PDBsum entry 2qs6

Go to PDB code: 
dna_rna links
Waters ×40
PDB id:
Name: DNA
Title: Structure of a hoogsteen antiparallel duplex with extra-heli thymines
Structure: DNA (5'-d( Dap Dtp Dap Dtp Dap Dtp Dcp Dt)-3'). Chain: a, b, c, d, e, f, g, h, i, j, k, l, m, n. Engineered: yes
Source: Synthetic: yes. Other_details: phosphoramidite method
3.08Å     R-factor:   0.214     R-free:   0.289
Authors: J.Pous,L.Urpi,J.A.Subirana,C.Gouyette,J.Navaza,J.L.Campos
Key ref: J.Pous et al. (2008). Stabilization by extra-helical thymines of a DNA duplex with Hoogsteen base pairs. J Am Chem Soc, 130, 6755-6760. PubMed id: 18447354 DOI: 10.1021/ja078022+
30-Jul-07     Release date:   25-Mar-08    


DOI no: 10.1021/ja078022+ J Am Chem Soc 130:6755-6760 (2008)
PubMed id: 18447354  
Stabilization by extra-helical thymines of a DNA duplex with Hoogsteen base pairs.
J.Pous, L.Urpí, J.A.Subirana, C.Gouyette, J.Navaza, J.L.Campos.
We present the crystal structure of the DNA duplex formed by d(ATATATCT). The crystals contain seven stacked antiparallel duplexes in the asymmetric unit with A.T Hoogsteen base pairs. The terminal CT sequences bend over so that the thymines enter the minor groove and form a hydrogen bond with thymine 2 of the complementary strand in the Hoogsteen duplex. Cytosines occupy extra-helical positions; they contribute to the crystal lattice through various kinds of interactions, including a unique CAA triplet. The presence of thymine in the minor groove apparently contributes to the stability of the DNA duplex in the Hoogsteen conformation. These observations open the way toward finding under what conditions the Hoogsteen duplex may be stabilized in vivo. The present crystal structure also confirms the tendency of A.T-rich oligonucleotides to crystallize as long helical stacks of duplexes.

Literature references that cite this PDB file's key reference

  PubMed id Reference
20179336 T.Moreno, J.Pous, J.A.Subirana, and J.L.Campos (2010).
Coiled-coil conformation of a pentamidine-DNA complex.
  Acta Crystallogr D Biol Crystallogr, 66, 251-257.
PDB code: 3ey0
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 code is shown on the right.