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PDBsum entry 112d
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DNA PDB id
112d

 

 

 

 

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Contents
DNA/RNA
Waters ×83
PDB id:
112d
Name: DNA
Title: Molecular structure of the g.A base pair in DNA and its implications for the mechanism of transversion mutations
Structure: DNA (5'-d( Cp Gp Cp Gp Ap Ap Tp Tp Ap Gp Cp G)-3'). Chain: a, b. Engineered: yes
Source: Synthetic: yes
Biol. unit: Dimer (from PQS)
Resolution:
2.50Å     R-factor:   0.170    
Authors: T.Brown,W.N.Hunter,G.Kneale,O.Kennard
Key ref: T.Brown et al. (1986). Molecular structure of the G.A base pair in DNA and its implications for the mechanism of transversion mutations. Proc Natl Acad Sci U S A, 83, 2402-2406. PubMed id: 3458205 DOI: 10.1073/pnas.83.8.2402
Date:
04-Jan-93     Release date:   15-Jul-93    
 Headers
 References

DNA/RNA chains
  C-G-C-G-A-A-T-T-A-G-C-G 12 bases
  C-G-C-G-A-A-T-T-A-G-C-G 12 bases

 

 
DOI no: 10.1073/pnas.83.8.2402 Proc Natl Acad Sci U S A 83:2402-2406 (1986)
PubMed id: 3458205  
 
 
Molecular structure of the G.A base pair in DNA and its implications for the mechanism of transversion mutations.
T.Brown, W.N.Hunter, G.Kneale, O.Kennard.
 
  ABSTRACT  
 
The synthetic deoxydodecamer d(C-G-C-G-A-A-T-T-A-G-C-G) was analyzed by x-ray diffraction methods, and the structure was refined to a residual error of R = 0.17 at 2.5-A resolution (2 sigma data) with 83 water molecules located. The sequence crystallizes as a full turn of a B-DNA helix and contains 2 purine X purine (G.A) base pairs and 10 Watson-Crick base pairs. The analysis shows conclusively that adenine is in the syn orientation with respect to the sugar moiety whereas guanine adopts the usual trans orientation. Nitrogen atoms of both bases are involved in hydrogen bonding with the N-1 of guanine 2.84 A from the N-7 of adenine and the N-6 of adenine within 2.74 A of the O-6 of guanine. The C-1'...C-1' separation is 10.7 A close to that for standard Watson-Crick base pairs. The incorporation of the purine.purine base pairs at two steps in the dodecamer causes little perturbation of either the local or the global conformation of the double helix. Comparison of the structural features with those of the G.T wobble pair and the standard G.C pair suggests a rationale for the differential enzymatic repair of the two types of base-pair mismatches.
 

