures of the Oligonucleotide d(ATGCGCAT)2: A Combined X-Ray and NMR Study.'' Nucleic Acids Res., 18, 5521-5528.

15. ADH034 [2.0Å, 12.7%] 5'-D(*GP*TP*GP*TP*AP*CP*AP*C)-3', Hexagonal
    S. C. Jain, G. Zon & M. Sundaralingam (1991) ``The Hexagonal Crystal Structure of the A-DNA Octamer d(GTGTACAC) and Its Comparison with the Tetragonal Structure Correlated Variations in Helical Parameters.'' Biochemistry, 30, 3567-3576.

16. ADH038 [1.4Å, 19.8%] 5'-D(*GP*TP*GP*TP*AP*CP*AP*C)-3', Spermine
    N. Thota, X. H. Li, C. Bingman & M. Sundaralingam (1993) ``High Resolution Refinement of the Hexagonal A-DNA Octamer d(GTGTACAC) at 1.4 Ångstroms Resolution.'' Acta Crystallogr., Sect. D, 49, 282-291.

17. ADH039 [1.4Å, 19.1%] 5'-D(*GP*TP*GP*TP*AP*CP*AP*C)-3', Spermidine
    N. Thota, X. H. Li, C. Bingman & M. Sundaralingam (1993) ``High Resolution Refinement of the Hexagonal A-DNA Octamer d(GTGTACAC) at 1.4 Ångstroms Resolution.'' Acta Crystallogr., Sect. D, 49, 282-291.

18. ADH047 [1.6Å, 15.4%] 5'-D(*GP*TP*GP*CP*GP*CP*AP*C)-3'
    C. Bingman, X. Li, G. Zon & M. Sundaralingam (1992) ``Crystal and Molecular Structure of d(GTGCGCAC): Investigation of the Effects of Base Sequence on the Conformation of Octamer Duplexes.'' Biochemistry, 31, 12803-12812.

19. ADH070 [1.9Å, 17.7%] 5'-D(*AP*CP*GP*TP*AP*CP*GP*T)-3'
    D. J. Wilcock, A. Adams, C. J. Cardin & L. P. G. Wakelin (1996) ``Structure of the DNA Octanucleotide d(ACGTACGT)2.'' Acta Crystallogr., Sect. D, 52, 481-485.

20. ADH078 [1.9Å, 16.4%] 5'-D(*CP*CP*CP*TP*AP*GP*GP*G)-3'
    D. B. Tippin & M. Sundaralingam (1996) ``Structure of d(CCTAGGG): Comparison with Nine Isomorphous Octamer Sequences Reveals Four Distinct Patterns of Sequence-Dependent Intermolecular Interactions.'' Acta Crystallogr., Sect. D, 52, 997-1003.

21. ADJ0102 [1.7Å, 19.0%] 5'-D(*GP*AP*CP*CP*GP*CP*GP*GP*TP*C)-3', Low Salt
    J.B. Finley & M. Luo (1998) ``X-ray Crystal Structures of Half the Human Papilloma Virus E2 Binding Site: d(GACCGCGGTC).'' Nucleic Acids Res., 26, 5719-5727.

22. ADJ0103 [1.9Å, 19.9%] 5'-D(*GP*AP*CP*CP*GP*CP*GP*GP*TP*C)-3', High Salt
    J.B. Finley & M. Luo (1998) ``X-ray Crystal Structures of Half the Human Papilloma Virus E2 Binding Site: d(GACCGCGGTC).'' Nucleic Acids Res., 26, 5719-5727.

23. ADJ0112 [1.9Å, 19.5%] 5'-D(*GP*TP*AP*CP*GP*CP*GP*TP*AP*C)-3'
    C. Ban, B. Ramakrishnan & M. Sundaralingam ``Crystal Structures of Two Isomorphous A-DNA Decamers d(GTACGCGTAC) and d(GGCCGCGGCC).'' To be Published.

24. ADJ0113 [1.8Å, 18.9%] 5'-D(*GP*GP*CP*CP*GP*CP*GP*GP*CP*C)-3'
    C. Ban, B. Ramakrishnan & M. Sundaralingam ``Crystal Structures of Two Isomorphous A-DNA Decamers d(GTACGCGTAC) and d(GGCCGCGGCC).'' To be Published.

