CITATIONS FOR PLAIN B-DNA'S ---------------------------------------------------------------------- NDB ID Citation ---------------------------------------------------------------------- 1S88 C.B.Nielsen, M.Petersen, E.B.Pedersen, P.E.Hansen, U.B.Christensen NMR structure determination of a modified DNA oligonucleotide containing a new intercalating nucleic acid. Bioconjug.Chem., 15, 260-269, 2004. 1SP6 I.Gomez-Pinto, E.Cubero, S.G.Kalko, V.Monaco, G.Van Der Marel, J.H.Van Boom, M.Orozco, C.Gonzalez Effect of bulky lesions on DNA: Solution structure of a DNA duplex containing a cholesterol adduct. To be published, n.a., n.a.-n.a., n.a.. 1SSJ I.Gomez-Pinto, E.Cubero, S.G.Kalko, V.Monaco, G.Van Der Marel, J.H.Van Boom, M.Orozco, C.Gonzalez Effect of bulky lesions on DNA: Solution structure of a DNA duplex containing a cholesterol adduct. To be published, n.a., n.a.-n.a., n.a.. BD0001 H.Rozenberg, D.Rabinovich, F.Frolow, R.S.Hegde, Z.Shakked Structural code for DNA recognition revealed in crystal structures of papillomavirus E2-DNA targets Proc.Nat.Acad.Sci.USA, 95, 15194-15199, 1998. BD0002 H.Rozenberg, D.Rabinovich, F.Frolow, R.S.Hegde, Z.Shakked Structural code for DNA recognition revealed in crystal structures of papillomavirus E2-DNA targets Proc.Nat.Acad.Sci.USA, 95, 15194-15199, 1998. BD0003 H.Rozenberg, D.Rabinovich, F.Frolow, R.S.Hegde, Z.Shakked Structural code for DNA recognition revealed in crystal structures of papillomavirus E2-DNA targets Proc.Nat.Acad.Sci.USA, 95, 15194-15199, 1998. BD0004 J.Liu, L.Malinina, T.Huynh-Dinh, J.A.Subirana The structure of the most studied DNA fragment changes under the influence of ions: A new packing of d(CGCGAATTCGCG) FEBS Lett., 438, 211-214, 1998. ---------------------------------------------------------------------- Page 1 created by the NDB Project on Wed May 26 14:26:20 2004 CITATIONS FOR PLAIN B-DNA'S ---------------------------------------------------------------------- NDB ID Citation ---------------------------------------------------------------------- BD0005 X.Shui, C. C.Sines, L.McFail-Isom, D.VanDerveer, L. D.Williams Structure of the Potassium Form of CGCGAATTCGCG: DNA Deformation by Electrostatic Collapse around Inorganic Cations Biochemistry, 37, 16877-16887, 1998. BD0007 V.Tereshko, G.Minasov, M.Egli The Dickerson-Drew B-DNA Dodecamer Revisited-At Atomic Resolution J.Am.Chem.Soc., 121, 470-471, 1999. BD0012 V.Tereshko, G.Minasov, M.Egli A "Hydrat-Ion Spine" in a B-DNA minor groove J.Am.Chem.Soc., 121, 3590-3595, 1999. BD0013 V.Tereshko, G.Minasov, M.Egli A "Hydrat-Ion Spine" in a B-DNA minor groove J.Am.Chem.Soc., 121, 3590-3595, 1999. BD0015 Y.Timsit, D.Moras DNA self-fitting: the double helix directs the geometry of its supramolecular assembly Embo J., 13, 2737-2746, 1994. BD0023 C. L.Kielkopf, S.Ding, P.Kuhn, D. C.Rees Conformational Flexibility of B-DNA at 0.74 A Resolution: d(CCAGTACTGG)2 J.Mol.Biol., 296, 787-801, 2000. BD0026 H.L.Ng, M.L.Kopka, R.E.Dickerson The structure of a stable intermediate in the A-B DNA helix transition Proc.Nat.Acad.Sci.USA, 97, 2035-2039, 2000. ---------------------------------------------------------------------- Page 2 created by the NDB Project on Wed May 26 14:26:20 2004 CITATIONS FOR PLAIN B-DNA'S ---------------------------------------------------------------------- NDB ID Citation ---------------------------------------------------------------------- BD0028 B.F.Eichman, J.M.Vargason, B.H.M.Mooers, P.S.Ho The Holliday Junction in an Inverted Repeat DNA Sequence: Sequence Effects on the Structure of Four-Way Junctions Proc.Nat.Acad.Sci.USA, 97, 3971-3976, 2000. BD0029 