纳米笔记丨纳米工程与肺癌的故事

Chem Commun Exterior modification of a DNA tetrahedron Guan-song Wang (2010)

Self-assembly of a DNA tetrahedron with hairpin spikes. DNA single strands (L, M, and S) stepwisely assemble into symmetric 3-point-star motifs with hairpins (tiles) and then into a hairpin tetrahedron in a one-pot process. Note that there are three single stranded loops (colored red) in the center of the complex to introduce flexibility to the hairpin-modified 3-point-star motifs. The purple segment in the second strand will form short hairpin structures during self-assembly. All hairpins stretch out from the struts of the DNA tetrahedron (purple) near the vertices with a three-fold rotational symmetry.

ACS Nano DNA polyhedra with T-linkage Guan-song Wang (2012)

Self-assembly of spiked DNA polyhedra with T-junction linkages. (a) Formation of a structurally well defined T-junction that joins a bulged DNA duplex (red) and a duplex (blue) with 5-base single-stranded overhang. (b) Self-assembly of spiked DNA tetrahedra from starshaped DNA motifs (tiles). Each motif contains an Ln strand and n copies of P strands. At the peripheral end of each branch of the star motif, there is a complementary T-junction pair: a single-stranded, 5-base-long overhang and a 5-base-long internal loop. T-junction interactions among the individual tiles would lead to the formation of DNA polyhedra. Each vertex of the polyhedra will be a DNA star motif, and one component star tile in each polyhedron is highlighted red. (c) Detailed structure of a strut [highlighted golden in the polyhedra shown in (b)] of the T-linked DNA polyhedra. There is a T-junction on each component of the DNA duplex. (d) Strut structure of the previously assembled, sticky-ended DNA polyhedra2831 is shown for comparison.

Angew Chem Int Ed Controlling the chirality of DNA Nanocages Guan-song Wang (2012)

Self-assembly of chiral DNA triangular prisms out of asymmetric three-point-star motifs. a) Schematic representation of the asymmetric three-point-star motifs. C=blue/red; M1, M2, and M3=green; S1, S2, and S3=black; L1, L2, and L3=red. For each motif, the two top branches have complementary sticky ends (green and yellow) and the bottom branch has self-complementary sticky ends (cyan). b) Scheme of the resulting chiral triangular prisms. In each prism, one component motif is highlighted. Note that the motifs and their resulting prisms are designated by the loop lengths in nucleotides.

J Am Chem Soc Artificial, parallel, left-handed DNA helices Guan-song Wang (2012)

Parallel, left-handed DNA duplexes with two half-turn domains. (a) Structural model (drawn with Nanoengineer, NanoRex Inc.). (b) Base stacking among the left-handed DNA duplexes leads to large aggregates (shown as an example). (c) Composition of one left handed DNA duplex studied here. It should be noted that the two component strands have identical sequences. (d) DNA sequences of the derived molecules. Mutated bases (red) introduce mismatches. In the names of the DNA strands, “2D” stands for two domains and “nT”indicates that the total number of extra T’s added is n.

Angew Chem Int Ed Directed self-assembly of DNA tiles into complex nanocages Guan-song Wang (2014)

Directed self-assembly of DNA tiles. a) A detailed structure (prepared from Tiamat[29]) of a 4-point-star motif (tile) that exemplifies all of the tiles used. It consists of one L4 strand (blue/red), four M strands (green), and four S strands (black). b) Simplified schemes of the assembly tiles (A-tiles) and directing tiles (D-tiles). An n-point-star tile for an A- or D-tile is termed An or Dn, respectively. For each tile, a simple scheme indicating all of the component strands (lines with the same color coding as in Figure 1a) and an even simpler ball and stick scheme are shown. The Dn tile has an n-fold rotational symmetry

and is assembled from three types of unique DNA strands: LDn, MD, and SD. The An tile has lower symmetry (an n 2-fold rotational symmetry) and is assembled from five types of DNA strands: LAn, MA1, MA2, SA1, and SA2. The sticky ends a/a’ are self-complementary and b and b’ are complementary to each other. c) A chart of the component tiles and the resulting DNA cages.

