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PDBsum entry 1b6y
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DNA PDB id
1b6y

 

 

 

 

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Contents
DNA/RNA
PDB id:
1b6y
Name: DNA
Title: 3,n4-etheno-2'-deoxycytidine opposite adenine in an 11-mer duplex, solution structure from nmr and molecular dynamics, 2 structures
Structure: 5'-d( Cp Gp Tp Ap Cp (Edc)p Cp Ap Tp Gp C)-3'. Chain: a. Engineered: yes. 5'-d( Gp Cp Ap Tp Gp Ap Gp Tp Ap Cp G)-3'. Chain: b. Engineered: yes
Source: Synthetic: yes. Synthetic: yes
NMR struc: 2 models
Authors: A.Korobka,D.Cullinan,M.Cosman,A.P.Grollman,D.J.Patel,M.Eisenberg,C.De Los Santos
Key ref:
A.Korobka et al. (1996). Solution structure of an oligodeoxynucleotide duplex containing the exocyclic lesion 3,N4-etheno-2'-deoxycytidine opposite 2'-deoxyadenosine, determined by NMR spectroscopy and restrained molecular dynamics. Biochemistry, 35, 13310-13318. PubMed id: 8873597 DOI: 10.1021/bi9605696
Date:
19-Jan-99     Release date:   27-Jan-99    
 Headers
 References

DNA/RNA chains
  C-G-T-A-C-EDC-C-A-T-G-C 11 bases
  G-C-A-T-G-A-G-T-A-C-G 11 bases

 

 
DOI no: 10.1021/bi9605696 Biochemistry 35:13310-13318 (1996)
PubMed id: 8873597  
 
 
Solution structure of an oligodeoxynucleotide duplex containing the exocyclic lesion 3,N4-etheno-2'-deoxycytidine opposite 2'-deoxyadenosine, determined by NMR spectroscopy and restrained molecular dynamics.
A.Korobka, D.Cullinan, M.Cosman, A.P.Grollman, D.J.Patel, M.Eisenberg, C.de los Santos.
 
  ABSTRACT  
 
The d(C-G-T-A-C-epsilon C-C-A-T-G-C).d(G-C-A-T-G-A-G-T-A-C-G) oligodeoxynucleotide duplex containing the 3, N4-etheno-2'-deoxycytidine adduct positioned opposite 2'-deoxyadenosine in the center of the helix has been analyzed by proton NMR spectroscopy and restrained molecular dynamics. The spectroscopic data establish a right-handed duplex, with sugar puckers in the C2'-endo/C3'-exo range, residues adopting an anti conformation around the glycosidic torsion angle and, with the exception of epsilon C.dA, Watson-Crick hydrogen bond alignment for all base pairs. Molecular dynamics simulations, restrained by the full relaxation matrix approach, produced a three-dimensional model with an NMR R-factor of 7%. The duplex structure shows no significant perturbation of the sugar-phosphate backbone, which remains in B-form. The exocyclic adduct and its partner dA are incorporated into the helix without producing a noticeable kink. The epsilon C.dA alignment adopts a staggered conformation with each residue displaced toward the 5'-terminus and intercalated between bases on the opposite strand, without increase of inter-phosphate distances. The partial intercalation of the epsilon C (anti).dA(anti) alignment allows stacking between the aromatic rings of epsilon C and dA and with base pairs adjacent to the lesion, suggesting an important role played by hydrophobic forces in the stabilization of the solution structure.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
18693701 G.Shanmugam, I.D.Kozekov, F.P.Guengerich, C.J.Rizzo, and M.P.Stone (2008).
Structure of the 1,N2-ethenodeoxyguanosine adduct opposite cytosine in duplex DNA: Hoogsteen base pairing at pH 5.2.
  Chem Res Toxicol, 21, 1795-1805.  
17941687 G.Shanmugam, A.K.Goodenough, I.D.Kozekov, F.P.Guengerich, C.J.Rizzo, and M.P.Stone (2007).
Structure of the 1,N2-etheno-2'-deoxyguanosine adduct in duplex DNA at pH 8.6.
  Chem Res Toxicol, 20, 1601-1611.  
11841206 B.Hang, G.Downing, A.B.Guliaev, and B.Singer (2002).
Novel activity of Escherichia coli mismatch uracil-DNA glycosylase (Mug) excising 8-(hydroxymethyl)-3,N4-ethenocytosine, a potential product resulting from glycidaldehyde reaction.
  Biochemistry, 41, 2158-2165.  
12490724 S.Smirnov, T.J.Matray, E.T.Kool, and C.de los Santos (2002).
Integrity of duplex structures without hydrogen bonding: DNA with pyrene paired at abasic sites.
  Nucleic Acids Res, 30, 5561-5569.
PDB codes: 1fzl 1fzs
10581234 T.E.Barrett, O.D.Schärer, R.Savva, T.Brown, J.Jiricny, G.L.Verdine, and L.H.Pearl (1999).
Crystal structure of a thwarted mismatch glycosylase DNA repair complex.
  EMBO J, 18, 6599-6609.
PDB code: 1mwj
9811839 B.Hang, M.Medina, H.Fraenkel-Conrat, and B.Singer (1998).
A 55-kDa protein isolated from human cells shows DNA glycosylase activity toward 3,N4-ethenocytosine and the G/T mismatch.
  Proc Natl Acad Sci U S A, 95, 13561-13566.  
9730823 C.A.Gelfand, G.E.Plum, A.P.Grollman, F.Johnson, and K.J.Breslauer (1998).
The impact of an exocyclic cytosine adduct on DNA duplex properties: significant thermodynamic consequences despite modest lesion-induced structural alterations.
  Biochemistry, 37, 12507-12512.  
9846123 E.T.Kool (1998).
Replication of non-hydrogen bonded bases by DNA polymerases: a mechanism for steric matching.
  Biopolymers, 48, 3.  
9671708 M.Saparbaev, and J.Laval (1998).
3,N4-ethenocytosine, a highly mutagenic adduct, is a primary substrate for Escherichia coli double-stranded uracil-DNA glycosylase and human mismatch-specific thymine-DNA glycosylase.
  Proc Natl Acad Sci U S A, 95, 8508-8513.  
9305987 D.Cullinan, F.Johnson, A.P.Grollman, M.Eisenberg, and C.de los Santos (1997).
Solution structure of a DNA duplex containing the exocyclic lesion 3,N4-etheno-2'-deoxycytidine opposite 2'-deoxyguanosine.
  Biochemistry, 36, 11933-11943.
PDB code: 1b6x
8942665 S.Shibutani, N.Suzuki, Y.Matsumoto, and A.P.Grollman (1996).
Miscoding properties of 3,N4-etheno-2'-deoxycytidine in reactions catalyzed by mammalian DNA polymerases.
  Biochemistry, 35, 14992-14998.  
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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