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Title: 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:
 [1];  [2];  [3];  [1]
  1. Univ. of Maryland, College Park, MD (United States)
  2. California State Polytechnic Univ., Pomona, CA (United States)
  3. 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:
Journal Article: 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. 2014. "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},
url = {https://www.osti.gov/biblio/1251232}, journal = {Nucleic Acids Research},
issn = {0305-1048},
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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Free Publicly Available Full Text
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Cited by: 28 works
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Works referenced in this record:

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A New Approach for Reversible RNA Photocrosslinking Reaction: Application to Sequence-Specific RNA Selection
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Cation-Dependent Conformational Switches in d-TGGCGGC Containing Two Triplet Repeats of Fragile X Syndrome: NMR Observations
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G-quadruplex nucleic acids as therapeutic targets
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“Nano-oddities”: Unusual Nucleic Acid Assemblies for DNA-Based Nanostructures and Nanodevices
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Solution structure of an unusually stable RNA tetraplex containing G- and U-quartet structures
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Three-Dimensional DNA Crystals with pH-Responsive Noncanonical Junctions
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Bulges in G-Quadruplexes: Broadening the Definition of G-Quadruplex-Forming Sequences
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Two DNA nanomachines map pH changes along intersecting endocytic pathways inside the same cell
journal, May 2013


First blueprint, now bricks: DNA as construction material on the nanoscale
journal, January 2006


DNA nanomachines and nanostructures involving quadruplexes
journal, January 2006


Base-tetrad swapping results in dimerization of RNA quadruplexes: Implications for formation of the i-motif RNA octaplex
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In vitro generated antibodies specific for telomeric guanine-quadruplex DNA react with Stylonychia lemnae macronuclei
journal, July 2001


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journal, May 1997


Intramolecular folding of a fragment of the cytosine-rich strand of telomeric DNA into an i-motif
journal, January 1994


Quadruplex DNA: sequence, topology and structure
journal, September 2006


G-quadruplexes in promoters throughout the human genome
journal, March 2007


Self-association of short DNA loops through minor groove C:G:G:C tetrads
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Works referencing / citing this record:

Mechanically rigid supramolecular assemblies formed from an Fmoc-guanine conjugated peptide nucleic acid
journal, November 2019


Structure and hydrodynamics of a DNA G-quadruplex with a cytosine bulge
journal, May 2018


High-resolution DNA quadruplex structure containing all the A-, G-, C-, T-tetrads
journal, October 2018


A DNA G-quadruplex/i-motif hybrid
posted_content, August 2019


A DNA G-quadruplex/i-motif hybrid
text, January 2019


A DNA G-quadruplex/i-motif hybrid
journal, November 2019


Mechanically rigid supramolecular assemblies formed from an Fmoc-guanine conjugated peptide nucleic acid
journal, November 2019


Structure and hydrodynamics of a DNA G-quadruplex with a cytosine bulge
journal, May 2018


High-resolution DNA quadruplex structure containing all the A-, G-, C-, T-tetrads
journal, October 2018


A DNA G-quadruplex/i-motif hybrid
posted_content, August 2019