Molecular Dynamics of DNA Origami Aleksei Aksimentiev, Physics - - PowerPoint PPT Presentation

Molecular Dynamics of DNA Origami

Aleksei Aksimentiev, Physics University of Illinois at Urbana-Champaign

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DNA origami

Han, Dongran et al., Science, 2011, 332 (6027), 342-346. Marras, Alexander E. et al., Proc. Natl. Acad. Sci. USA, 2015, 112 (3) 713-718 Gerling, Thomas et al., Science, 2015, 347 (6229), 1446-1452.

Scaffold: long ssDNA Staple: short (17~50 bp) ssDNA, connecting different parts.

Video credit: Shawn Douglas

Design ¡and ¡ ¡characterization ¡of ¡DNA ¡ nanostructures

= = z x y i i ii i ii ii iii iii i ii iii i ii

a b d c

Computer-aided design of DNA origami with caDNAno (Shih group, Harvard U.)

c b a

Transmission electron microscopy and/or atomic force microscopy validates the design Cryo-EM reconstruction, the

• nly experimentally

derived structural model caDNAno

All-atom molecular dynamics simulations

• f DNA nanostructures

Massive parallel computer Blue Waters (UIUC): ~200,000 CPUs Atoms move according to ¡ classical mechanics (F= ma)

Interaction between atoms is ¡ defined by molecular force field Time scale: ~ 0.1-100 µs Length scale: 10K - 100M ¡atoms or (< 50 nm)3 Time resolution: 2 fs Spacial resolution: 0.1 A ACS Nano 9:1420-1433 (2015)

C D D A

crossover plane ii crossover plane iii

y z x

i ii iii i ii iii

1 2 3 4 5 6 13 1415 16 17 18 1211 10 9 8 7

B

y x

⊗

crossover plane i

18 17 16 15 14 13 12 11 10 9 8 7 6 5 4 3 2 1

E

i ii iii i ii iii i ii iii i 5

✴ CHARMM36 force field ✴ Explicit water ✴ [MgCl2] ~ 10 mM ✴ NAMD ✴ 1 to 3M atoms ✴ 500 to 1,000 CPUs

y z x

From caDNAno to all-atom

• caDNAno returns topology (json) and

sequence (csv) information.

• cadnano2pdb.pl combines json and

csv files into a PDB file.

Jejoong ¡Yoo ¡

All-atom MD simulation

• f L-shape DNA origami

10 8 6 4 2 Bend per 7-bp array cell (°) 24 20 16 12 8 4 Array cell index Programmed bend 120 110 100 90 80 70 60 End-end angle (°) 30 25 20 15 10 5 Time (ns)

18 17 16 15 14 13 12 11 10 9 8 7 6 5 4 3 2 1

ˆ t1 ˆ t2 ˆ t3 ˆ t3 ˆ t3

2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 s = L s = 0 1 26 27

Programmed bend

Experiment Dietz, H. et al, Science, 325

Structural dynamics

Structural fluctuations reveal local mechanical properties

30 28 26 24 22 20 18 DNA-DNA distance (Å)

80 60 40 20 HC0 SQ0 pers

lp

µm

Persistence length

• f DNA origami

MD trajectories allow us to compute natural bending and torsion as well as persistence length

Our simulations predict higher rigidity for honeycomb-lattice design.

• Chicken wire frame represents center line of helices &

junction

• Inter-DNA distance in color map

Yoo ¡and ¡AA, ¡PNAS ¡110:20099 ¡(2013)

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MD simulation of DNA origami conductivity

PDMS

5 nA 150 ms

caDNAno all-atom

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DNA Mg(H2O)62+ H2O K+ Cl- PDMS

5 nA 150 ms

MD simulation of DNA origami conductivity

Electric field

Li, Chen-Yu et al. ACS Nano 9:1420-1433 (2015)

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PDMS

5 nA 150 ms

MD simulation of DNA origami conductivity

Instantaneous current:

500mV

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Factors affecting ionic conductivity of DNA origami

Number of DNA layers: Lattice type:

500mV

More layer -> less leakage current SQ2 has lower projected DNA density and a higher leakage current Nonlinear because of the edge effect