25. ADJ022 [2.0Å, 18.0%] 5'-D(*AP*CP*CP*GP*GP*CP*CP*GP*GP*T)-3'
    C. A. Frederick, G. J. Quigley, M. -K. Teng, M. Coll, G. A. Van Der Marel, J. H. Van Boom, A. Rich & A. H. -J. Wang (1989) ``Molecular Structure of an A-DNA Decamer d(ACCGGCCGGT).'' Eur. J. Biochem., 181, 295-307.

26. ADJ049 [1.6Å, 18.5%] 5'-D(*CP*CP*CP*GP*GP*CP*CP*GP*GP*G)-3'
    B. Ramakrishnan & M. Sundaralingam (1993) ``High Resolution Crystal Structure of the A-DNA Decamer d(CCCGGCCGGG): Novel Intermolecular Base-Paired G*(G·C) Triplets.'' J. Mol. Biol., 231, 431-444.

27. ADJ050 [1.7Å, 18.5%] 5'-D(*GP*CP*GP*GP*GP*CP*CP*CP*GP*C)-3', Orthorhombic
    B. Ramakrishnan & M. Sundaralingam (1993) ``Evidence for Crystal Environment Dominating Base Sequence Effects on DNA Conformation: Crystal Structures of the Orthorhombic and Hexagonal Polymorphs of the A-DNA Decamer d(GCGGGCCCGC) and Comparison with Their Isomorphous Crystal Structures.'' Biochemistry, 32, 11458-11468.

28. ADJ051 [1.8Å, 18.3%] 5'-D(*GP*CP*GP*GP*GP*CP*CP*CP*GP*C)-3', Hexagonal
    B. Ramakrishnan & M. Sundaralingam (1993)``Evidence for Crystal Environment Dominating Base Sequence Effects on DNA Conformation: Crystal Structures of the Orthorhombic and Hexagonal Polymorphs of the A-DNA Decamer d(GCGGGCCCGC) and Comparison with Their Isomorphous Crystal Structures.'' Biochemistry, 32, 11458-11468.

29. ADJ065 [1.9Å, 19.4%] 5'-D(*AP*CP*CP*GP*GP*CP*CP*GP*GP*T)-3', [CO(NH3)6]3+
    Y. -G. Gao, H. Robinson, J. H. Van Boom & A. H. -J. Wang (1995) ``Influence of Counter-Ions on the Crystal Structures of DNA Decamers: Binding of [Co(NH3)6]3+ and Ba2+ to A-DNA.'' Biophys. J., 69, 559-568.

30. ADJ066 [2.0Å, 20.6%] 5'-D(*AP*CP*CP*CP*GP*CP*GP*GP*GP*T)-3', BA2+
    Y. -G. Gao, H. Robinson, J. H. Van Boom & A. H. -J. Wang (1995) ``Influence of Counter-Ions on the Crystal Structures of DNA Decamers: Binding of [Co(NH3)6]3+ and Ba2+ to A-DNA.'' Biophys. J., 69, 559-568.

31. ADJ067 [1.9Å, 20.0%] 5'-D(*AP*CP*CP*GP*GP*CP*CP*GP*GP*T)-3'
    Y. -G. Gao, H. Robinson, J. H. Van Boom & A. H. -J. Wang (1995) ``Influence of Counter-Ions on the Crystal Structures of DNA Decamers: Binding of [Co(NH3)6]3+ and Ba2+ to A-DNA.'' Biophys. J., 69, 559-568.

32. ADJ075 [1.9Å, 18.6%] 5'-D(*GP*CP*AP*CP*GP*CP*GP*TP*GP*C)-3'
    C. Ban, & M. Sundaralingam (1996) ``Crystal Structure of the Self-Complementary 5'-Purine Start Decamer d(GCACGCGTGC) in the A-DNA Conformation-Part II.'' Biophys. J., 71, 1222-1227.

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Last modified: Fri Apr 7 18:56:26 2000