Literature references that cite this PDB file's key reference

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PDB code: 1i6j
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Use of an N-terminal fragment from moloney murine leukemia virus reverse transcriptase to facilitate crystallization and analysis of a pseudo-16-mer DNA molecule containing G-A mispairs.
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PDB code: 1d1u
10985772 N.Sugimoto, M.Nakano, and S.Nakano (2000).
Thermodynamics-structure relationship of single mismatches in RNA/DNA duplexes.
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10052954 B.Pan, S.N.Mitra, and M.Sundaralingam (1999).
Crystal structure of an RNA 16-mer duplex R(GCAGAGUUAAAUCUGC)2 with nonadjacent G(syn).A+(anti) mispairs.
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PDB code: 420d
9485363 H.T.Allawi, and J.SantaLucia (1998).
Nearest neighbor thermodynamic parameters for internal G.A mismatches in DNA.
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Structure of d(GT)n.d(GA)n sequences: formation of parallel stranded duplex DNA.
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PDB code: 355d
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Structural features of the DNA hairpin d(ATCCTA-GTTA-TAGGAT): formation of a G-A base pair in the loop.
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PDB code: 1ac7
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Cloning, overexpression, and biochemical characterization of the catalytic domain of MutY.
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A thymidine triphosphate shape analog lacking Watson-Crick pairing ability is replicated with high sequence selectivity.
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DNA structural forms.
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Tetraplex folding of telomere sequences and the inclusion of adenine bases.
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Crystal and molecular structure of r(CGCGAAUUAGCG): an RNA duplex containing two G(anti).A(anti) base pairs.
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PDB code: 157d
7859713 H.Pulyaeva, S.F.Zakharov, M.M.Garner, and A.Chrambach (1994).
Detection of a single base mismatch in double-stranded DNA by electrophoresis on uncrosslinked polyacrylamide gel.
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Formation of sheared G:A base pairs in an RNA duplex modelled after ribozymes, as revealed by NMR.
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Mutations in a shuttle vector exposed to activated mitomycin C.
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Alternating d(GA)n DNA sequences form antiparallel stranded homoduplexes stabilized by the formation of G.A base pairs.
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Biochemical basis of DNA replication fidelity.
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NMR studies of G:A mismatches in oligodeoxyribonucleotide duplexes modelled after ribozymes.
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DNA methylation by N-methyl-N-nitrosourea: methylation pattern changes in single- and double-stranded DNA, and in DNA with mismatched or bulged guanines.
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Influence of nearest neighbor sequence on the stability of base pair mismatches in long DNA; determination by temperature-gradient gel electrophoresis.
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The conformational variability of an adenosine.inosine base-pair in a synthetic DNA dodecamer.
  Nucleic Acids Res, 20, 4753-4759.
PDB code: 1d81
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The influence of local DNA sequence and DNA repair background on the mutational specificity of 1-nitroso-8-nitropyrene in Escherichia coli: inferences for mutagenic mechanisms.
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1382298 J.J.Tsai-Wu, H.F.Liu, and A.L.Lu (1992).
Escherichia coli MutY protein has both N-glycosylase and apurinic/apyrimidinic endonuclease activities on A.C and A.G mispairs.
  Proc Natl Acad Sci U S A, 89, 8779-8783.  
1386670 L.S.Kappen, and I.H.Goldberg (1992).
Neocarzinostatin acts as a sensitive probe of DNA microheterogeneity: switching of chemistry from C-1' to C-4' by a G.T mismatch 5' to the site of DNA damage.
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1837078 J.A.Cognet, J.Gabarro-Arpa, M.Le Bret, G.A.van der Marel, J.H.van Boom, and G.V.Fazakerley (1991).
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Nucleotide sequence of the Escherichia coli micA gene required for A/G-specific mismatch repair: identity of micA and mutY.
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The vinyl chloride DNA derivative N2,3-ethenoguanine produces G----A transitions in Escherichia coli.
  Proc Natl Acad Sci U S A, 88, 9974-9978.  
2216754 G.A.Leonard, E.D.Booth, and T.Brown (1990).
Structural and thermodynamic studies on the adenine.guanine mismatch in B-DNA.
  Nucleic Acids Res, 18, 5617-5623.  
2395870 G.D.Webster, M.R.Sanderson, J.V.Skelly, S.Neidle, P.F.Swann, B.F.Li, and I.J.Tickle (1990).
Crystal structure and sequence-dependent conformation of the A.G mispaired oligonucleotide d(CGCAAGCTGGCG).
  Proc Natl Acad Sci U S A, 87, 6693-6697.
PDB code: 1dnm
2197596 M.L.Michaels, L.Pham, Y.Nghiem, C.Cruz, and J.H.Miller (1990).
MutY, an adenine glycosylase active on G-A mispairs, has homology to endonuclease III.
  Nucleic Acids Res, 18, 3841-3845.  
2275970 T.Umehara, S.Kuwabara, S.Mashimo, and S.Yagihara (1990).
Dielectric study on hydration of B-, A-, and Z-DNA.
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  2687237 B.A.Learn, and R.H.Grafstrom (1989).
Methyl-directed repair of frameshift heteroduplexes in cell extracts from Escherichia coli.
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2682664 K.G.Au, S.Clark, J.H.Miller, and P.Modrich (1989).
Escherichia coli mutY gene encodes an adenine glycosylase active on G-A mispairs.
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2674904 M.Yarus, J.Levine, G.B.Morin, and T.R.Cech (1989).
A Tetrahymena intron nucleotide connected to the GTP/arginine site.
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2695962 O.Kennard, and W.N.Hunter (1989).
Oligonucleotide structure: a decade of results from single crystal X-ray diffraction studies.
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2911488 W.B.Cruse, J.Aymani, O.Kennard, T.Brown, A.G.Jack, and G.A.Leonard (1989).
Refined crystal structure of an octanucleotide duplex with I.T. mismatched base pairs.
  Nucleic Acids Res, 17, 55-72.
PDB code: 1d90
3041378 D.L.Sloane, M.F.Goodman, and H.Echols (1988).
The fidelity of base selection by the polymerase subunit of DNA polymerase III holoenzyme.
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3060357 F.J.Van de Ven, and C.W.Hilbers (1988).
Nucleic acids and nuclear magnetic resonance.
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Kinds and spectrum of mutations induced by 1-nitrosopyrene adducts during plasmid replication in human cells.
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An NMR study of polymorphous behaviour of the mismatched DNA octamer d(m5C-G-m5C-G-A-G-m5C-G) in solution. The B-duplex and hairpin forms.
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3671069 P.W.Corfield, W.N.Hunter, T.Brown, P.Robinson, and O.Kennard (1987).
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PDB code: 114d
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PDB code: 1d99
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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.

 

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