Crystal structure of a DNA/Ba2+ G-quadruplex containing a water-mediated C-tetrad
Abstract
We have determined the 1.50 Å crystal structure of the DNA decamer, d(CCACNVKGCGTGG) (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.
- Authors:
-
- Univ. of Maryland, College Park, MD (United States)
- California State Polytechnic Univ., Pomona, CA (United States)
- St. John's Univ., Queens, NY (United States)
- Publication Date:
- Research Org.:
- Argonne National Laboratory (ANL), Argonne, IL (United States)
- Sponsoring Org.:
- National Science Foundation (NSF)
- OSTI Identifier:
- 1251232
- Grant/Contract Number:
- DMR1149665
- Resource Type:
- Accepted Manuscript
- Journal Name:
- Nucleic Acids Research
- Additional Journal Information:
- Journal Volume: 42; Journal Issue: 21; Journal ID: ISSN 0305-1048
- Publisher:
- Oxford University Press
- Country of Publication:
- United States
- Language:
- ENGLISH
- Subject:
- 59 BASIC BIOLOGICAL SCIENCES
Citation Formats
Zhang, Diana, Huang, Terry, Lukeman, Philip S., and Paukstelis, Paul J. Crystal structure of a DNA/Ba2+ G-quadruplex containing a water-mediated C-tetrad. United States: N. p., 2014.
Web. doi:10.1093/nar/gku1122.
Zhang, Diana, Huang, Terry, Lukeman, Philip S., & Paukstelis, Paul J. Crystal structure of a DNA/Ba2+ G-quadruplex containing a water-mediated C-tetrad. United States. https://doi.org/10.1093/nar/gku1122
Zhang, Diana, Huang, Terry, Lukeman, Philip S., and Paukstelis, Paul J. Tue .
"Crystal structure of a DNA/Ba2+ G-quadruplex containing a water-mediated C-tetrad". United States. https://doi.org/10.1093/nar/gku1122. https://www.osti.gov/servlets/purl/1251232.
@article{osti_1251232,
title = {Crystal structure of a DNA/Ba2+ G-quadruplex containing a water-mediated C-tetrad},
author = {Zhang, Diana and Huang, Terry and Lukeman, Philip S. and Paukstelis, Paul J.},
abstractNote = {We have determined the 1.50 Å crystal structure of the DNA decamer, d(CCACNVKGCGTGG) (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.},
doi = {10.1093/nar/gku1122},
journal = {Nucleic Acids Research},
number = 21,
volume = 42,
place = {United States},
year = {Tue Nov 11 00:00:00 EST 2014},
month = {Tue Nov 11 00:00:00 EST 2014}
}
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Guanine base stacking in G-quadruplex nucleic acids
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Mechanically rigid supramolecular assemblies formed from an Fmoc-guanine conjugated peptide nucleic acid
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- Nucleic Acids Research, Vol. 46, Issue 21
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posted_content, August 2019
- Chu, Betty; Zhang, Daoning; Paukstelis, Paul J.
- bioRxiv