Molecular Dynamics of DNA origami nanostructures

Transcription

1 Molecular Dynamics of DNA origami nanostructures Christopher Maffeo PI: Aleksei Aksimentiev Department of Physics University of Illinois at Urbana-Champaign Blue Waters Symposium June 5, 2018

2 All-atom Molecular Dynamics (MD) U = Atoms modeled as classical point particles Interactions prescribed by CHARMM36 force field bonded + i>j with CUFIX corrections Simulations run using NAMD on Blue Waters k(r ij r 0 ) 2 + k ( 0 ) 2 + k(1 + cos(n + )) U min Rmin r ij 12 + Cq iq j 0r ij 2 R 6 min r ij bond angle dihedral Lennard-Jones (van der Waals) electrostatic Phillips et.al. J. Com. Chem. 26:1781

3 Single-stranded DNA hybridizes with sequence specificity phosphate sugar. adenine. guanine thymine cytosine

4 DNA origami Building a structure with nanoscale precision by folding DNA 2.5 nm Viral DNA (scaffold) Synthetic DNA (staples) ~30 40 nucleotides

5 Downloaded fr to I, and S41 to S49). Increasing the concentrainterfaces, create rich opportunities for adjusting ntarity, including dimers, trimers, and a teands8n to+s21). 1, and nthe+ conformational 1 and tion of cations shifts the equilibrium toward the equilibrium, and changing it merthe (Fig.planes 1D; fig. defined S7, B to F;by andnfigs. closed state by predominantly reducing the avreversibly and rapidly, by global parameters such o illustrate the ability of finely the click-in shape n + 2 can not be tuned, and ~34.3 /bp asthat cation ognition for precisely defining conis thescheme smallest increment of curvature canconcentration and solution temperature. erage time that the switch dwells in the open state (fig. S23I). We test these options in detail using ensemble and mational states within a multidomain DNA be achieved. The greater the strength of the designed insingle-molecule fluorescence resonance energy ct, we designed a switchlike DNA object conteraction between the shape-complementary transfer (FRET) experiments, as well as TEM imng of two rigid beams connected by a pivot interfaces of the switch, the lower the cation conaging and electrophoretic mobility analysis per. 1E and fig. S22). The switch can dwell either centration necessary for stabilizing the closed formed as a function of cation concentration and n ensemble of open states or in a closed state. state (Fig. 2B and fig. S23, B and C). In the switch temperature with the switch object and for a distructure of the closed state is prescribed by version with 16 stacking bonds, the transition meric brick complex. For both the switch and the pe-complementary patterns of double-helical occurred over a narrow concentration interval dimeric bricks, increasing the cation concentraa domains that can click into each other when ranging from 6 to 12 mm MgCl2. For stronger tion shifted the conformational equilibrium fromdietz two beams draw together (Fig. 1E, right). and coworkers, the open or monomeric states to the closed or Science ect imaging by negative-stain TEM confirms hybridization-based interactions at all comple(2012) dimeric states, respectively (Fig. 2, A and B, and the switch adopts open and closed conformentary sites instead of the minimal stacking DNA origami structures Fig. 1. Synthetic DNA membr D REPORTS channel formed by 54 doublelattice. Cylinders indicate double brane stem; orange strands with oligonucleotides that hybridize Geometric specifications of the tr = 6 nm, inner diame Yan and diameter coworkers, D Science (2013) fully surrounded by DNA helices of a 7-base strand extension actin for mutant M1 and l = 14 nm f B Fig. 1. Synthetic DNA membrane channels. (A) Schematic illustration of the channel formed by 54 double-helical DNA domains packed on a honeycomb lattice. Cylinders indicate double-helical DNA domains. Red denotes transmembrane stem; orange strands with orange ellipsoids indicate cholesterol-modified oligonucleotides that hybridize to single-stranded DNA adaptor strands. (B) Geometric specifications of the transmembrane channel. Length L = 47 nm, tube diameter D = 6 nm, inner diameter d = 2 nm. The length of the central channel fully surrounded by DNA helices is 42 nm. The star symbol indicates the position of a 7-base strand extension acting as a defect in channel mutants [l = 15 nm for mutant M1 and l = 14 nm for mutant M2; see text S6 and cadnano maps Yan and coworkers, Science (2011) rvatures. (A) Schematic representation of the hem(c) Schematic representation of the ellipsoid. (D) TEM EM grids. The concave surface is visible as a dark area. d on TEM grids. Due to the spherical symmetry, the of the ellipsoid. The outline of the ellipsoid is visible. 0 nm. (G) Schematic representation of the nanoflask.. (I) TEM images of the nanoflask, randomly deposited om of the flask are clearly visible in the images. Scale emag.org on September 27, SCIENCE (figs. S22 to S24)]. (C) Cross-sectio porated in a lipid bilayer. (D) Averag purified DNA channel structures ( displayed in figs. S1 and S2). (E an adhering to small unilamellar vesic oleoyl-sn-glycero-3-phosphocholine of vesicle size distribution and bindin to S9. (G) TEM image of DNA channe upper right part of the image. DNA covered areas or sticking to SUVs (s VOL NOVEMBER 2 Fig. 4. Schematics (left), (middle), and TEM images (right)30ofmm(a) an and (C), the diam 12.5AFM mm MgCl MgCl S-shaped structure, a sphere, (C) aspherical screw. All scale bars indicate 200 nm, images compared Fig. 4. Bending enables the design of intricate nonlinear shapes. Red single scaffold strand(b) designed to fold into aand 50-nm-wide wireframe 25 nm emag.org nanorobot (15 MD) that can be reversibly reconfigured in three different con4. Reversibly reconfigurable non base pairing multistate DNA devices segments indicate regions in which deletions and insertions are installed. capsule resembling a beach ball and four typical particles representing Shih and coworkers, Science (2009) and all zoom-in images (images without scale bars) are 200 by 200 nm. In (B) flattening of the Scaleshapes. bars, 20 nm. Modelrow: of a schematic 3-by-6 helix DNA-origami bundle different of the beach ball. The design states: folds as six Dietz bent crosses and coworkers, Science formational disassembled, and assembled with (2015) open or closed arms, h arbitrary (A)(A)Top representations of aprojections reconfig5 mm MgCl2 designed to bend into a half-circle with a 25-nm radius that bears three 2 (inset) connected on a single scaffold. (D) A concave triangle that is folded 2

