PDBsum entry 284d

Go to PDB code: 
dna_rna metals links
_BA ×11
Waters ×105
PDB id:
Name: DNA
Title: The bi-loop, a new general four-stranded DNA motif
Structure: DNA (5'-cd( P Ap Tp Tp Cp Ap Tp Tp C)-3'). Chain: a, b. Engineered: yes
Source: Synthetic: yes
1.10Å     R-factor:   0.228    
Authors: S.A.Salisbury,S.E.Wilson,H.R.Powell,O.Kennard,P.Lubini, G.M.Sheldrick,N.Escaja,E.Alazzouzi,A.Grandas,E.Pedroso
Key ref:
S.A.Salisbury et al. (1997). The bi-loop, a new general four-stranded DNA motif. Proc Natl Acad Sci U S A, 94, 5515-5518. PubMed id: 9159103 DOI: 10.1073/pnas.94.11.5515
11-Sep-96     Release date:   11-Jun-97    


DOI no: 10.1073/pnas.94.11.5515 Proc Natl Acad Sci U S A 94:5515-5518 (1997)
PubMed id: 9159103  
The bi-loop, a new general four-stranded DNA motif.
S.A.Salisbury, S.E.Wilson, H.R.Powell, O.Kennard, P.Lubini, G.M.Sheldrick, N.Escaja, E.Alazzouzi, A.Grandas, E.Pedroso.
The crystal structure of the cyclic octanucleotide d<pATTCATTC> contains two independent molecules that form a novel quadruplex by means of intermolecular Watson-Crick A.T pairs and base stacking. A virtually identical quadruplex composed of G.C pairs was found by earlier x-ray analysis of the linear heptamer d(GCATGCT), when the DNA was looped in the crystal. The close correspondence between these two structures of markedly dissimilar oligonucleotides suggests that they are both examples of a previously unrecognized motif. Their nucleotide sequences have little in common except for two separated 5'-purine-pyrimidine dinucleotides forming the quadruplex, and by implication these so-called "bi-loops" could occur widely in natural DNA. Such structures provide a mechanism for noncovalent linking of polynucleotides in vivo. Their capacity to associate by base stacking, demonstrated in the crystal structure of d(GCATGCT), creates a compact molecular framework made up of four DNA chains within which strand exchange could take place.
  Selected figure(s)  
Figure 2.
Fig. 2. Schematic representation (19) in which the sugar-phosphate backbone atoms of the dimer are replaced by ribbons. Interactions in the farther stack, where bases are indicated by darker colors, are the same as in the nearer.
Figure 4.
Fig. 4. (A) Two dimers of the cyclic octamer arranged so that the thymine rings of T3 and T17 of one are in van der Waals contact with those of T7 and T13 of the other. For clarity, only backbone^ atoms are shown as spheres. (B) Side view showing only the nearer molecule of each dimer. Putative new phosphodiester bonds between O3 of T2 and P of T3 are represented as dashed lines. (C) Proposed^ course of recombination according to this mechanism between two duplexes containing the self-complementary sequence d(GCATGC).
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
19321501 J.Viladoms, N.Escaja, M.Frieden, I.Gómez-Pinto, E.Pedroso, and C.González (2009).
Self-association of short DNA loops through minor groove C:G:G:C tetrads.
  Nucleic Acids Res, 37, 3264-3275.
PDB codes: 2k8z 2k90 2k97
17913750 D.J.Patel, A.T.Phan, and V.Kuryavyi (2007).
Human telomere, oncogenic promoter and 5'-UTR G-quadruplexes: diverse higher order DNA and RNA targets for cancer therapeutics.
  Nucleic Acids Res, 35, 7429-7455.  
16607659 N.Escaja, I.Gómez-Pinto, J.Viladoms, M.Rico, E.Pedroso, and C.González (2006).
Induced-fit recognition of DNA by small circular oligonucleotides.
  Chemistry, 12, 4035-4042.  
12560479 J.H.Thorpe, S.C.Teixeira, B.C.Gale, and C.J.Cardin (2003).
Crystal structure of the complementary quadruplex formed by d(GCATGCT) at atomic resolution.
  Nucleic Acids Res, 31, 844-849.
PDB code: 1mf5
12682360 V.Dapić, V.Abdomerović, R.Marrington, J.Peberdy, A.Rodger, J.O.Trent, and P.J.Bates (2003).
Biophysical and biological properties of quadruplex oligodeoxyribonucleotides.
  Nucleic Acids Res, 31, 2097-2107.  
12202780 J.Jaumot, N.Escaja, R.Gargallo, C.González, E.Pedroso, and R.Tauler (2002).
Multivariate curve resolution: a powerful tool for the analysis of conformational transitions in nucleic acids.
  Nucleic Acids Res, 30, e92.  
11405476 R.K.Sigel, S.M.Thompson, E.Freisinger, F.Glahé, and B.Lippert (2001).
Metal-modified nucleobase sextet: joining four linear metal fragments (trans-a2PtII) and six model nucleobases to an exceedingly stable entity.
  Chemistry, 7, 1968-1980.  
11745109 M.A.Keniry (2000).
Quadruplex structures in nucleic acids.
  Biopolymers, 56, 123-146.  
9914254 S.Longhi, M.Czjzek, and C.Cambillau (1998).
Messages from ultrahigh resolution crystal structures.
  Curr Opin Struct Biol, 8, 730-737.  
9559582 S.Pospísilová, and J.Kypr (1998).
UV light-induced duplex-to-duplex crosslinking of DNA molecules in aqueous ethanol solutions.
  Photochem Photobiol, 67, 386-390.  
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.