Molecular Dynamics of DNA Origami Aleksei Aksimentiev, Physics University of Illinois at Urbana-Champaign
DNA origami Scaffold: long ssDNA Staple: short (17~50 bp) ssDNA, connecting different parts. Video credit: Shawn Douglas 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 2 Gerling, Thomas et al ., Science , 2015, 347 (6229), 1446-1452.
Design ¡and ¡ ¡characterization ¡of ¡DNA ¡ nanostructures Computer-aided design of DNA origami a b y = = with caDNAno (Shih group, Harvard U.) x z a b c i ii iii i ii caDNAno i ii iii i ii c d i ii iii Transmission electron microscopy and/or atomic force microscopy Cryo-EM validates the design reconstruction, the only experimentally derived structural model
All-atom molecular dynamics simulations of DNA nanostructures Atoms move according to ¡ Massive parallel computer classical mechanics (F= ma) Blue Waters (UIUC): ~200,000 CPUs Time scale: ~ 0.1-100 µ s Interaction between atoms is ¡ Length scale: 10K - 100M ¡ atoms or (< 50 nm) 3 defined by molecular force field Time resolution: 2 fs ACS Nano 9:1420-1433 (2015) Spacial resolution: 0.1 A
From caDNAno to all-atom C A B i ii iii i ii iii i ii iii i crossover plane i Jejoong ¡Yoo ¡ 1 3 5 1 2 4 6 2 3 5 4 6 1211 11 9 7 9 8 7 10 10 8 12 x 13 1415 17 13 15 17 16 x 18 z 18 ii iii 14 16 ii iii i y ⊗ i y crossover plane ii crossover plane iii D E x z D y • caDNAno returns topology (json) and ✴ CHARMM36 force field sequence (csv) information. ✴ Explicit water ✴ [MgCl 2 ] ~ 10 mM ✴ NAMD ✴ 1 to 3M atoms • cadnano2pdb.pl combines json and ✴ 500 to 1,000 CPUs csv files into a PDB file. 5
All-atom MD simulation of L-shape DNA origami Experiment Dietz, H. et al, Science , 325 120 s = L 110 27 End-end angle (°) 26 3 5 100 1 ˆ t 3 25 6 2 4 ˆ 90 24 t 2 23 11 9 ˆ 80 t 1 7 22 12 70 10 8 21 15 17 60 13 20 0 5 10 15 20 25 30 Time (ns) 19 ˆ 14 16 18 t 3 10 Programmed bend 18 Bend per 7-bp array cell (°) Programmed 8 17 s = 0 16 6 ˆ t 3 15 4 14 bend 13 12 2 11 10 9 5 4 3 1 8 7 6 2 0 0 4 8 12 16 20 24 Array cell index
Structural dynamics
Structural fluctuations reveal local mechanical properties MD trajectories allow us to compute 80 l p pers natural bending and torsion as well as 30 60 DNA-DNA distance (Å) persistence length 28 26 µm 40 24 - Inter-DNA distance in color map 22 - Chicken wire frame represents center line of helices & 20 20 junction 18 0 HC0 SQ0 Persistence length of DNA origami Our simulations predict higher rigidity for honeycomb-lattice design. Yoo ¡and ¡AA, ¡ PNAS ¡110:20099 ¡(2013)
MD simulation of DNA origami conductivity caDNAno 5 nA 150 ms all-atom PDMS 9
MD simulation of DNA origami conductivity 5 nA DNA 150 ms Mg(H 2 O) 62+ H 2 O K + Cl - Electric field PDMS Li, Chen-Yu et al. ACS Nano 9:1420-1433 (2015) 10
MD simulation of DNA origami conductivity 5 nA 150 ms Instantaneous current: PDMS 11
Factors affecting ionic conductivity of DNA origami Number of DNA layers: Lattice type: SQ2 has lower projected DNA density and a higher leakage More layer -> less leakage current current 500mV 500mV Nonlinear because of the edge effect 12
Higher [Mg 2+ ] makes DNA origami Effect of Mg 2+ less conductive. a) 1 M KCl, 0.5x TBE 2 1 100 mM MgCl 2 Elisa A. Hemmig - SQ2, m13 a) 1 M KCl, 0.5x TBE sequence 1 2 100 mM MgCl 2 30 ms 1 nA - Silvia Hernández-Ainsa 30 ms [Mg 2+ ] 1 nA + + ~2 times less V=500 mV conductive than Ulrich F. 5.5 mM MgCl2 [Mg 2+ ] 25 mM MgCl2 50 mM MgCl2 Keyser + 0 M [Mg 2+ ] + V=500 mV 5.5 mM 25 mM 50 mM 100 mM 1 nA a) 1 M KCl, 0.5x TBE 30 ms 1 2 5.5 mM MgCl2 25 mM MgCl2 50 mM MgCl2 100 mM MgCl 2 3 nA 1 nA - b) 30 ms 90 ms 30 ms 1 nA b) Higher [Mg 2+ ], higher current drop. 13 + + V=500 mV 5.5 mM MgCl2 25 mM MgCl2 50 mM MgCl2 1 nA 30 ms b) c) c) c)
Mg 2+ makes DNA origami more compact, by screening the DNA- Mechanism of Mg 2+ DNA repulsion. 0 mM 131 mM 250 mM FRET: Elisa A. Silvia Ulrich F. Hemmig Hernández-Ainsa Keyser Cy3 (0,0) Cy5 (2,0) pendicular c Mean 58 54 53 (nm 2 ) area Higher [Mg 2+ ], lower inter-DNA distance h f 0.4 FRET efficiency 105.5 mM 205.5 mM 105.5 mM 205.5 mM 0.3 55.5 mM 55.5 mM 5.5 mM 5.5 mM 0.2 [MgCl 2 ] 14 i e
Anisotropic conductivity Ulrich F. Jinglin Kong Keyser b AFM E x E y X σ σ o,x o,y Y Li, Chen-Yu et al. ACS Nano 9:1420-1433 (2015) 15
Programmable ionic conductivity of DNA origami Structural design Ionic environment Number of DNA layers Direction MD has Lattice type Electro- Leak-proof Electric Z predicting mechanical plates field gates a) a) 1 M KCl, 0.5x TBE 1 M KCl, 0.5x TBE power! X 1 1 2 2 100 mM MgCl 2 100 mM MgCl 2 Nucleotide content Y - - Magnitude 30 ms 30 ms - - 1 nA 1 nA A A + + + + V=500 mV V=500 mV 5.5 mM MgCl2 5.5 mM MgCl2 25 mM MgCl2 25 mM MgCl2 50 mM MgCl2 50 mM MgCl2 16 1 nA 1 nA 30 ms 30 ms b) b) c) c)
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 Bai et al , PNAS 109:20012 (2012) 130 ns MD trajectory
MD simulation of the cryo-EM object starting from a caDNAno design 7M atom solvated model Bai et al , PNAS 109:20012 (2012) 130 ns MD trajectory
MD simulation of the cryo-EM object starting from a caDNAno design Bai et al , PNAS 109:20012 (2012) 7M atom solvated model 130 ns MD trajectory
Preliminary analysis indicates excellent agreement between the two methods Cryo-EM reconstruction All-atom MD simulation
Ongoing projects \ Ion ¡channels Locking ¡ ¡ nanocontainers DNA ¡bricks 24
Acknowledgement Collaborator (Keyser’s group) Chen Yu Li Dr. Ulrich F. Keyser Dr. Silvia Hernández-Ainsa Dr. Jejoong Yoo Elisa A. Hemmig Jinglin Kong Dr. Chris Maffeo 25
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