K.K.Woods, L.McFail-Isom, C.C.Sines, S.B.Howerton, R.K.Stephens, L.D.Williams Monovalent Cations Sequester within the A-Tract Minor Groove of [d(CGCGAATTCGCG)]2 J.Am.Chem.Soc., 122, 1546-1547, 2000. BD0030 M.Egli, V.Tereshko, M.Teplova, G.Minasov, A.Joachimiak, R.Sanishvili, C.M.Weeks, R.Miller, M.A.Maier, H.An, P.Dan Cook, M.Manoharan X-Ray Crystallographic Analysis of the Hydration of A-and B- Form DNA at Atomic resolution Biopolymers, 48, 234-252, 1998. BD0033 T.K.Chiu, R.E.Dickerson 1 A crystal structures of B-DNA reveal sequence-specific binding and groove-specific bending of DNA by magnesium and calcium J.Mol.Biol., 301, 915-945, 2000. BD0034 T.K.Chiu, R.E.Dickerson 1 A crystal structures of B-DNA reveal sequence-specific binding and groove-specific bending of DNA by magnesium and calcium J.Mol.Biol., 301, 915-945, 2000. BD0035 T.K.Chiu, R.E.Dickerson 1 A crystal structures of B-DNA reveal sequence-specific binding and groove-specific bending of DNA by magnesium and calcium J.Mol.Biol., 301, 915-945, 2000. BD0036 T.K.Chiu, R.E.Dickerson 1 A crystal structures of B-DNA reveal sequence-specific binding and groove-specific bending of DNA by magnesium and calcium J.Mol.Biol., 301, 915-945, 2000. ---------------------------------------------------------------------- Page 3 created by the NDB Project on Wed May 26 14:26:20 2004 CITATIONS FOR PLAIN B-DNA'S ---------------------------------------------------------------------- NDB ID Citation ---------------------------------------------------------------------- BD0038 G.Minasov, M.Teplova, P.Nielsen, J.Wengel, M.Egli Structural Basis of Cleavage by RNase H of Hybrids of Arabinonucleic Acids and RNA Biochemistry, 39, 3525-3532, 2000. BD0039 J.M.Vargason, B.F.Eichman, P.S.Ho The extended and eccentric E-DNA structure induced by cytosine methylation or bromination Nat.Struct.Biol., 7, 758-761, 2000. BD0040 J.M.Vargason, B.F.Eichman, P.S.Ho The extended and eccentric E-DNA structure induced by cytosine methylation or bromination Nat.Struct.Biol., 7, 758-761, 2000. BD0041 C.C.Sines, L.McFail-Isom, S.B.Howerton, D.VanDerveer, L.D.Williams Cations Mediate B-DNA Conformational Heterogeneity J.Am.Chem.Soc., 122, 11048-11056, 2000. BD0047 S.Chen, H.M.Berman Crystallographic Structure of a DNA Dodecamer d- (GCAAACGTTTGC)2 To be Published, n.a., n.a.-n.a., n.a.. BD0050 J.M.Vargason, K.Henderson, P.S.Ho A Crystallographic Map of the Transition from B-DNA to A-DNA Proc.Nat.Acad.Sci.USA, 98, 7265-7270, 2001. BD0051 D.R.Mack, T.K.Chiu, R.E.Dickerson Intrinsic Bending and Deformability at the T-A step of CCTTTAAAGG: A Comparative Analysis of T-A and A-T steps within A-tracts J.Mol.Biol., 312, 1037-1049, 2001. ---------------------------------------------------------------------- Page 4 created by the NDB Project on Wed May 26 14:26:20 2004 CITATIONS FOR PLAIN B-DNA'S ---------------------------------------------------------------------- NDB ID Citation ---------------------------------------------------------------------- BD0052 J.Hizver, H.Rozenberg, F.Frolow, D.Rabinovich, Z.Shakked DNA Bending by an Adenine-Thymine Tract and Its Role in Gene Regulation. Proc.Nat.Acad.Sci.USA, 98, 8490-8495, 2001. BD0054 S.B.Howerton, C.C.Sines, D.VanDerveer, L.D.Williams Locating Monovalent Cations in the Grooves of B-DNA Biochemistry, 40, 10023-10031, 2001. BD0055 A.A.Lipanov, M.L.Kopka, M.Kaczor-Grzeskowiak, R.E.Dickerson The Structure of a /B-DNA Decamer with an I(Slash)A Mismatch and Comparison with the G(Slash)A Mismatch To be Published, n.a., n.a.-n.a., n.a.. BD0057 A.K.Todd, S.Neidle Crystal Structure of a Non-Self Complementary DNA Dodecamer Containing an A/T Tract: Analysis of the Effect of Crystal Environment on Local Helical Parameters To be Published, n.a., n.a.