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Title: Tuning the Cavity Size and Chirality of Self-Assembling 3D DNA Crystals

Abstract

The foundational goal of structural DNA nanotechnology—the field that uses oligonucleotides as a molecular building block for the programmable self-assembly of nanostructured systems—was to use DNA to construct three-dimensional (3D) lattices for solving macromolecular structures. The programmable nature of DNA makes it an ideal system for rationally constructing self-assembled crystals and immobilizing guest molecules in a repeating 3D array through their specific stereospatial interactions with the scaffold. In this work, we have extended a previously described motif (4 × 5) by expanding the structure to a system that links four double-helical layers; we use a central weaving oligonucleotide containing a sequence of four six-base repeats (4 × 6), forming a matrix of layers that are organized and dictated by a series of Holliday junctions. In addition, we have assembled mirror image crystals (l-DNA) with the identical sequence that are completely resistant to nucleases. Bromine and selenium derivatives were obtained for the l- and d-DNA forms, respectively, allowing phase determination for both forms and solution of the resulting structures to 3.0 and 3.05 Å resolution. Both right- and left-handed forms crystallized in the trigonal space groups with mirror image 3-fold helical screw axes P32 and P31 for each motif, respectively. Themore » structures reveal a highly organized array of discrete and well-defined cavities that are suitable for hosting guest molecules and allow us to dictate a priori the assembly of guest–DNA conjugates with a specified crystalline hand.« less

Authors:
; ; ; ; ; ;  [1]; ORCiD logo
  1. Department of Chemistry, New York University, New York, New York 10003, United States
Publication Date:
Research Org.:
Argonne National Lab. (ANL), Argonne, IL (United States). Advanced Photon Source (APS)
Sponsoring Org.:
National Institutes of Health (NIH)
OSTI Identifier:
1377917
Resource Type:
Journal Article
Resource Relation:
Journal Name: Journal of the American Chemical Society; Journal Volume: 139; Journal Issue: 32
Country of Publication:
United States
Language:
ENGLISH
Subject:
59 BASIC BIOLOGICAL SCIENCES; 37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CHEMISTRY

Citation Formats

Simmons, Chad R., Zhang, Fei, MacCulloch, Tara, Fahmi, Noureddine, Stephanopoulos, Nicholas, Liu, Yan, Seeman, Nadrian C., and Yan, Hao. Tuning the Cavity Size and Chirality of Self-Assembling 3D DNA Crystals. United States: N. p., 2017. Web. doi:10.1021/jacs.7b06485.
Simmons, Chad R., Zhang, Fei, MacCulloch, Tara, Fahmi, Noureddine, Stephanopoulos, Nicholas, Liu, Yan, Seeman, Nadrian C., & Yan, Hao. Tuning the Cavity Size and Chirality of Self-Assembling 3D DNA Crystals. United States. doi:10.1021/jacs.7b06485.
Simmons, Chad R., Zhang, Fei, MacCulloch, Tara, Fahmi, Noureddine, Stephanopoulos, Nicholas, Liu, Yan, Seeman, Nadrian C., and Yan, Hao. Wed . "Tuning the Cavity Size and Chirality of Self-Assembling 3D DNA Crystals". United States. doi:10.1021/jacs.7b06485.
@article{osti_1377917,
title = {Tuning the Cavity Size and Chirality of Self-Assembling 3D DNA Crystals},
author = {Simmons, Chad R. and Zhang, Fei and MacCulloch, Tara and Fahmi, Noureddine and Stephanopoulos, Nicholas and Liu, Yan and Seeman, Nadrian C. and Yan, Hao},
abstractNote = {The foundational goal of structural DNA nanotechnology—the field that uses oligonucleotides as a molecular building block for the programmable self-assembly of nanostructured systems—was to use DNA to construct three-dimensional (3D) lattices for solving macromolecular structures. The programmable nature of DNA makes it an ideal system for rationally constructing self-assembled crystals and immobilizing guest molecules in a repeating 3D array through their specific stereospatial interactions with the scaffold. In this work, we have extended a previously described motif (4 × 5) by expanding the structure to a system that links four double-helical layers; we use a central weaving oligonucleotide containing a sequence of four six-base repeats (4 × 6), forming a matrix of layers that are organized and dictated by a series of Holliday junctions. In addition, we have assembled mirror image crystals (l-DNA) with the identical sequence that are completely resistant to nucleases. Bromine and selenium derivatives were obtained for the l- and d-DNA forms, respectively, allowing phase determination for both forms and solution of the resulting structures to 3.0 and 3.05 Å resolution. Both right- and left-handed forms crystallized in the trigonal space groups with mirror image 3-fold helical screw axes P32 and P31 for each motif, respectively. The structures reveal a highly organized array of discrete and well-defined cavities that are suitable for hosting guest molecules and allow us to dictate a priori the assembly of guest–DNA conjugates with a specified crystalline hand.},
doi = {10.1021/jacs.7b06485},
journal = {Journal of the American Chemical Society},
number = 32,
volume = 139,
place = {United States},
year = {Wed Aug 02 00:00:00 EDT 2017},
month = {Wed Aug 02 00:00:00 EDT 2017}
}