Reconstructed 3D structural models of the DNA complexes that resulted from directed self-assembly. For each structure, four views at different orientations are shown.

Nat Commun Construction of RNA nanocages by re-engineering the packaging RNA of Phi29 bacteriophage Guan-song Wang (2014)

Self-assembly of RNA nanoprisms I and II by re-engineering pRNA. (a) Secondary structure of the wild-type pRNA (packaging RNA of bacteriophage phi29). CE- and D-loops can interact with each other via the highlighted, complementary bases (red and golden). (b) Re-engineered pRNA molecules: shortened A-helix with a self-complementary sticky-end (green) and mutated CE- and D-loops (red and golden). (c) A 3D model of pRNA mutants. (d) Four pairs of complementary sequences used for the interacting loops of the pRNA mutants. Self-assembly of (e) a triangular RNA prism (I) and (f) a tetragonal prism (II). pRNAs can bind to each other through both loop–loop interaction and sticky-end cohesion. The mutant pRNAs are named according to the interacting loop sequence; for example, pRNA a–b0 has sequences a at CE-loop (red bases) and b0 at D-loop (golden bases).

Self-assembly of RNA nanoprism III by re-engineering pRNA. (a) A re-engineered pRNA molecule: capping A-helix with a loop and adding a self-complementary sticky end (green) to E-helix. (b) Predicted 3D structure of pRNA mutant. (c) Self-assembly of triangular RNA prism III.

* in the name of a pRNA mutant indicates that the RNA has a sticky

end on E-helix.

Nat Commun De novo design of an-RNA tile that self-assembles into a homo-octameric nanoprism Guan-song Wang (2015)

Self-assembly of a de novo designed RNA tile into a homooctameric prism. (a) Sequence and secondary structure of the design, twostranded RNA tile (R1–R2). All structural elements (three duplex regions Pa, Pb and Pc; two tails Ta and Tc; two internal bulges loops Lab and Lbc) are indicated. Note that Ta (yellow) and Lab (yellow) are complementary to each other and Tc (red) is self complementary. (b) A detailed scheme of a T-junction structure formed by hybridization between a Ta tail and Lab loop. Both are coloured yellow. The black and yellow lines represent the RNA backbones and the short grey lines represent base pairs. (c) Selfoligomerization of the RNA tile. The tile can tetramerize into tetrameric square via T-junction formation (Ta–Lab hetero-hybridization) and dimerize via sticky-end cohesion (Tc–Tc hybridization). The two types of interactions together lead to the formation of an octameric nanoprism. For both the square and prism, a top view and a near side view are

shown. The structural models were prepared with a computer program Coot. (d) A 2D diagram showing the connectivity of the tiles. Each tile contains two strands represented by a thick line and a thin line, which share the same colour.

J Control Release Self-assembled triangular DNA nanoparticles are an efficient system for gene delivery Guan-song Wang (2016)

Complexes of self-assembly triangular nanoparticles loaded with mTOR single-stranded siRNA (ssRNA-TNP). A, Schematic representation of ssRNA-TNP nanocomplex. There are three unique strands, the 27-mer red strands (mTOR single-stranded siRNA), present three times, the 47-mer blue strands (mTOR-2A), also present three times, and the inner dark green strand (mTOR-1A), with a 3-fold repeating sequence. B, Analysis of ssRNA-TNP samples by atomic force microscope (AFM). 1) A raw AFM image. 2) A zoom-in AFM image. C. Comparison of the close-up views of individual particles (left) with supposed triangular models (right) at same orientations.