-n.a., n.a.. BD0059 H.Park, K.Zhang, Y.Ren, S.Nadji, N.Sinha, J.-S.Taylor, C.Kang Crystal Structure of a DNA Decamer Containing a cis-syn Thymine-dimer Proc.Nat.Acad.Sci.USA, 99, 15965-15970, 2002. BD0060 C.J.Wilds, Z.Wawrzak, R.Krishnamurthy, A.Eschenmoser, M.Egli Crystal Structure of a B-Form DNA Duplex Containing (L)- alpha-Threofuranosyl (3'-->2') Nucleosides: A Four-Carbon Sugar Is Easily Accommodated into the Backbone of DNA J.Am.Chem.Soc., 124, 13716-13721, 2002. BD0062 K.K.Woods, T.Lan, L.W.McLaughlin, L.D.Williams The Role of Minor Groove Functional Groups in DNA Hydration Nucleic Acids Res., 31, 1536-1540, 2003. ---------------------------------------------------------------------- Page 5 created by the NDB Project on Wed May 26 14:26:20 2004 CITATIONS FOR PLAIN B-DNA'S ---------------------------------------------------------------------- NDB ID Citation ---------------------------------------------------------------------- BD0063 S.L.Labiuk, L.T.Delbaere, J.S.Lee Cobalt(II), nickel(II) and zinc(II) do not bind to intra- helical N(7) guanine positions in the B-form crystal structure of d(GGCGCC) J.Biol.Inorg.Chem., 8, 715-720, 2003. BD0064 S.L.Labiuk, L.T.Delbaere, J.S.Lee Cobalt(II), nickel(II) and zinc(II) do not bind to intra- helical N(7) guanine positions in the B-form crystal structure of d(GGCGCC) J.Biol.Inorg.Chem., 8, 715-720, 2003. BD0065 S.L.Labiuk, L.T.Delbaere, J.S.Lee Cobalt(II), nickel(II) and zinc(II) do not bind to intra- helical N(7) guanine positions in the B-form crystal structure of d(GGCGCC) J.Biol.Inorg.Chem., 8, 715-720, 2003. BD0066 N.Valls, G.Wright, R.A.Steiner, G.N.Murshudov, J.A.Subirana DNA variability in five crystal structures of d(CGCAATTGCG). Acta Crystallogr., Sect.D, 60, 680-685, 2004. BD0067 K.K.Woods, S.B.Howerton, S.Tannenbaum, L.D.Williams A High Resolution Crystal Structure of [d(CGCAAATTTGCG)]2 TO BE PUBLISHED, n.a., n.a.-n.a., n.a.. BD0072 K.Kimura, A.Ono, K.Watanabe, A.Takenaka X-Ray analyses of oligonucleotides of containing 5- formylcytosine, suggesting a structural reason for codon- anticodon recognition of mitochondrial tRNA-Met To be Published, n.a., n.a.-n.a., n.a.. BDH071 L.Urpi, V.Tereshko, L.Malinina, T.Huynh-Dinh, J.A.Subirana Structural Comparison Between the d(CTAG) Sequence in Oligonucleotides and Trp and Met Repressor-Operator Complexes Nat.Struct.Biol., 3, 325-328, 1996. ---------------------------------------------------------------------- Page 6 created by the NDB Project on Wed May 26 14:26:20 2004 CITATIONS FOR PLAIN B-DNA'S ---------------------------------------------------------------------- NDB ID Citation ---------------------------------------------------------------------- BDJ017 U.Heinemann, C.Alings Crystallographic Study of One Turn of G/C-Rich B-DNA J.Mol.Biol., 210, 369-381, 1989. BDJ019 G.G.Prive, K.Yanagi, R.E.Dickerson 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, 1991. BDJ025 K.Grzeskowiak, K.Yanagi, G.G.Prive, R.E.Dickerson 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, 1991. BDJ031 J.R.Quintana, K.Grzeskowiak, K.Yanagi, R.E.Dickerson 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, 1992. BDJ036 H.Yuan, J.Quintana, R.E.Dickerson 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, 1992. BDJ037 H.Yuan, J.Quintana, R.E.Dickerson 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, 1992. BDJ039 U.Heinemann, C.Alings, M.Bansal Double Helix Conformation Groove Dimensions and Ligand Binding Potential of a G/C-Stretch in B-DNA Embo J., 11, 1931-1939, 