PDBsum entry 2o1i

Go to PDB code: 
dna_rna ligands links
R1C ×3
Waters ×75
PDB id:
Name: DNA
Title: Rh(bpy)2chrysi complexed to mismatched DNA
Structure: 5'-d( Cp Gp Gp Ap Ap Ap Tp Tp Cp Cp Cp G)-3'. Chain: a. Engineered: yes
Source: Synthetic: yes. Other_details: solid phase synthesis
1.10Å     R-factor:   0.151     R-free:   0.204
Authors: V.C.Pierre,J.T.Kaiser,J.K.Barton
Key ref:
V.C.Pierre et al. (2007). Insights into finding a mismatch through the structure of a mispaired DNA bound by a rhodium intercalator. Proc Natl Acad Sci U S A, 104, 429-434. PubMed id: 17194756 DOI: 10.1073/pnas.0610170104
28-Nov-06     Release date:   09-Jan-07    


DOI no: 10.1073/pnas.0610170104 Proc Natl Acad Sci U S A 104:429-434 (2007)
PubMed id: 17194756  
Insights into finding a mismatch through the structure of a mispaired DNA bound by a rhodium intercalator.
V.C.Pierre, J.T.Kaiser, J.K.Barton.
We report the 1.1-A resolution crystal structure of a bulky rhodium complex bound to two different DNA sites, mismatched and matched in the oligonucleotide 5'-(dCGGAAATTCCCG)2-3'. At the AC mismatch site, the structure reveals ligand insertion from the minor groove with ejection of both mismatched bases and elucidates how destabilized mispairs in DNA may be recognized. This unique binding mode contrasts with major groove intercalation, observed at a matched site, where doubling of the base pair rise accommodates stacking of the intercalator. Mass spectral analysis reveals different photocleavage products associated with the two binding modes in the crystal, with only products characteristic of mismatch binding in solution. This structure, illustrating two clearly distinct binding modes for a molecule with DNA, provides a rationale for the interrogation and detection of mismatches.
  Selected figure(s)  
Figure 2.
Fig. 2. Insertion of the bulky rhodium complex in the mismatch site. (a) Insertion of -[Rh(bpy)[2]chrysi]^3+ (red) via the minor groove and replacement of the AC mismatch bases. The ejected adenosine (green) remains in the minor groove, whereas the ejected cytosine (blue) is in the major groove. (b) Representative omit |F[o]| – |F[c]| electron density map for two intertwined and crystallographically related oligonucleotides (orange and cyan). The ejected mismatched adenosine of one strand (red) -stacks with the 2,2'-bipyridine and ejected adenosine of the related strand (blue).
Figure 4.
Fig. 4. Distortion of the rhodium complex upon intercalation and insertion in DNA. The crystal structures of -[Rh(bpy)[2]chrysi]^3+"free" (without DNA, gray carbon atoms), inserted via the minor groove (light blue carbon atoms), and intercalated via the major groove (red carbon atoms) were superimposed by using the central ring of the chrysi ligand.
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20736180 S.Komeda, T.Moulaei, M.Chikuma, A.Odani, R.Kipping, N.P.Farrell, and L.D.Williams (2011).
The phosphate clamp: a small and independent motif for nucleic acid backbone recognition.
  Nucleic Acids Res, 39, 325-336.  
19938008 A.Granzhan, E.Largy, N.Saettel, and M.P.Teulade-Fichou (2010).
Macrocyclic DNA-mismatch-binding ligands: structural determinants of selectivity.
  Chemistry, 16, 878-889.  
20697625 G.Song, and J.Ren (2010).
Recognition and regulation of unique nucleic acid structures by small molecules.
  Chem Commun (Camb), 46, 7283-7294.  
19374348 B.M.Zeglis, V.C.Pierre, J.T.Kaiser, and J.K.Barton (2009).
A bulky rhodium complex bound to an adenosine-adenosine DNA mismatch: general architecture of the metalloinsertion binding mode.
  Biochemistry, 48, 4247-4253.
PDB codes: 3gsj 3gsk
19122895 D.R.Boer, A.Canals, and M.Coll (2009).
DNA-binding drugs caught in action: the latest 3D pictures of drug-DNA complexes.
  Dalton Trans, (), 399-414.  
19453124 M.H.Lim, H.Song, E.D.Olmon, E.E.Dervan, and J.K.Barton (2009).
Sensitivity of Ru(bpy)2dppz2+ luminescence to DNA defects.
  Inorg Chem, 48, 5392-5397.  
19175313 R.J.Ernst, H.Song, and J.K.Barton (2009).
DNA mismatch binding and antiproliferative activity of rhodium metalloinsertors.
  J Am Chem Soc, 131, 2359-2366.  
19006320 A.E.Rumora, K.M.Kolodziejczak, A.Malhowski Wagner, and M.E.Núñez (2008).
Thymine dimer-induced structural changes to the DNA duplex examined with reactive probes (†).
  Biochemistry, 47, 13026-13035.  
18491905 B.M.Zeglis, J.A.Boland, and J.K.Barton (2008).
Targeting abasic sites and single base bulges in DNA with metalloinsertors.
  J Am Chem Soc, 130, 7530-7531.  
18576614 B.M.Zeglis, and J.K.Barton (2008).
Binding of Ru(bpy)2(eilatin)2+ to matched and mismatched DNA.
  Inorg Chem, 47, 6452-6457.  
18658249 M.Bahr, V.Gabelica, A.Granzhan, M.P.Teulade-Fichou, and E.Weinhold (2008).
Selective recognition of pyrimidine-pyrimidine DNA mismatches by distance-constrained macrocyclic bis-intercalators.
  Nucleic Acids Res, 36, 5000-5012.  
18535698 Y.Osakada, K.Kawai, M.Fujitsuka, and T.Majima (2008).
Charge transfer in DNA assemblies: effects of sticky ends.
  Chem Commun (Camb), (), 2656-2658.  
17406597 B.M.Zeglis, and J.K.Barton (2007).
DNA base mismatch detection with bulky rhodium intercalators: synthesis and applications.
  Nat Protoc, 2, 357-371.  
17989802 B.M.Zeglis, V.C.Pierre, and J.K.Barton (2007).
Metallo-intercalators and metallo-insertors.
  Chem Commun (Camb), (), 4565-4579.  
17877349 C.Cordier, V.C.Pierre, and J.K.Barton (2007).
Insertion of a bulky rhodium complex into a DNA cytosine-cytosine mismatch: an NMR solution study.
  J Am Chem Soc, 129, 12287-12295.  
17918931 M.H.Lim, I.H.Lau, and J.K.Barton (2007).
DNA strand cleavage near a CC mismatch directed by a metalloinsertor.
  Inorg Chem, 46, 9528-9530.  
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.