Abstract
Although many models have been developed to guide the design and implementation of DNA tile-based self-assembly systems with increasing complexity, the fundamental assumptions of the models have not been thoroughly tested. To expand the quantitative understanding of DNA tile-based self-assembly and to test the fundamental assumptions of self-assembly models, we investigated DNA tile attachment to preformed "multi-tile" arrays in real time and obtained the thermodynamic and kinetic parameters of single tile attachment in various sticky end association scenarios. With more sticky ends, tile attachment becomes more thermostable with an approximately linear decrease in the free energy change (more negative). The total binding free energy of sticky ends is partially compromised by a sequence-independent energy penalty when tile attachment forms a constrained configuration: "loop". The minimal loop is a 2 × 2 tetramer (Loop4). The energy penalty of loops of 4, 6, and 8 tiles was analyzed with the independent loop model assuming no interloop tension, which is generalizable to arbitrary tile configurations. More sticky ends also contribute to a faster on-rate under isothermal conditions when nucleation is the rate-limiting step. Incorrect sticky end contributes to neither the thermostability nor the kinetics. The thermodynamic and kinetic parameters of DNA tile attachment elucidated here will contribute to the future improvement and optimization of tile assembly modeling, precise control of experimental conditions, and structural design for error-free self-assembly.
| Original language | English |
|---|---|
| Pages (from-to) | 9370-9381 |
| Number of pages | 12 |
| Journal | ACS Nano |
| Volume | 11 |
| Issue number | 9 |
| DOIs | |
| Publication status | Published - Sep 26 2017 |
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Keywords
- DNA nanotechnology
- double-crossover tile
- kinetics
- self-assembly
- thermodynamics
ASJC Scopus subject areas
- Materials Science(all)
- Engineering(all)
- Physics and Astronomy(all)
Cite this
Understanding the Elementary Steps in DNA Tile-Based Self-Assembly. / Jiang, Shuoxing; Hong, Fan; Hu, Huiyu; Yan, Hao; Liu, Yan.
In: ACS Nano, Vol. 11, No. 9, 26.09.2017, p. 9370-9381.Research output: Contribution to journal › Article
}
TY - JOUR
T1 - Understanding the Elementary Steps in DNA Tile-Based Self-Assembly
AU - Jiang, Shuoxing
AU - Hong, Fan
AU - Hu, Huiyu
AU - Yan, Hao
AU - Liu, Yan
PY - 2017/9/26
Y1 - 2017/9/26
N2 - Although many models have been developed to guide the design and implementation of DNA tile-based self-assembly systems with increasing complexity, the fundamental assumptions of the models have not been thoroughly tested. To expand the quantitative understanding of DNA tile-based self-assembly and to test the fundamental assumptions of self-assembly models, we investigated DNA tile attachment to preformed "multi-tile" arrays in real time and obtained the thermodynamic and kinetic parameters of single tile attachment in various sticky end association scenarios. With more sticky ends, tile attachment becomes more thermostable with an approximately linear decrease in the free energy change (more negative). The total binding free energy of sticky ends is partially compromised by a sequence-independent energy penalty when tile attachment forms a constrained configuration: "loop". The minimal loop is a 2 × 2 tetramer (Loop4). The energy penalty of loops of 4, 6, and 8 tiles was analyzed with the independent loop model assuming no interloop tension, which is generalizable to arbitrary tile configurations. More sticky ends also contribute to a faster on-rate under isothermal conditions when nucleation is the rate-limiting step. Incorrect sticky end contributes to neither the thermostability nor the kinetics. The thermodynamic and kinetic parameters of DNA tile attachment elucidated here will contribute to the future improvement and optimization of tile assembly modeling, precise control of experimental conditions, and structural design for error-free self-assembly.
AB - Although many models have been developed to guide the design and implementation of DNA tile-based self-assembly systems with increasing complexity, the fundamental assumptions of the models have not been thoroughly tested. To expand the quantitative understanding of DNA tile-based self-assembly and to test the fundamental assumptions of self-assembly models, we investigated DNA tile attachment to preformed "multi-tile" arrays in real time and obtained the thermodynamic and kinetic parameters of single tile attachment in various sticky end association scenarios. With more sticky ends, tile attachment becomes more thermostable with an approximately linear decrease in the free energy change (more negative). The total binding free energy of sticky ends is partially compromised by a sequence-independent energy penalty when tile attachment forms a constrained configuration: "loop". The minimal loop is a 2 × 2 tetramer (Loop4). The energy penalty of loops of 4, 6, and 8 tiles was analyzed with the independent loop model assuming no interloop tension, which is generalizable to arbitrary tile configurations. More sticky ends also contribute to a faster on-rate under isothermal conditions when nucleation is the rate-limiting step. Incorrect sticky end contributes to neither the thermostability nor the kinetics. The thermodynamic and kinetic parameters of DNA tile attachment elucidated here will contribute to the future improvement and optimization of tile assembly modeling, precise control of experimental conditions, and structural design for error-free self-assembly.
KW - DNA nanotechnology
KW - double-crossover tile
KW - kinetics
KW - self-assembly
KW - thermodynamics
UR - http://www.scopus.com/inward/record.url?scp=85029911977&partnerID=8YFLogxK
UR - http://www.scopus.com/inward/citedby.url?scp=85029911977&partnerID=8YFLogxK
U2 - 10.1021/acsnano.7b04845
DO - 10.1021/acsnano.7b04845
M3 - Article
C2 - 28813590
AN - SCOPUS:85029911977
VL - 11
SP - 9370
EP - 9381
JO - ACS Nano
JF - ACS Nano
SN - 1936-0851
IS - 9
ER -