DNAオリガミ設計例 (rectangle)
Learn more about the details:
https://doi.org/10.1273/cbij.18.96
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caDNAno desgin
caDNAno desgin
Rectangle (no linker model)
20 rows of duplex DNA having 352 bp length
Neighboring three lanes bound by 32 bp length staples forming a double crossover.
Designed by S. Kishi (Konagaya-lab)
Image area 2x2μm2
Observed width ~ 110-120nm, height ~ 60-70nm, thickness ~ 2nm
Typical cationic strength
Observation under deionized and TAE buffer conditions have been started.
TAE buffer contains EDTA
Taken by S. Kishi (Konagaya-lab)
A profile of normalized histograms of Zp' obtained from a MD run under normal ionic strength.
The distribution shows a strong peak initially at 0 ps, which reflects the facts that DNA origami is prepared using a canonical B-DNA atomic model.
The correlation to the initial condition becomes almost negligible after 0.6 ns of simulation time.
Analized by R. Azuma (Konagaya-lab)
Helix form analysis Comparison among different ionic strength / water permittivity
Helix form analysis Comparison among different ionic strength / water permittivity
In the presence of cations
-Sharpest peak
-Maximum centered around a peak of canonical B-DNA.
ε=1
-Broader shape with multiple humps.
-Resulting from the strain in response to the stress force applied on each strand.
ε>>1
-Exhibit similar delta shaped peaks
-Maxima are centered around the peak of canonical B-DNA.
Analized by R. Azuma (Konagaya-lab)
Size profiles of DNA origami “rectangle” in deionized water under (ε: dielectric constant = 60)
Lx : purple
Ly: green
Lz: blue
Lx(t)/Lx(0) : purple
Ly(t)/Ly(0) : green
Lz(t)/Lz(0) : blue
Analized by R. Azuma (Konagaya-lab)
Molecular Dynamics simulation in deionized water
(ε: dielectric constant = 1)
Damaged structures in top and bottom halves.
Scaffolds loose their counterpart staple strands
They exhibit arched conformations
Simulated by R. Azuma (Konagaya-lab)
Molecular Dynamics simulation in deionized water
(ε: dielectric constant = 60)
Remain undamaged while it keeps growing.
As a result, regular pattern associated with “argyle lattice” develops.
Simulated by R. Azuma (Konagaya-lab)
Molecular Dynamics simulation in explicit solvent water
[Na+]=150mM and [Mg2+]=30 mMRemain undamaged
Simulated by R. Azuma (Konagaya-lab)
CC BY 4.0
Ryuzo Azuma, Sae Kishi, Greg Gutmann, Akihiko Konagaya: All-atom molecular dynamics of film supported flat-shaped DNA origami in water, Chem-Bio Informatics Journal/Volume 18 (2018)
https://doi.org/10.1273/cbij.18.96
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