6 Cryo-electron microscopy and all-atom simulation for DNA origami structure prediction Reference structure docked into cryo-em 2 RMSD of scaffold (nm) time (ns) PNAS 109:20012 Nucleic Acids Research 44:3013

7 Comparison between simulation and experiment EM density psuedo-atomic model Nucleic Acids Research 44:3013 simulation

8 Interactions in a simple coarse-grained DNA model 4 nm cutoff 100 mm

9 Coarse-grained model captures programmed curvature Design and TEM: Science 325:725

10 Adaptive resolution simulation of DNA origami systems Andersen et al., Nature 2009 Birkedal Group

11 DNA-based Voltage sensing Keyser Group Experimental setup All-atom MD simulation 5 na 150 ms ACS Nano 9: (2015) Idea: use DNA origami as a local voltage probe

12 Design of a nanoscale voltage sensor Keyser and Tinnefeld Groups Nano Lett., doi: /acs.nanolett.7b05354 (2018)

13 Coarse-grained simulations of a FRET plate capture ~5 bp/bead CG model 40 µs simulations 100 mv 200 mv 300 mv 400 mv 600 mv Nano Lett., doi: /acs.nanolett.7b05354 (2018)

14 CG simulation of FRET efficiency 2 beads/bp CG model 1 µs simulations 100 mv 400 mv 200 mv Design A1 300 mv Nano Lett., doi: /acs.nanolett.7b05354 (2018)

15 Voltage sensing with DNA origami Experiment: Simulation: Nano Lett., doi: /acs.nanolett.7b05354 (2018)

16 DNA Ion Channels Jejoong Yoo Nano Letters, 13: 2351 Porins, 1 ns conductance Yoo & Aksimentiev, JPCL 6, 4680 (2015)

17 DNA Ion Channels Conductance < 0.1 ns Membrane channel made of a single DNA duplex (0.1 ns) Nano Letters 16:4665 (2016) Gramicidin ion channels Chen-Yu Li Porin-like DNA channel 40 ns Keyser Group ACS Nano 10:8207 (2016)

18 All-atom MD simulation of lipid-dna interface Chen Yu Li No applied electric field Lipid molecule around the DNA channel can translocate to the other leaflet.

19 Lipid translocation through toroidal pores is very common and very fast

20 Lipid translocation through toroidal pores is very common and very fast DPhPE DPhPC 3-5 orders of magnitude faster than natural scramblases scramblase

21 Experimental verification Scale bars are 10 µm Keyser Group Ohmann, Li, Ulrich F. Keyser, Aksimentiev,

22 Works in human cells Annexin V binds specifically to PS lipids found in inner leaflet of human cells Breast cancer cells from the cell line MDA-MB-231 Positive control: apoptosis-inducing microbial alkaloid staurosporine Negative control: DNA folding buffer Scale bar is 20 µm

23 Acknowledgements Aksimentiev Group Aleksei Aksimentiev Chen-Yu Li Jejoong Yoo Center for Macromolecular Modeling and Bioinformatics Victoria Birkedal Ulrich Keyser Philip Tinnefeld