J Am Chem Soc Retrosynthetic analysis-guided breaking tile symmetry for the assembly of complex DNA Nanostructures Guan-song Wang (2016)

(a) Schematics of three asymmetric three-point-star DNA motifs. Motif-O: each branch is 2.25 turns long and has self complementary sticky ends. Motif-EOE: the two bottom branches are 2 turns long and have complementary sticky ends; the top branch is 2.25 turns long and has self-complementary sticky ends. Motif-E: each branch is 2 turns long; the two bottom branches have complementary sticky ends; the top branch has self-complementary sticky ends. The loop lengths of each motif are indicated in parentheses. The central strand (C), medium strands (M), and short strands (S) are colored blue/red, green, and black, respectively. Note that there are three red, central, single-stranded loops (L1, L2, and L3). The number of halfturns of the edge formed is labeled beside each branch. (b) Schematic illustration of the O-edge and E-edge. For the O-edge, neighboring motifs are related by a 2-fold rotational axis as indicated by a pair of black arrows. Light blue and purple hexagons indicate motifs facing up

and down, respectively. (c−f) A set of four rules have been established to guide the design of DNA nanostructures.

Truncated octahedron assembled from Motif-O (3,7,3). (a) Retrosynthetic analysis of a truncated octahedron. (b) Native agarose gel analysis of Motif-O (3,7,3) assembly. A DNA cube assembled from Motif-O (5,5,5) is used as the reference in lane 2. (c) AFM imaging of the truncated octahedron. Particles that have similar projections onto the structural model of the truncated octahedron are highlighted in white boxes and presented in the right panel. (d) Representative cryoEM image of the truncated octahedron. White boxes indicate the DNA particles. (e) Four views of the reconstructed structural model of the truncated octahedron. (f) Pairwise comparison between raw cryoEM images of individual particles (left) and the corresponding projections (right) of the reconstructed structural model. The raw particles were selected from different image frames to represent views at different orientations.

Chem Sci Protecting microRNAs from RNase degradation with steric DNA nanostructures Guan-song Wang (2018)

Design and characterization of the DNA shuriken. (a) A schematic illustration of the DNA shuriken design. The DNA shuriken is a DNA star motif carrying 3 miR-145 strands.

Chem Sci Capturing intracellular oncogenic microRNAs with self-assembledDNA nanostructures for microRNA based cancer therapy Guan-song Wang (2018)

Functional DNA nanotube design. (A) Scheme of a DNA Y-motif design. The red DNA segment of strand M is the capturing unit in single-stranded form. (B) Two DNA Y-motifs bend by 90 degrees to form a nanotube structure. Each DNA nanotube carries 6 capturing units. The designed DNA nanotube is approximately 13.9 nm long and 5.8 nm wide (diameter). (C) DNA nanotubes carrying capturing units with different configurations: overhang, duplex and hairpin structures.

Nat Commun Invivo production of RNA nanostructures via programmed folding of single-stranded RNAs Guan-song Wang (2018)

Component motifs of RNA structures. For each motif, a schematic drawing and a 3D model are shown. The thick colored lines and thin gray lines represent RNA backbones and basepairs, respectively

Designs, folding, and characterization of an RNA square (S) and an RNA double square (S2). a, b The molecular design and single-stranded folding pathways for S and S2, respectively. The RNA single strands are colored in a rainbow gradient from 5′ (red) to 3′ end (purple). Red, green, and blue boxes with dashed lines highlight a 90°-kink, a KL interaction, and a 3WL interaction, respectively. Each edge is composed of a two-turn RNA duplex. Characterization of c, d RNA square and e, f RNA double square. c, e electrophoretic analysis; d, f Atomic force microscopy (AFM) imaging. Note that S* has the same sequence as S except that one loop sequence is altered so that no KL interaction can form. (Scale bar: 20 nm)

Folding of complex RNA nanostructures from single RNA strands. a Structural design of an RNA 5-petal flower, which contains six KL interactions, ten 90°-kinks, and ten 3WJs. b AFM images of the RNA flowers. Left: transcription mixture from a PCR mixture. Right: thermal annealed, purified RNA nanoflower molecule. Scale of inset: 60 nm. c Structural design of an RNA tetra-square (S4), which contains four 3WLs, four 90°-kinks, and a 4WJ. d AFM images of the RNA S4. Left: transcription mixture. Right: thermal annealed, purified RNA S4. Scale of inset: 25 nm. (Scale bar: 50 nm)