1992. ---------------------------------------------------------------------- Page 7 created by the NDB Project on Wed May 26 14:26:20 2004 CITATIONS FOR PLAIN B-DNA'S ---------------------------------------------------------------------- NDB ID Citation ---------------------------------------------------------------------- BDJ051 D.S.Goodsell, M.L.Kopka, D.Cascio, R.E.Dickerson Crystal Structure of CATGGCCATG and Its Implications for A- Tract Bending Models Proc.Nat.Acad.Sci.USA, 90, 2930-2934, 1993. BDJ052 K.Grzeskowiak, D.S.Goodsell, M.Kaczor-Grzeskowiak, D.Cascio, R.E.Dickerson 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, 1993. BDJ055 D.S.Goodsell, M.Kaczor-Grzeskowiak, R.E.Dickerson The Crystal Structure of C-C-A-T-T-A-A-T-G-G: Implications for Bending of B-DNA at T-A Steps J.Mol.Biol., 239, 79-96, 1994. BDJ060 D.S.Goodsell, K.Grzeskowiak, R.E.Dickerson 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, 1995. BDJ061 Z.Shakked, G.Guzikevich-Guerstein, F.Frolow, D.Rabbinovich, A.Joachimiak, P.B.Sigler Determinants of Repressor/Operator Recognition from the Structure of the Trp Operator Binding Site Nature, 368, 469-473, 1994. BDJ069 A.A.Wood, C.M.Nunn, J.O.Trent, S.Neidle Sequence-Dependent Crossed Helix Packing in the Crystal Structure of the B-DNA Decamer Yields a Detailed Model for the Holliday Junction J.Mol.Biol., 269, 827-841, 1997. BDJ081 G.W.Han, M.L.Kopka, D.Cascio, K.Grzeskowiak, R.E.Dickerson Structure of a DNA Analog of the Primer for HIV-1 RT Second Strand Synthesis J.Mol.Biol., 269, 811-826, 1997. ---------------------------------------------------------------------- Page 8 created by the NDB Project on Wed May 26 14:26:20 2004 CITATIONS FOR PLAIN B-DNA'S ---------------------------------------------------------------------- NDB ID Citation ---------------------------------------------------------------------- BDL001 H.R.Drew, R.M.Wing, T.Takano, C.Broka, S.Tanaka, K.Itakura, R.E.Dickerson Structure of a B-DNA Dodecamer. Conformation and Dynamics Proc.Nat.Acad.Sci.USA, 78, 2179-2183, 1981. BDL002 H.R.Drew, S.Samson, R.E.Dickerson Structure of a B-DNA Dodecamer at 16 Kelvin Proc.Nat.Acad.Sci.USA, 79, 4040-4044, 1982. BDL005 S.R.Holbrook, R.E.Dickerson, S.-H.Kim Anisotropic Thermal-Parameter Refinement of the DNA Dodecamer CGCGAATTCGCG by the Segmented Rigid-Body Method Acta Crystallogr.,Sect.B, 41, 255-262, 1985. BDL006 H.C.M.Nelson, J.T.Finch, B.F.Luisi, A.Klug The Structure of an Oligo(dA).Oligo(dT) Tract and Its Biological Implications Nature, 330, 221-226, 1987. BDL007 C.Yoon, G.G.Prive, D.S.Goodsell, R.E.Dickerson Structure of an Alternating-B DNA Helix and Its Relationship to A-Tract DNA Proc.Nat.Acad.Sci.USA, 85, 6332-6336, 1988. BDL015 A.D.DiGabriele, M.R.Sanderson, T.A.Steitz Crystal Lattice Packing Is Important in Determining the Bend of a DNA Dodecamer Containing an Adenine Tract Proc.Nat.Acad.Sci.USA, 86, 1816-1820, 1989. BDL016 M.Coll, C.A.Frederick, A.H.-J.Wang, A.Rich A Bifurcated Hydrogen-Bonded Conformation in the d(A.T) Base Pairs of the DNA Dodecamer d(CGCAAATTTGCG) and Its Complex with Distamycin Proc.Nat.Acad.Sci.USA, 84, 8385-8389, 1987. ---------------------------------------------------------------------- Page 9 created by the NDB Project on Wed May 26 14:26:20 2004 CITATIONS FOR PLAIN B-DNA'S ---------------------------------------------------------------------- NDB ID Citation ---------------------------------------------------------------------- BDL018 Y.Timsit, E.Westhof, R.P.P.Fuchs, D.Moras Unusual Helical Packing in Crystals of DNA Bearing A Mutation Hot Spot Nature, 341, 459-462, 1989. BDL020 E.Westhof 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, 