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Nucleic Acid Standards

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

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



  1. BD0001 [1.6Å 17.3%] 5'-d(ApCpCpGpApCpGpTpCpGpGpT)-3'
    H. Rozenberg, D. Rabinovich, F. Frolow, R.S. Hegde & Z. Shakked (1998) ``Structural Code for DNA Recognition Revealed in Crystal Structures of Papillomavirus E2-DNA Targets.'' Proc. Nat. Acad. Sci. USA., 95, 15194-15199.
  2. BD0005 [1.5Å 21.8%] 5'-d(CpGpCpGpApApTpTpCpGpCpG)-3'
    X. Shui, C. C. Sines, L. McFail-Isom, D. VanDerveer & L. D. Williams (1998) ``Structure of the Potassium Form of CGCGAATTCGCG: DNA Deformation by Electrostatic Collapse around Inorganic Cations.'' Biochemistry, 37, 16877-16887.
  3. BD0006 [1.15Å] 5'-d(GpGpCpCpApApTpTpGpG)-3'
    D. Vlieghe, J.P. Turkenburg & L. Van Meervelt (1999) ``B-DNA at Atomic Resolution Reveals Extended Hydration Patterns.'' Acta Crystallogr., Sect. D, 55, 1495-1502.
  4. BD0014 [1.45Å 21.72%] 5'-D(*CP*GP*CP*GP*AP*AP*TP*TP*CP*GP*CP*G)-3'
    J.Liu & J.A.Subirana (1999) ``Structure of d(CGCGAATTCGCG) in the Presence of Ca2+ Ions.'' J. Biol. Chem., 274, 24749-24752.
  5. BD0016 [0.9Å 14.5%] 5'-d(GpCpGpApApTpTpCpG)-3'
    M. Soler-Lopez, L. Malinina, J. Liu, T. Huynh-Dinh & J.A. Subirana (1999) ``Water and ions in a high resolution structure of B-DNA.'' J. Biol. Chem., 274, 23683-23686.
  6. BD0018 [1.3Å] 5'-d(GpCpGpApApTpTpCpGpCpG)-3'
    G. Minasov, V. Tereshko & M. Egli (1999) ``Atomic-resolution Crystal Structures of B-DNA Reveal Specific Influences of Divalent Metal Ions on Conformation and Packing.'' J. Mol. Biol.., 291, 83-99.
  7. BD0019 [1.7Å, 19.4%] 5'-d(GpGpCpGpApApTpTpCpGpCpG)-3'
    G. Minasov, V. Tereshko & M. Egli (1999) ``Atomic-resolution Crystal Structures of B-DNA Reveal Specific Influences of Divalent Metal Ions on Conformation and Packing.'' J. Mol. Biol.., 291, 83-99.
  8. BD0023 [0.7Å, 10.5%] 5'-d(CpCpApGpTpApCpTpGpG)-3'
    C. L. Kielkopf, S. Ding, P. Kuhn & D. C. Rees (2000) ``Conformational Flexibility of B-DNA at 0.74 A Resolution: d(CCAGTACTGG)2.'' J. Mol. Biol.., 296, 787-801.
  9. BD0029 [1.8Å, 20.9%] 5'-d(CpGpCpGpApApTpTpCpGpCpG)-3'
    K.K. Woods, L. McFail-Isom, C.C. Sines, S.B. Howerton, R.K. Stephens & L.D. Williams (to be published).
  10. BDJ017 [1.6Å 16.0%] 5'-D(*CP*CP*AP*GP*GP*CP*CP*TP*GP*G)-3'
    U. Heinemann & C. Alings (1989) ``Crystallographic Study of One Turn of G/C-Rich B-DNA.'' J. Mol. Biol., 210, 369-381.
  11. BDJ019 [1.4Å 16.0%] 5'-D(*CP*CP*AP*AP*CP*GP*TP*TP*GP*G)-3'
    G. G. Prive, K. Yanagi & R. E. Dickerson (1991) ``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-C-T-G-G.'' J. Mol. Biol., 217, 177-199.
  12. BDJ025 [1.5Å 16.1%] 5'-D(*CP*GP*AP*TP*CP*GP*AP*TP*CP*G)-3'
    K. Grzeskowiak, K. Yanagi, G. G. Prive & R. E. Dickerson (1991) ``The Structure of B-Helical C-G-A-T-C-G-A-T-C-G and Comparison with C-C-A-A-C-G-T-T-G-G. The Effect of Base Pair Reversals.'' J. Biol. Chem., 266, 8861-8883.
  13. BDJ031 [1.5Å 15.7%] 5'-D(*CP*GP*AP*TP*TP*AP*AP*TP*CP*G)-3'