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Effect of Mg2+

25 mM MgCl2 50 mM MgCl2 5.5 mM MgCl2 1 nA 30 ms

1 2

1 M KCl, 0.5x TBE 100 mM MgCl2

a) b) c)

+ +

• 1 nA

30 ms

V=500 mV

[Mg2+]

Elisa A. Hemmig Silvia Hernández-Ainsa Ulrich F. Keyser

5.5 mM 100 mM 50 mM 25 mM [Mg2+]

25 mM MgCl2 50 mM MgCl2 5.5 mM MgCl2 1 nA 30 ms

1 2

1 M KCl, 0.5x TBE 100 mM MgCl2

a) b) c)

+ +

• 1 nA

30 ms

V=500 mV

25 mM MgCl2 50 mM MgCl2 5.5 mM MgCl2 1 nA 30 ms

1 2

1 M KCl, 0.5x TBE 100 mM MgCl2

a) b) c)

+ +

• 1 nA

30 ms

V=500 mV

90 ms 3 nA

Higher [Mg2+] makes DNA origami less conductive.

Higher [Mg2+], higher current drop. SQ2, m13 sequence ~2 times less conductive than 0 M [Mg2+]

58 54 53 (nm2)

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Mechanism of Mg2+

c e

0 mM 131 mM 250 mM

[MgCl2] 0.4 0.3 0.2

f h i

5.5 mM 55.5 mM 105.5 mM 205.5 mM

pendicular

Cy5 (2,0) Cy3 (0,0)

FRET efficiency

Elisa A. Hemmig Silvia Hernández-Ainsa Ulrich F. Keyser

FRET:

205.5 mM 105.5 mM 55.5 mM 5.5 mM

Mean area

Higher [Mg2+], lower inter-DNA distance

Mg2+ makes DNA origami more compact, by screening the DNA- DNA repulsion.

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Anisotropic conductivity

b

σ σ

• ,x
• ,y

Ulrich F. Keyser Jinglin Kong

Ex Ey X Y AFM

Li, Chen-Yu et al. ACS Nano 9:1420-1433 (2015)

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Programmable ionic conductivity of DNA origami

Number of DNA layers Lattice type

Structural design

Nucleotide content Ionic environment Direction

X Y Z

Magnitude

25 mM MgCl2 50 mM MgCl2 5.5 mM MgCl2 1 nA 30 ms

1 2

1 M KCl, 0.5x TBE 100 mM MgCl2

a) b) c)

+ +

• 1 nA

30 ms

V=500 mV

• A

25 mM MgCl2 50 mM MgCl2 5.5 mM MgCl2 1 nA 30 ms

1 2

1 M KCl, 0.5x TBE 100 mM MgCl2

a) b) c)

+ +

• 1 nA

30 ms

V=500 mV

• A

Electric field Leak-proof plates Electro- mechanical gates

MD has predicting power!

Cryo-EM reconstruction versus all-atom simulation

Bai et al, PNAS 109:20012 (2012)

Cryo-EM reconstruction versus all-atom simulation

Bai et al, PNAS 109:20012 (2012)

Cryo-EM reconstruction versus all-atom simulation

Bai et al, PNAS 109:20012 (2012)

MD simulation of the cryo-EM object starting from a caDNAno design

7M atom solvated model 130 ns MD trajectory Bai et al, PNAS 109:20012 (2012)

7M atom solvated model 130 ns MD trajectory Bai et al, PNAS 109:20012 (2012)

MD simulation of the cryo-EM object starting from a caDNAno design

7M atom solvated model 130 ns MD trajectory Bai et al, PNAS 109:20012 (2012)

MD simulation of the cryo-EM object starting from a caDNAno design

Preliminary analysis indicates excellent agreement between the two methods

Cryo-EM reconstruction All-atom MD simulation

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Ion ¡channels

\

Locking ¡ ¡ nanocontainers

Ongoing projects

DNA ¡bricks

25

Acknowledgement

Collaborator (Keyser’s group)

• Dr. Jejoong Yoo

Chen Yu Li

• Dr. Ulrich F. Keyser
• Dr. Silvia Hernández-Ainsa

Elisa A. Hemmig Jinglin Kong

• Dr. Chris Maffeo