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Title: Characterizing the length-dependence of DNA nanotube end-to-end joining rates

Abstract

DNA nanotechnology provides a route towards the synthesis of custom nano-structured materials and circuits through hierarchical assembly processes. Although predictive kinetic models are being developed for the assembly of DNA nanostructures from small monomeric components, a general model for the hierarchical assembly of DNA nanostructures remains elusive. DNA tile nanotubes provide an ideal model system for the study of hierarchical assembly via end-to-end joining. In this study, we experimentally characterize the length-dependence of the end-to-end joining rate of DNA tile nanotubes. We then test the ability of three different models of polymer end-to-end joining to reproduce experimentally measured changes in nanotube lengths during a joining reaction using an ODE model for nanotube joining. All three models predict physically realistic joining rates that are consistent with prior measurements, with a length-independent end-to-end joining rate model providing the best fit to the experimental data. A length-independent constant joining rate is consistent with other DNA self-assembly processes across a broad range of length scales and also suggests how tractable models for hierarchical DNA nanostructure could be developed.

Authors:
ORCiD logo [1];  [2];  [2];  [1];  [3];  [4];  [2];  [1]
  1. Johns Hopkins Univ., Baltimore, MD (United States)
  2. Univ. of California, Los Angeles, CA (United States)
  3. Baltimore Polytechnic Inst., Baltimore, MD (United States)
  4. Ultivue, Cambridge, MA (United States)
Publication Date:
Research Org.:
Univ. of California, Riverside, CA (United States)
Sponsoring Org.:
USDOE Office of Science (SC), Basic Energy Sciences (BES) (SC-22)
OSTI Identifier:
1595293
Grant/Contract Number:  
SC0010595
Resource Type:
Accepted Manuscript
Journal Name:
Molecular Systems Design & Engineering
Additional Journal Information:
Journal Name: Molecular Systems Design & Engineering; Journal ID: ISSN 2058-9689
Publisher:
Royal Society of Chemistry
Country of Publication:
United States
Language:
English

Citation Formats

Pacella, Michael S., Mardanlou, Vahid, Agarwal, Siddharth, Patel, Anusha, Jelezniakov, Elizabeth, Mohammed, Abdul M., Franco, Elisa, and Schulman, Rebecca. Characterizing the length-dependence of DNA nanotube end-to-end joining rates. United States: N. p., 2019. Web. doi:10.1039/C9ME00068B.
Pacella, Michael S., Mardanlou, Vahid, Agarwal, Siddharth, Patel, Anusha, Jelezniakov, Elizabeth, Mohammed, Abdul M., Franco, Elisa, & Schulman, Rebecca. Characterizing the length-dependence of DNA nanotube end-to-end joining rates. United States. doi:10.1039/C9ME00068B.
Pacella, Michael S., Mardanlou, Vahid, Agarwal, Siddharth, Patel, Anusha, Jelezniakov, Elizabeth, Mohammed, Abdul M., Franco, Elisa, and Schulman, Rebecca. Wed . "Characterizing the length-dependence of DNA nanotube end-to-end joining rates". United States. doi:10.1039/C9ME00068B.
@article{osti_1595293,
title = {Characterizing the length-dependence of DNA nanotube end-to-end joining rates},
author = {Pacella, Michael S. and Mardanlou, Vahid and Agarwal, Siddharth and Patel, Anusha and Jelezniakov, Elizabeth and Mohammed, Abdul M. and Franco, Elisa and Schulman, Rebecca},
abstractNote = {DNA nanotechnology provides a route towards the synthesis of custom nano-structured materials and circuits through hierarchical assembly processes. Although predictive kinetic models are being developed for the assembly of DNA nanostructures from small monomeric components, a general model for the hierarchical assembly of DNA nanostructures remains elusive. DNA tile nanotubes provide an ideal model system for the study of hierarchical assembly via end-to-end joining. In this study, we experimentally characterize the length-dependence of the end-to-end joining rate of DNA tile nanotubes. We then test the ability of three different models of polymer end-to-end joining to reproduce experimentally measured changes in nanotube lengths during a joining reaction using an ODE model for nanotube joining. All three models predict physically realistic joining rates that are consistent with prior measurements, with a length-independent end-to-end joining rate model providing the best fit to the experimental data. A length-independent constant joining rate is consistent with other DNA self-assembly processes across a broad range of length scales and also suggests how tractable models for hierarchical DNA nanostructure could be developed.},
doi = {10.1039/C9ME00068B},
journal = {Molecular Systems Design & Engineering},
number = ,
volume = ,
place = {United States},
year = {2019},
month = {12}
}

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