TY - JOUR
T1 - Ethanol-Induced Condensation and Decondensation in DNA-Linked Nanoparticles
T2 - A Nucleosome-like Model for the Condensed State
AU - Xiong, Qinsi
AU - Lee, One Sun
AU - Mirkin, Chad A.
AU - Schatz, George
N1 - Funding Information:
This work was supported by the Center for Bio-Inspired Energy Science (CBES), an Energy Frontier Research Center funded by the U.S. Department of Energy (DOE) Office of Basic Energy Sciences (DE-SC0000989). We thank Nikhil Chellam for helpful discussions.
Publisher Copyright:
© 2022 American Chemical Society.
PY - 2023/1/11
Y1 - 2023/1/11
N2 - Inspired by the conventional use of ethanol to induce DNA precipitation, ethanol condensation has been applied as a routine method to dynamically tune "bond"lengths (i.e., the surface-to-surface distances between adjacent nanoparticles that are linked by DNA) and thermal stabilities of colloidal crystals involving DNA-linked nanoparticles. However, the underlying mechanism of how the DNA bond that links gold nanoparticles changes in this class of colloidal crystals in response to ethanol remains unclear. Here, we conducted a series of all-atom molecular dynamic (MD) simulations to explore the free energy landscape for DNA condensation and decondensation. Our simulations confirm that DNA condensation is energetically much more favorable under 80% ethanol conditions than in pure water, as a result of ethanol's role in enhancing electrostatic interactions between oppositely charged species. Moreover, the condensed DNA adopts B-form in pure water and A-form in 80% ethanol, which indicates that the higher-order transition does not affect DNA's conformational preferences. We further propose a nucleosome-like supercoiled model for the DNA condensed state, and we show that the DNA end-to-end distance derived from this model matches the experimentally measured DNA bond length of about 3 nm in the fully condensed state for DNA where the measured length is 16 nm in water. Overall, this study provides an atomistic understanding of the mechanism underlying ethanol-induced condensation and water-induced decondensation, while our proposed nucleosome-like model allows the design of new strategies for interpreting experimental studies of DNA condensation.
AB - Inspired by the conventional use of ethanol to induce DNA precipitation, ethanol condensation has been applied as a routine method to dynamically tune "bond"lengths (i.e., the surface-to-surface distances between adjacent nanoparticles that are linked by DNA) and thermal stabilities of colloidal crystals involving DNA-linked nanoparticles. However, the underlying mechanism of how the DNA bond that links gold nanoparticles changes in this class of colloidal crystals in response to ethanol remains unclear. Here, we conducted a series of all-atom molecular dynamic (MD) simulations to explore the free energy landscape for DNA condensation and decondensation. Our simulations confirm that DNA condensation is energetically much more favorable under 80% ethanol conditions than in pure water, as a result of ethanol's role in enhancing electrostatic interactions between oppositely charged species. Moreover, the condensed DNA adopts B-form in pure water and A-form in 80% ethanol, which indicates that the higher-order transition does not affect DNA's conformational preferences. We further propose a nucleosome-like supercoiled model for the DNA condensed state, and we show that the DNA end-to-end distance derived from this model matches the experimentally measured DNA bond length of about 3 nm in the fully condensed state for DNA where the measured length is 16 nm in water. Overall, this study provides an atomistic understanding of the mechanism underlying ethanol-induced condensation and water-induced decondensation, while our proposed nucleosome-like model allows the design of new strategies for interpreting experimental studies of DNA condensation.
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U2 - 10.1021/jacs.2c11834
DO - 10.1021/jacs.2c11834
M3 - Article
C2 - 36573457
AN - SCOPUS:85145331773
SN - 0002-7863
VL - 145
SP - 706
EP - 716
JO - Journal of the American Chemical Society
JF - Journal of the American Chemical Society
IS - 1
ER -