PDBsum entry 212d

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dna_rna ligands links
NCO ×3
Waters ×66
PDB id:
Name: DNA
Title: Influence of counter-ions on the crystal structures of DNA decamers: binding of [co(nh3)6]3+ and ba2+ to a-DNA
Structure: DNA (5'-d( Ap Cp Cp Gp Gp Cp Cp Gp Gp T)-3'). Chain: a. Engineered: yes
Source: Synthetic: yes
1.90Å     R-factor:   0.194    
Authors: Y.-G.Gao,H.Robinson,J.H.Van Boom,A.H.-J.Wang
Key ref: Y.G.Gao et al. (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. PubMed id: 8527670
26-Jun-95     Release date:   31-Jan-96    


Biophys J 69:559-568 (1995)
PubMed id: 8527670  
Influence of counter-ions on the crystal structures of DNA decamers: binding of [Co(NH3)6]3+ and Ba2+ to A-DNA.
Y.G.Gao, H.Robinson, J.H.van Boom, A.H.Wang.
A-DNA is a stable alternative right-handed double helix that is favored by certain sequences (e.g., (dG)n.(dC)n) or under low humidity conditions. Earlier A-DNA structures of several DNA oligonucleotides and RNA.DNA chimeras have revealed some conformational variation that may be the result of sequence-dependent effects or crystal packing forces. In this study, four crystal structures of three decamer oligonucleotides, d(ACCGGCCGGT), d(ACCCGCGGGT), and r(GC)d(GTATACGC) in two crystal forms (either the P6(1)22 or the P2(1)2(1)2(1) space group) have been analyzed at high resolution to provide the molecular basis of the structural difference in an experimentally consistent manner. The study reveals that molecules crystallized in the same space group have a more similar A-DNA conformation, whereas the same molecule crystallized in different space groups has different (local) conformations. This suggests that even though the local structure is influenced by the crystal packing environments, the DNA molecule adjusts to adopt an overall conformation close to canonical A-DNA. For example, the six independent CpG steps in these four structures have different base-base stacking patterns, with their helical twist angles (omega) ranging from 28 degrees to 37 degrees. Our study further reveals the structural impact of different counter-ions on the A-DNA conformers. [Co(NH3)6]3+ has three unique A-DNA binding modes. One binds at the major groove side of a GpG step at the O6/N7 sites of guanine bases via hydrogen bonds. The other two modes involve the binding of ions to phosphates, either bridging across the narrow major groove or binding between two intra-strand adjacent phosphates. Those interactions may explain the recent spectroscopic and NMR observations that [Co(NH3)6]3+ is effective in inducing the B- to A-DNA transition for DNA with (G)n sequence. Interestingly, Ba2+ binds to the same O6/N7 sites on guanine by direct coordinations.

Literature references that cite this PDB file's key reference

  PubMed id Reference
  19255472 R.M.Leal, S.C.Teixeira, M.P.Blakeley, E.P.Mitchell, and V.T.Forsyth (2009).
A preliminary neutron crystallographic study of an A-DNA crystal.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 65, 232-235.  
15597210 J.Golebiowski, S.Antonczak, J.Fernandez-Carmona, R.Condom, and D.Cabrol-Bass (2004).
Closing loop base pairs in RNA loop-loop complexes: structural behavior, interaction energy and solvation analysis through molecular dynamics simulations.
  J Mol Model, 10, 408-417.  
12056901 M.Kaul, and D.S.Pilch (2002).
Thermodynamics of aminoglycoside-rRNA recognition: the binding of neomycin-class aminoglycosides to the A site of 16S rRNA.
  Biochemistry, 41, 7695-7706.  
10790193 A.Rodger, K.J.Sanders, M.J.Hannon, I.Meistermann, A.Parkinson, D.S.Vidler, and I.S.Haworth (2000).
DNA structure control by polycationic species: polyamine, cobalt ammines, and di-metallo transition metal chelates.
  Chirality, 12, 221-236.  
11031289 T.E.Cheatham, and P.A.Kollman (2000).
Molecular dynamics simulation of nucleic acids.
  Annu Rev Phys Chem, 51, 435-471.  
10215851 Y.G.Gao, H.Robinson, and A.H.Wang (1999).
High-resolution A-DNA crystal structures of d(AGGGGCCCCT). An A-DNA model of poly(dG) x poly(dC).
  Eur J Biochem, 261, 413-420.
PDB codes: 440d 441d
10600106 Y.G.Gao, H.Robinson, R.Sanishvili, A.Joachimiak, and A.H.Wang (1999).
Structure and recognition of sheared tandem G x A base pairs associated with human centromere DNA sequence at atomic resolution.
  Biochemistry, 38, 16452-16460.
PDB codes: 1d8x 1d9r 1dcr
9788937 B.Schneider, K.Patel, and H.M.Berman (1998).
Hydration of the phosphate group in double-helical DNA.
  Biophys J, 75, 2422-2434.  
9564052 C.Mayer-Jung, D.Moras, and Y.Timsit (1998).
Hydration and recognition of methylated CpG steps in DNA.
  EMBO J, 17, 2709-2718.
PDB codes: 382d 383d 384d
9635768 I.Rouzina, and V.A.Bloomfield (1998).
DNA bending by small, mobile multivalent cations.
  Biophys J, 74, 3152-3164.  
9493396 S.Neidle, and C.M.Nunn (1998).
Crystal structures of nucleic acids and their drug complexes.
  Nat Prod Rep, 15, 1.  
9687367 W.Shepard, W.B.Cruse, R.Fourme, la Fortelle, and T.Prangé (1998).
A zipper-like duplex in DNA: the crystal structure of d(GCGAAAGCT) at 2.1 A resolution.
  Structure, 6, 849-861.
PDB code: 376d
9195889 J.S.Kieft, and I.Tinoco (1997).
Solution structure of a metal-binding site in the major groove of RNA complexed with cobalt (III) hexammine.
  Structure, 5, 713-721.
PDB code: 1ajf
9097733 M.C.Wahl, and M.Sundaralingam (1997).
Crystal structures of A-DNA duplexes.
  Biopolymers, 44, 45-63.  
9351805 T.E.Cheatham, and P.A.Kollman (1997).
Insight into the stabilization of A-DNA by specific ion association: spontaneous B-DNA to A-DNA transitions observed in molecular dynamics simulations of d[ACCCGCGGGT]2 in the presence of hexaamminecobalt(III).
  Structure, 5, 1297-1311.  
8604309 H.Robinson, and A.H.Wang (1996).
Neomycin, spermine and hexaamminecobalt (III) share common structural motifs in converting B- to A-DNA.
  Nucleic Acids Res, 24, 676-682.  
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB codes are shown on the right.