Thermodynamics and Kinetics of DNA Tile Binding During the Nucleation Process of DNA Self-Assembly
Fan Hong#, Shuoxing Jiang, Hao Yan*, Yan Liu*
Center for Molecular Design and Biomimetics, The Biodesign Institute, and Department of Chemistry and Biochemistry, Arizona State University,
Tempe, Arizona 85287, United States
#Poster Presenter(PhD student): fhong5@asu.edu *Corresponding authors: Hao.Yan@asu.edu, yan_liu@asu.edu.
Abstract
Thermodynamic Study
Table 2. Arrhenius fitting results.
• DX (double crossover) DNA tile is the most widely used building block for
2D array formation, nanotube engineering, and algorithmic self-assembly.
The versatilities of DX tiles predominantly rely on the thermodynamic and
kinetic control of binding during the assembly process.
• Fluorescence dye is introduced to preformed DNA structure to monitor
binding process in real time and thermodynamic and kinetic parameters are
obtained for 4 kinds of binding scenarios during the nucleation process of
DNA self-assembly.
• DX tile binding behaves differently in thermodynamics and kinetics among
4 kinds of scenarios, even with the same number of sticky ends due to the
different geometric arrangement.
• The relative rates of nucleation process in different directions affects the
circumference of DNA nanotubes.
ln(A)
Ea (kcal/mol)
2B-S
38.5±0.5
13.8±0.3
2B-L
25.5±0.7
6.9±0.4
3B
32.1±0.4
10.2±0.2
4B
36.4±0.6
12.4±0.4
Figure 5. Arrhenius plot of DX tile binding in all scenarios in this study. Rate
constants were measured at 5 different temperatures.
The Relative rates of Nucleation Process Affects the
Circumference of DNA Nanotube
The Nucleation Process of DX Tile Self-Assembly
Figure 3. Illustration of a typical FRET data processing for DX binding of 2BL scenario. θ, normalized FRET efficiency.
Figure 6. The nucleation
process
controls
DNA
nanotube formation. (A) The
scheme of DNA nanotube
formation process. (B-C)
AFM images of opened
nanotubes that are 10 and 6
tiles
in
circumference
respectively. The scale bars
are
50
nm.
(D)
Circumference distribution of
DNA nanotubes formed at 20,
24, 28°C. As the assembly
temperature increases, the
main circumference of the
formed tubes increases as
well.
Table 1. Melting temperature and thermodynamic data of DX tile binding
at all 4 scenarios.
W/2 (°C) ΔH (kcal/mol) ΔS (kcal/mol*K) TΔS (kcal/mol)
ΔG (25 oC)
(kcal/mol)
2B-S 28.2±0.1 28.3±0.1
4.0±0.1
-92.1±3.6
-0.272±0.012
-81.0±3.6
-11.1±0.1
2B-L 32.9±0.1 32.9±0.1
4.3±0.1
-108.8±0.8
-0.321±0.003
-95.7±0.8
-13.0±0.1
3B
37.8±0.1 37.9±0.1
3.7±0.2
-110.8±4.6
-0.323±0.015
-96.3±4.5
-14.5±0.1
4B
40.6±0.1 40.7±0.1
3.0±0.1
-124.6±10.7
-0.364±0.034
-108.5±10.2
-16.1±0.5
Tm (°C)
Figure 1. The nucleation process of DX tile self-assembly and DNA helix
model of favorable binding steps in this study. The green dots and red five star
indicate 6-FAM and TAMRA modification, respectively
AFM Characterization
Tf (°C)
Kinetic Study
References
Figure 2. The morphology observations of the multi-tile intermediates before
and after DX tile binding by AFM. All the scale bars are 20 nm.
Figure 4. A) Kinetic measurements and non-linear fitting. B) The rate
constants of 2B-S and 2B-L binding.
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Acknowledgement:
This work was supported by grants from the Army Research Office, Office of Naval Research
and National Science Foundation to Y.L. and H.Y.