Folding of a single-stranded, 4-turn, RNA tetrahedron (T4). a Structural design of T4. An RNA single strand is rainbow colored from 5′ to 3′ end. It contains four 3WJs and will fold from a 2D branching structure into a 3D tetrahedron upon the three pairs of KL interactions (indicated by dashed, double-arrowed lines). Each edge is four helical turns long. Scale bar, 50 nm. b A control molecule T4*. One loop sequence is altered to prevent one KL interaction. Thus T4* will assemble into a flat, double triangular shape instead of a tetrahedron. The models were built with Coot39 and Chimera37. All KLs are colored orange in the model. Scale bar, 50 nm. c, d AFM images of T4 and T4*, respectively. For each structure , three particles are zoomed-in and fitted with corresponding shapes. e, g Cryogenic electron microscopy (cryoEM) characterization of T4. e A raw cryoEM image. Each white box indicates an individual RNA particle. Scale

bar, 50 nm. f Four different views of the reconstructed structural model of the RNA tetrahedron (top) and corresponding views of the simulated model (bottom). Scale bar, 5 nm. g Pairwise comparison between raw cryoEM

images of individual particles (left) and the corresponding projections (right) of the reconstructed structural model. The raw particles were selected from different images to represent views at different orientations

Cloning and in vivo expression of RNA nanostructures. a Overall scheme. An expression vector (pET23a, orange) carrying an S2-coding DNA sequence (green) is transformed into E. coli cells. Upon IPTG induction, the S2 gene gets transcribed into RNAs, which self-fold into the designed double square structure in the cell. b Structural model of the S2 structure. c AFM imaging of cell lysates from E. coli without the expression vector (- Plasmid), or

with the vector but without S2 gene expression induction (- IPTG), or with S2 gene expression ( +IPTG). (Scale bar: 20 nm)

Acs Appl Mater Inter Isothermal self-assembly of spermidine/DNA Nanostructure complex as a functional platform for cancer therapy Guan-song Wang (2018)

Schematic illustration of the designed DNA nanoprism. (A) A DNA triangle consists of one core strand P1 and three copies of side strand P2. One protruding segment of P2 (at the 5' end) hybridizes to mTOR siRNA; the

other segment is intended to link to another DNA triangle. (B) Two DNA triangles form a DNA prism by the base pairing between P2 and P2' (Yellow). (C) SNP further hybridizes with mTOR siRNA at a molar ratio of 1:6 to form

an mTOR siRNA-loaded DNA nanoprism. Typically, a spermidine concentration of 100 μM at pH 7.0 was applied to facilitate the DNA nanoprism self-assembly.

DLS analysis of the DNA triangle, naked DNA prism and DNA prism. (A) Structures of the DNA triangle (half-prism), naked nanoprism and nanoprism.

ChemBioChem Targeted delivery of Rab26 siRNA with precisely tailored DNA prism for lung cancer therapy Guan-song Wang (2019)

Design and self-assembly pathway of DNA nanoprism. The distance between the two triangles is approximately 6.8 nm, and each edge of the triangle is also roughly 6.8 nm. A) One core DNA P1 and three PA or PR assemble into a triangular-shaped DNA structure. Strand PA has a segment of aptamer sequence at its 5’, whereas PR carries an overhang that can hybridize with Rab26 siRNA. B) DNA nanoprism carries three aptamer and three Rab26 siRNA-binding overhang. Rab26 siRNA can be easily attached on the nanoprism by mixing it with the prism at room temperature for 30 min. C) DNA nanoprisms with six MUC-1 aptamers.

Small Assembling defined DNA Nanostructure with Nitrogen-enriched carbon dots for theranostic cancer applications Guan-song Wang (2020)

Ethylenediamine-derived cationic CDs-assisted DNA NP self-assembly. A) NCDs were synthesized through a hydrothermal reaction using ethylenediamine as the precursor. B) The as-prepared cationic CDs mediate the Mg2+-free, isothermal self-assembly of DNA NP. P1 hybridizes with P2 or P3 to form a triangle-shaped structure. Two triangles dimerize into a prism by base-pairing of two intruding segments of P2 and P3. NPNCDK was obtained by mixing KRAS siRNA and NP at a molar ratio of 6:1.