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

Zhang, Diana; Huang, Terry; Lukeman, Philip S.; Paukstelis, Paul J.

doi:10.1093/nar/gku1122

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

Journal Article · Tue Nov 11 00:00:00 EST 2014 · Nucleic Acids Research

DOI:https://doi.org/10.1093/nar/gku1122· OSTI ID:1251232

Zhang, Diana ^[1]; Huang, Terry ^[2]; Lukeman, Philip S. ^[3]; Paukstelis, Paul J. ^[1]

Univ. of Maryland, College Park, MD (United States)
California State Polytechnic Univ., Pomona, CA (United States)
St. John's Univ., Queens, NY (United States)

We have determined the 1.50 Å crystal structure of the DNA decamer, d(CCA^CNVKGCGTGG) (^CNVK, 3-cyanovinylcarbazole), which forms a G-quadruplex structure in the presence of Ba²⁺. 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 Ba²⁺ ions to occupy adjacent steps in the central ion channel. One ordered Mg²⁺ 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 ^CNVK 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.

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Research Organization:: Argonne National Laboratory (ANL), Argonne, IL (United States)

Sponsoring Organization:: National Science Foundation (NSF)

Grant/Contract Number:: DMR1149665

OSTI ID:: 1251232

Journal Information:: Nucleic Acids Research, Vol. 42, Issue 21; ISSN 0305-1048

Publisher:: Oxford University PressCopyright Statement

Country of Publication:: United States

Language:: ENGLISH

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Cited by: 28 works

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