    J. R. Quintana, K. Grzeskowiak, K. Yanagi & R. E. Dickerson (1992) ``The 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.
  14. BDJ036 [1.7Å 17.8%] 5'-D(*CP*GP*AP*TP*AP*TP*AP*TP*CP*G)-3', Calcium
    H. Yuan, J. Quintana & R. E. Dickerson (1992) ``Alternative Structures for Alternating Poly(dA-dT) Tracts: the Structure of the B-DNA Decamer C-G-A-T-A-T-A-T-C-G'' Biochemistry, 31, 8009-8021.
  15. BDJ037 [2.0Å 16.5%] 5'-D(*CP*GP*AP*TP*AP*TP*AP*TP*CP*G)-3', Magnesium
    H. Yuan, J. Quintana & R. E. Dickerson (1992) ``Alternative Structures for Alternating Poly(dA-dT) Tracts: the Structure of the B-DNA Decamer C-G-A-T-A-T-A-T-C-G.'' Biochemistry, 31, 8009-8021.
  16. BDJ051 [2.0Å 19.6%] 5'-D(*CP*AP*TP*GP*GP*CP*CP*AP*TP*G)-3'
    D. S. Goodsell, M. L. Kopka, D. Cascio & R. E. Dickerson (1993) ``Crystal Structure of CATGGCCATG and Its Implications for A-Tract Bending Models.'' Proc. Nat. Acad. Sci. USA, 90, 2930-2934.
  17. BDJ052 [1.9Å 17.9%] 5'-D(*CP*CP*AP*AP*GP*CP*TP*TP*GP*G)-3', Calcium
    K. Grzeskowiak, D. S. Goodsell, M. Kaczor-Grzeskowiak, D. Cascio & R. E. Dickerson (1993) ``Crystallographic Analysis of C-C-A-A-G-C-T-T-G-G and Its Implications for Bending in B-DNA.'' Biochemistry, 32, 8923-8931.
  18. BDJ060 [1.7Å 20.0%] 5'-D(*CP*TP*CP*TP*CP*GP*AP*GP*AP*G)-3'
    D. S. Goodsell, K. Grzeskowiak & R. E. Dickerson (1995) ``Crystal Structure of C-T-C-T-C-G-A-G-A-G: Implications for the Structure of the Holliday Junction.'' Biochemistry, 34, 1022-1029.
  19. BDJ061 [1.9Å 17.0%] 5'-D(*CP*CP*AP*CP*TP*AP*GP*TP*GP*G)-3'
    Z. Shakked, G. Guzikevich-Guerstein, F. Frolow, D. Rabbinovich, A. Joachimiak & P. B. Sigler (1994) ``Determinants of Repressor/Operator Recognition from the Structure of the Trp Operator Binding Site.'' Nature, 368, 469-473.
  20. BDJ081 [1.8Å 23.3%] 5'-D(*CP*AP*AP*AP*GP*AP*AP*AP*AP*G)-3'
    G. W. Han, M. L. Kopka, D. Cascio, K. Grzeskowiak &, R. E. Dickerson (1997) ``Structure of a DNA Analog of the Primer for HIV-1 RT Second Strand Synthesis.'' J. Mol. Biol., 269, 811-826.
  21. BDL001 [1.9Å 17.8%] 5'-D(*CP*GP*CP*GP*AP*AP*TP*TP*CP*GP*CP*G)-3', 290 K
    H. R. Drew, R. M. Wing, T. Takano, C. Broka, S. Tanaka, K. Itakura & R. E. Dickerson (1981) ``Structure of a B-DNA Dodecamer. Conformation and Dynamics.'' Proc. Nat. Acad. Sci. USA, 78, 2179-2183.
  22. BDL005 [1.9Å 14.9%] 5'-D(*CP*GP*CP*GP*AP*AP*TP*TP*CP*GP*CP*G)-3', 290 K, Using Anisotropic Thermal Motion Model
    S. R. Holbrook, R. E. Dickerson & S. -H. Kim (1985) ``Anisotropic Thermal-Parameter Refinement of the DNA Dodecamer CGCGAATTCGCG by the Segmented Rigid-Body Method.'' Acta Crystallogr., Sect. B, 41, 255-262.
  23. BDL020 [1.9Å 18.8%] 5'-D(*CP*GP*CP*GP*AP*AP*TP*TP*CP*GP*CP*G)-3', Re-Refinement
    E. Westhof (1987) ``Re-Refinement of the B-Dodecamer d(CGCGAATTCGCG) with a Comparative Analysis of the Solvent in It and in the Z-Hexamer d(5BrCG5BrCG5BrCG).'' J. Biomol. Struct. Dyn., 5, 581-600.
  24. BDL084 [1.4Å 19.7%] 5'-D(*CP*GP*CP*GP*AP*AP*TP*TP*CP*GP*CP*G)-3'
    X. Shui, L. McFail-Isom, G. G. Hu & L. D. Williams (1998) ``The B-DNA Dodecamer at High Resolution Reveals a Spine of Water on Sodium.'' Biochemistry, 37, 8341-8355.