4U92

Crystal structure of a DNA/Ba2+ G-quadruplex containing a water-mediated C-tetrad

Summary for 4U92

• Entry DOI: 10.2210/pdb4u92/pdb
• Descriptor: DNA (5'-D(*CP*CP*AP*KP*GP*CP*GP*TP*GP*G)-3'), BARIUM ION, MAGNESIUM ION, ... (4 entities in total)
• Functional Keywords: dna quadruplex barium c-tetrad, dna
• Biological source: synthetic construct
• Total number of polymer chains: 2
• Total formula weight: 6460.32

Authors

Paukstelis, P.J.,Zhang, D.,Huang, T.,Lukeman, P. (deposition date: 2014-08-05, release date: 2014-11-26, Last modification date: 2023-12-27)

Primary citation

Zhang, D.,Huang, T.,Lukeman, P.S.,Paukstelis, P.J.
Crystal structure of a DNA/Ba2+ G-quadruplex containing a water-mediated C-tetrad.
Nucleic Acids Res., 42:13422-13429, 2014

PubMed Abstract: We have determined the 1.50 Å crystal structure of the DNA decamer, d(CCA(CNV)KGCGTGG) ((CNV)K, 3-cyanovinylcarbazole), which forms a G-quadruplex structure in the presence of Ba(2+). The structure contains several unique features including a bulged nucleotide and the first crystal structure observation of a C-tetrad. The structure reveals that water molecules mediate contacts between the divalent cations and the C-tetrad, allowing Ba(2+) ions to occupy adjacent steps in the central ion channel. One ordered Mg(2+) facilitates 3'-3' stacking of two quadruplexes in the asymmetric unit, while the bulged nucleotide mediates crystal contacts. Despite the high diffraction limit, the first four nucleotides including the (CNV)K nucleoside are disordered though they are still involved in crystal packing. This work suggests that the bulky hydrophobic groups may locally influence the formation of non-Watson-Crick structures from otherwise complementary sequences. These observations lead to the intriguing possibility that certain types of DNA damage may act as modulators of G-quadruplex formation.

PubMed: 25389267
DOI: 10.1093/nar/gku1122

Experimental method

X-RAY DIFFRACTION (1.5 Å)