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Title: An intercalation-locked parallel-stranded DNA tetraplex

Abstract

DNA has proved to be an excellent material for nanoscale construction because complementary DNA duplexes are programmable and structurally predictable. However, in the absence of Watson–Crick pairings, DNA can be structurally more diverse. Here, we describe the crystal structures of d(ACTCGGATGAT) and the brominated derivative, d(ACBrUCGGABrUGAT). These oligonucleotides form parallel-stranded duplexes with a crystallographically equivalent strand, resulting in the first examples of DNA crystal structures that contains four different symmetric homo base pairs. Two of the parallel-stranded duplexes are coaxially stacked in opposite directions and locked together to form a tetraplex through intercalation of the 5'-most A–A base pairs between adjacent G–G pairs in the partner duplex. The intercalation region is a new type of DNA tertiary structural motif with similarities to the i-motif. 1H–1H nuclear magnetic resonance and native gel electrophoresis confirmed the formation of a parallel-stranded duplex in solution. Finally, we modified specific nucleotide positions and added d(GAY) motifs to oligonucleotides and were readily able to obtain similar crystals. This suggests that this parallel-stranded DNA structure may be useful in the rational design of DNA crystals and nanostructures.

Authors:
; ;
Publication Date:
Research Org.:
Argonne National Laboratory (ANL), Argonne, IL (United States). Advanced Photon Source (APS)
Sponsoring Org.:
USDOE Office of Science (SC), Basic Energy Sciences (BES); National Science Foundation (NSF)
OSTI Identifier:
1171850
Resource Type:
Accepted Manuscript
Journal Name:
Nucleic Acids Research
Additional Journal Information:
Journal Volume: 43; Journal Issue: 3; Journal ID: ISSN 0305-1048
Publisher:
Oxford University Press
Country of Publication:
United States
Language:
English

Citation Formats

Tripathi, S., Zhang, D., and Paukstelis, P. J. An intercalation-locked parallel-stranded DNA tetraplex. United States: N. p., 2015. Web. doi:10.1093/nar/gkv033.
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Tripathi, S., Zhang, D., & Paukstelis, P. J. An intercalation-locked parallel-stranded DNA tetraplex. United States. https://doi.org/10.1093/nar/gkv033
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Tripathi, S., Zhang, D., and Paukstelis, P. J. Tue . "An intercalation-locked parallel-stranded DNA tetraplex". United States. https://doi.org/10.1093/nar/gkv033. https://www.osti.gov/servlets/purl/1171850.
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@article{osti_1171850,
title = {An intercalation-locked parallel-stranded DNA tetraplex},
author = {Tripathi, S. and Zhang, D. and Paukstelis, P. J.},
abstractNote = {DNA has proved to be an excellent material for nanoscale construction because complementary DNA duplexes are programmable and structurally predictable. However, in the absence of Watson–Crick pairings, DNA can be structurally more diverse. Here, we describe the crystal structures of d(ACTCGGATGAT) and the brominated derivative, d(ACBrUCGGABrUGAT). These oligonucleotides form parallel-stranded duplexes with a crystallographically equivalent strand, resulting in the first examples of DNA crystal structures that contains four different symmetric homo base pairs. Two of the parallel-stranded duplexes are coaxially stacked in opposite directions and locked together to form a tetraplex through intercalation of the 5'-most A–A base pairs between adjacent G–G pairs in the partner duplex. The intercalation region is a new type of DNA tertiary structural motif with similarities to the i-motif. 1H–1H nuclear magnetic resonance and native gel electrophoresis confirmed the formation of a parallel-stranded duplex in solution. Finally, we modified specific nucleotide positions and added d(GAY) motifs to oligonucleotides and were readily able to obtain similar crystals. This suggests that this parallel-stranded DNA structure may be useful in the rational design of DNA crystals and nanostructures.},
doi = {10.1093/nar/gkv033},
journal = {Nucleic Acids Research},
number = 3,
volume = 43,
place = {United States},
year = {Tue Jan 27 00:00:00 EST 2015},
month = {Tue Jan 27 00:00:00 EST 2015}
}
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https://doi.org/10.1093/nar/gkv033
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Folding DNA to create nanoscale shapes and patterns
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  • Zheng, Jianping; Birktoft, Jens J.; Chen, Yi
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DNA nanotubes self-assembled from triple-crossover tiles as templates for conductive nanowires
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journal, February 2006

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Circuits and programmable self-assembling DNA structures
journal, September 2002

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5'-CGA sequence is a strong motif for homo base-paired parallel-stranded DNA duplex as revealed by NMR analysis.
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Crystal structure of the complementary quadruplex formed by d(GCATGCT) at atomic resolution
journal, February 2003

The poly dA helix: a new structural motif for high performance DNA-based molecular switches
journal, March 2009

  • Chakraborty, Saikat; Sharma, Suruchi; Maiti, Prabal K.
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X-ray structure of d(CGAA), parallel-stranded DNA duplex with homo base pairs
journal, November 2002

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DNA-Templated Self-Assembly of Protein Arrays and Highly Conductive Nanowires
journal, September 2003

Rapid Chiral Assembly of Rigid DNA Building Blocks for Molecular Nanofabrication
journal, December 2005

Programming DNA Tube Circumferences
journal, August 2008

DNA Origami with Complex Curvatures in Three-Dimensional Space
journal, April 2011

The anatomy of A-, B-, and Z-DNA
journal, April 1982

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