Origami conductivity and structural stability

1. The ionic conductivity
and structural stability
of DNA origami
Chen-Yu Li
2014/7/7

2. 2
Content
Introduction
Results:
(1) DNA origami expands under electric field
(2) [Mg2+] dependence of conductivity
(3) Voltage dependence of conductivity
Summary

3. 3
22
= =
z
x
y
i
i
ii
i
ii
ii
iii
iii
i ii iii i ii
a b
dc
ure 1 | Design of three-dimensional DNA origami. a, Double helices
mprised of scaffold (grey) and staple strands (orange, white, blue) run
rallel to the z-axis to form an unrolled two-dimensional schematic of the
get shape. Phosphate linkages form crossovers between adjacent helices,
h staple crossovers bridging different layers shown as semicircular arcs.
Cylinder model of a half-rolled conceptual intermediate. Cylinders
represent double helices, with loops of unpaired scaffold strand linking the
ends of adjacent helices. c, Cylinder model of folded target shape. The
honeycomb arrangement of parallel helices is shown in cross-sectional slices
(i–iii) parallel to the x–y plane, spaced apart at seven base-pair intervals that
repeat every 21 base pairs. All potential staple crossovers are shown for each
cross-section. d, Atomistic DNA model of shape from c.
ATURE|Vol 459|21 May 2009 LETTERS
© 2006 Nature Publishing Group
Conceptually, the second step (illustrated in Fig. 1b) proceeds by
folding a single long scaffold strand (900 nucleotides (nt) in Fig. 1b)
back and forth in a raster fill pattern so that it comprises one of the
two strands in every helix; progression of the scaffold from one helix
to another creates an additional set of crossovers, the ‘scaffold
crossovers’ (indicated by small red crosses in Fig. 1b). The funda-
mental constraint on a folding path is that the scaffold can form a
crossover only at those locations where the DNA twist places it at a
are represented as lists of DNA lengths and offsets in units of half-
turns. These lists, along with the DNA sequence of the actual scaffold
to be used, are input to a computer program. Rather than assuming
10.5 base pairs (bp) per turn (which corresponds to standard B-DNA
twist), the program uses an integer number of bases between periodic
crossovers (for example, 16 bp for 1.5 turns). It then performs the
third step, the design of a set of ‘staple strands’ (the coloured DNA
strands in Fig. 1c) that provide Watson–Crick complements for the
Figure 1 | Design of DNA origami. a, A shape (red) approximated by parallel
double helices joined by periodic crossovers (blue). b, A scaffold (black) runs
through every helix and forms more crossovers (red). c, As first designed,
most staples bind two helices and are 16-mers. d, Similar to c with strands
drawn as helices. Red triangles point to scaffold crossovers, black triangles to
periodic crossovers with minor grooves on the top face of the shape, blue
triangles to periodic crossovers with minor grooves on bottom. Cross-
sections of crossovers (1, 2, viewed from left) indicate backbone positions
with coloured lines, and major/minor grooves by large/small angles between
them. Arrows in c point to nicks sealed to create green strands in d. Yellow
diamonds in c and d indicate a position at which staples may be cut and
resealed to bridge the seam. e, A finished design after merges and
rearrangements along the seam. Most staples are 32-mers spanning three
helices. Insets show a dumbbell hairpin (d) and a 4-T loop (e), modifications
used in Fig. 3.
298
DNA origami
Rothemund, P.W., 2006, Folding DNA to create nanoscale shapes and patterns, Nature, 440(7082), pp. 297-302.
Douglas, S.M., Dietz, H., Liedl, T., Högberg, B., Graf, F. & Shih, W.M., 2009, Self-assembly of DNA into nanoscale three-dimensional shapes, Nature, 459(7245), pp. 414-8.
Scaffold: long ssDNA
Staple: short (17~50 bp) ssDNA,
connecting different parts.

4. The hybrid nanopore
4
5nm
~15 nm
K
+ Cl
-K
+
K
+
K
+ K
+
K
+
K
+K
+
K
+ Cl
-
Cl
- Cl
-Cl
-
Cl
-
Cl
-
Ea
→~20 nm
b
10nm10nm
~20 nm
1 M KCl
~5 nm
Advantage:
1. better pore size control
2. modification around the pore
Disadvantage:
1. leakage
2. structurally more dynamic

5. 5
Content
Introduction
Results:
(1) DNA origami expands under electric field
(2) [Mg2+] dependence of conductivity
(3) Voltage dependence of conductivity
Summary

6. Build a DNA origami system
6
(2) Introduce Mg2+ ion to
neutralize the DNA
(3) Add water by VMD
solvate plugin
(4) Add 1MKCl by VMD
autoionize plugin
(1) Design the origami form
caDNAno, make pdb file by
cadnano2pdb[1], and make
scaffold periodic
X
Y
Z
[1]Yoo, Jejoong, and Aleksei Aksimentiev. "In situ structure and dynamics of DNA origami determined through molecular dynamics simulations." Proc Natl Acad Sci USA
110, no. 50 (2013): 20099-104. DOI: 10.1073/pnas.1316521110

7. 7
Ion movement under electric field
E
K+ Cl-
Orchard: K+; Cyan: Cl-; Pink:Mg2+

8. D
*
(c)(b)(a)
E
D
8
Nano accordion
HX2* HC2 SQ2
D
*
(c)(b)(a)
E
D

9. 9
Content
Introduction
Results:
(1) DNA origami expands under electric field
(2) [Mg2+] dependence of conductivity
(3) Voltage dependence of conductivity
Summary

10. 10
0mM [Mg2+] 131mM [Mg2+] 246mM [Mg2+]
526453655883Area(angstrom2) =
[Mg2+] affects Conductivity by changing area

11. 11
[MgCl2]
=
V
?
Experimental results

12. 12
Content
Introduction
Results:
(1) DNA origami expands under electric field
(2) [Mg2+] dependence of conductivity
(3) Voltage dependence of conductivity
Summary

13. 13
V V
VS
SMD constrain
The contradiction may result from system setup

14. 14
(a)
(b)
(e)
(c)
equilibrated 5 ns 100 nsE
(f)
(d)
X
Z
Y
0.3 5.5 mM MgCl2
(g)
Einitial setup
H
The (SQ2 + SiO2) hybrid system

15. 15
(a)
(b)
(e)
(c)
equilibrated 5 ns 100 nsE
(f)
(d)
X
Z
Y
0.3 5.5 mM MgCl2
(g)
Einitial setup
H
(b)
(e)
(c)
(f)
(d)
X
Z
Y
300 400 500
0.1
0.2
0.3 5.5 mM MgCl2
25 mM MgCl2
50 mM MgCl2
100 mM MgCl2
G
Voltage (mV)
(g)
H
5 ns 100 nsE
(d)
0.3 5.5 mM MgCl2
(g)
E
The results are consistent with experiment

16. 16
Content
Introduction
Results:
(1) DNA origami expands under electric field
(2) [Mg2+] dependence of conductivity
(3) Voltage dependence of conductivity
Summary

17. 17
Summary
(1) DNA origami would expand under electric field.
!
(2) The conductivity of DNA origami would be affected
by ion concentration, voltage and other factors.