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Title: Designing Higher Resolution Self-Assembled 3D DNA Crystals via Strand Terminus Modifications

Abstract

DNA tensegrity triangles self-assemble into rhombohedral three-dimensional crystals via sticky ended cohesion. Crystals containing two-nucleotide (nt) sticky ends (GA:TC) have been reported previously, and those crystals diffracted to 4.9 Å at beam line NSLS-I-X25. Here, we analyze the effect of varying sticky end lengths and sequences, as well as the impact of 5’- and 3’-phosphates on crystal formation and resolution. Tensegrity triangle motifs having 1-, 2- and 3-nt sticky ends all form crystals. X-ray diffraction data from the same beam line reveal that the crystal resolution for a 1-nt sticky end (G:C) and a 3-nt sticky end (GAT:ATC) were 3.4 Å and 4.2 Å respectively. Resolutions were determined from complete data sets in each case. We also conducted trials that examined every possible combination of 1-nucleotide and 2-nucleotide sticky-ended phosphorylated strands and successfully crystallized all 16 possible combinations of strands. We observed the position of the 5’-phosphate on either the crossover (1), helical (2), or central strand (3) affected the resolution of the self-assembled crystals for the 2-turn monomer (3.0 Å for 1-2P-3P) and 2-turn dimer sticky ended (4.1 Å for 1-2-3P) systems. Here, we have also examined the impact of the identity of the base flanking the sticky ends,more » as well as the use of 3'-sticky ends. We conclude that crystal resolution is not a simple consequence of the thermodynamics of the direct nucleotide pairing interactions involved in molecular cohesion in this system.« less

Authors:
 [1];  [1]; ORCiD logo [1];  [1];  [1];  [1];  [1]; ORCiD logo [1];  [1]; ORCiD logo [2];  [1];  [3]; ORCiD logo [4]; ORCiD logo [1]
  1. New York Univ., New York, NY (United States)
  2. St. John’s Univ., New York, NY (United States)
  3. Argonne National Lab. (ANL), Argonne, IL (United States)
  4. Purdue Univ., West Lafayette, IN (United States)
Publication Date:
Research Org.:
New York Univ., New York, NY (United States)
Sponsoring Org.:
USDOE
OSTI Identifier:
1532763
Grant/Contract Number:  
SC0007991
Resource Type:
Accepted Manuscript
Journal Name:
ACS Nano
Additional Journal Information:
Journal Name: ACS Nano; Journal ID: ISSN 1936-0851
Publisher:
American Chemical Society (ACS)
Country of Publication:
United States
Language:
English
Subject:
DNA crystals; self-assembly; crystalline order optimization; sticky ends; terminal phosphates

Citation Formats

Ohayon, Yoel P., Hernandez, Carina, Chandrasekaran, Arun Richard, Wang, Xinyu, Abdallah, Hatem O., Jong, Michael Alexander, Mohsen, Michael G., Sha, Ruojie, Birktoft, Jens J., Lukeman, Philip S., Chaikin, Paul M., Ginell, Stephen L., Mao, Chengde, and Seeman, Nadrian C. Designing Higher Resolution Self-Assembled 3D DNA Crystals via Strand Terminus Modifications. United States: N. p., 2019. Web. doi:10.1021/acsnano.9b02430.
Ohayon, Yoel P., Hernandez, Carina, Chandrasekaran, Arun Richard, Wang, Xinyu, Abdallah, Hatem O., Jong, Michael Alexander, Mohsen, Michael G., Sha, Ruojie, Birktoft, Jens J., Lukeman, Philip S., Chaikin, Paul M., Ginell, Stephen L., Mao, Chengde, & Seeman, Nadrian C. Designing Higher Resolution Self-Assembled 3D DNA Crystals via Strand Terminus Modifications. United States. doi:10.1021/acsnano.9b02430.
Ohayon, Yoel P., Hernandez, Carina, Chandrasekaran, Arun Richard, Wang, Xinyu, Abdallah, Hatem O., Jong, Michael Alexander, Mohsen, Michael G., Sha, Ruojie, Birktoft, Jens J., Lukeman, Philip S., Chaikin, Paul M., Ginell, Stephen L., Mao, Chengde, and Seeman, Nadrian C. Tue . "Designing Higher Resolution Self-Assembled 3D DNA Crystals via Strand Terminus Modifications". United States. doi:10.1021/acsnano.9b02430.
@article{osti_1532763,
title = {Designing Higher Resolution Self-Assembled 3D DNA Crystals via Strand Terminus Modifications},
author = {Ohayon, Yoel P. and Hernandez, Carina and Chandrasekaran, Arun Richard and Wang, Xinyu and Abdallah, Hatem O. and Jong, Michael Alexander and Mohsen, Michael G. and Sha, Ruojie and Birktoft, Jens J. and Lukeman, Philip S. and Chaikin, Paul M. and Ginell, Stephen L. and Mao, Chengde and Seeman, Nadrian C.},
abstractNote = {DNA tensegrity triangles self-assemble into rhombohedral three-dimensional crystals via sticky ended cohesion. Crystals containing two-nucleotide (nt) sticky ends (GA:TC) have been reported previously, and those crystals diffracted to 4.9 Å at beam line NSLS-I-X25. Here, we analyze the effect of varying sticky end lengths and sequences, as well as the impact of 5’- and 3’-phosphates on crystal formation and resolution. Tensegrity triangle motifs having 1-, 2- and 3-nt sticky ends all form crystals. X-ray diffraction data from the same beam line reveal that the crystal resolution for a 1-nt sticky end (G:C) and a 3-nt sticky end (GAT:ATC) were 3.4 Å and 4.2 Å respectively. Resolutions were determined from complete data sets in each case. We also conducted trials that examined every possible combination of 1-nucleotide and 2-nucleotide sticky-ended phosphorylated strands and successfully crystallized all 16 possible combinations of strands. We observed the position of the 5’-phosphate on either the crossover (1), helical (2), or central strand (3) affected the resolution of the self-assembled crystals for the 2-turn monomer (3.0 Å for 1-2P-3P) and 2-turn dimer sticky ended (4.1 Å for 1-2-3P) systems. Here, we have also examined the impact of the identity of the base flanking the sticky ends, as well as the use of 3'-sticky ends. We conclude that crystal resolution is not a simple consequence of the thermodynamics of the direct nucleotide pairing interactions involved in molecular cohesion in this system.},
doi = {10.1021/acsnano.9b02430},
journal = {ACS Nano},
number = ,
volume = ,
place = {United States},
year = {2019},
month = {6}
}

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This content will become publicly available on June 25, 2020
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