1987. BDL028 N.Narayana, S.L.Ginell, I.M.Russu, H.M.Berman Crystal and Molecular Structure of a DNA Fragment: d(CGTGAATTCACG) Biochemistry, 30, 4449-4455, 1991. BDL029 T.A.Larsen, M.L.Kopka, R.E.Dickerson Crystal Structure Analysis of the B-DNA Dodecamer CGTGAATTCACG Biochemistry, 30, 4443-4449, 1991. BDL035 Y.Timsit, E.Vilbois, D.Moras Base-Pairing Shift in the Major Groove of (CA)n Tracts by B- DNA Crystal Structures Nature, 354, 167-170, 1991. BDL038 K.J.Edwards, D.G.Brown, N.Spink, S.Neidle Molecular Structure of the B-DNA Dodecamer d(CGCAAATTTGCG)2; An Examination of Propeller Twist and Minor-Groove Water Structure at 2.2 Angstroms Resolution J.Mol.Biol., 226, 1161-1173, 1992. BDL042 G.A.Leonard, W.N.Hunter Crystal and Molecular Structure of d(CGTAGATCTACG) at 2.25 Angstroms Resolution J.Mol.Biol., 234, 198-208, 1993. ---------------------------------------------------------------------- Page 10 created by the NDB Project on Wed May 26 14:26:20 2004 CITATIONS FOR PLAIN B-DNA'S ---------------------------------------------------------------------- NDB ID Citation ---------------------------------------------------------------------- BDL047 A.D.DiGabriele, T.A.Steitz A DNA Dodecamer Containing an Adenine Tract Crystallizes in a Unique Lattice and Exhibits a New Bend J.Mol.Biol., 231, 1024-1039, 1993. BDL059 K.Balendiran, S.T.Rao, C.Y.Sekharudu, G.Zon, M.Sundaralingam X-Ray Structures of the B-DNA Dodecamer d(CGCGTTAACGCG) with an Inverted Central Tetranucleotide and Its Netropsin Complex Acta Crystallogr.,Sect.D, 51, 190-198, 1995. BDL070 L.Urpi, V.Tereshko, L.Malinina, T.Huynh-Dinh, J.A.Subirana Structural Comparison Between the d(CTAG) Sequence in Oligonucleotides and trp and met Repressor-Operator Complexes Nat.Struct.Biol., 3, 325-328, 1996. BDL075 B.L.Partridge, S.A.Salisbury n.a. To be Published, n.a., n.a.-n.a., 1996. BDL078 M.Shatzky-Schwartz, N.D.Arbuckle, M.Eisenstein, D.Rabinovich, A.Bareket-Samish, T.E.Haran, B.F.Luisi, Z.Shakked X-ray and Solution Studies of DNA Oligomers and Implications for the Structural Basis of A-Tract-Dependent Curvature J.Mol.Biol., 267, 595-623, 1997. BDL084 X.Shui, L.McFail-Isom, G.G.Hu, L.D.Williams The B-DNA Dodecamer at High Resolution Reveals a Spine of Water on Sodium Biochemistry, 37, 8341-8355, 1998. DD0054 C.Temperini, L.Messori, P.Orioli, C.Di Bugno, F.Animati, G.Ughetto The crystal structure of the complex between a disaccharide anthracycline and the DNA hexamer d(CGATCG) reveals two different binding sites involving two DNA duplexes Nucleic Acids Res., 31, 1464-1469, 2003. ---------------------------------------------------------------------- Page 11 created by the NDB Project on Wed May 26 14:26:20 2004 CITATIONS FOR PLAIN B-DNA'S ---------------------------------------------------------------------- NDB ID Citation ---------------------------------------------------------------------- DD0059 C.J.Squire, G.R.Clark B-DNA Dodecamer d(CGCGAATTCGCG)2 complexed with proamine To be published, n.a., n.a.-n.a., n.a.. DD0060 C.J.Squire, G.R.Clark B-DNA Dodecamer d(CGCGAATTCGCG)2 complexed with proamine To be published, n.a., n.a.-n.a., n.a.. UD0029 F.A.Hays, J.M.Vargason, P.S.Ho Effect of Sequence on the Conformation of DNA Holliday Junctions Biochemistry, 42, 9586-9597, 2003. UD0041 C.J.Cardin, Y.GAN, J.H.Thorpe, S.C.M.Teixeira, B.C.Gale, M.I.A.Moraes Metal Ion Distribution and Stabilisation of the DNA Quadruplex Structure Formed by d(GCATGCT) To be Published, n.a., n.a.-n.a., n.a.. ---------------------------------------------------------------------- Page 12 created by the NDB Project on Wed May 26 14:26:20 2004