Arrays of modular DNA units can broadcast advice by transforming their centralized appearance in acknowledgment to bounden of DNA activate strands. Song et al. actinic ellipsoidal arrays of double-stranded DNA (see the Perspective by Yang and Lin). Transient aboveboard configurations transform into two abiding ellipsoidal structures by avidity beyond a brace of opposing vertices. Bounden of DNA activate strands causes switching into the accession abiding configuration. The tiles appropriately actualize a avalanche of transformations forth a accurate pathway, thereby transmitting advice about breadth bounden occurred.
Science, this affair p. eaan3377; see additionally p. 352
Information broadcast at the diminutive akin is an capital abnormality in abundant actinic and biological processes. A key claiming in complete diminutive self-assembly is to accumulate bogus structures that imitate these circuitous activating behaviors in controllable systems. One able avenue is DNA self-assembly, a almighty access for the architecture and architecture of arbitrary-shaped bogus nanostructures with accretion complication and precision. Nonetheless, admitting contempo advance in the architecture of reconfigurable DNA nanostructures that abide tailored postassembly transformations in acknowledgment to adapted concrete or actinic cues, the activating behaviors of massive, circuitous DNA structures abide limited. The absolute systems about display almost simple activating behaviors that absorb a distinct footfall or a few accomplish of transformation. Moreover, abounding of these structures board mainly changeless segments abutting by a few baby reconfigurable domains.
Here, we approved prescribed, all-embracing advice broadcast in bogus diminutive arrays accumulated from modular DNA antijunction units. The baby activating antijunction assemblage contains four DNA double-helix domains of according breadth and four activating nicking points, and can about-face amid two abiding conformations, through an boilerplate accessible conformation. In an array, the active force of advice broadcast is abject stacking: The conformational about-face of one antijunction assemblage will account the interface amid the adapted assemblage and its adjoining units to become a high-energy anatomy with attenuated abject stacking, arch to transformations in the adjoining units. The adjustment transformation is agnate to a diminutive “domino array”: Once able at a few alleged units, the transformation again propagates, afterwards the accession of added “trigger strands,” to adjoining units and eventually the absolute array. The specific advice pathways by which this transformation occurs can be controlled by abacus activate strands to specific units, or by altering the architecture of alone units, the access amid units, and the geometry of the array.
The reconfigurable DNA broadcast arrays were complete by application both origami and single-strand–brick approaches. In one-pot assembly, we empiric that the arrays congenital from antijunction units apparent a spectrum of shapes to board adapted combinations of antijunction conformations. With the assimilation of set strands, we could lock the arrays into assigned conformations. The added set strands were added, the greater the accumulation confused against the agnate adjustment conformation. Added factors, including the admeasurement and aspect adjustment of an array, the abutting adjustment of an array, DNA sequences of an array, cation concentration, and temperature, accept been apparent to affect the aftereffect of one-pot assembly.
The transformation avalanche was approved with preassembled arrays. Aback starting from one conformation, accession of the activate fiber at alleged locations of the adjustment initiates structural transformation from the alleged sites and propagates to the blow of the adjustment in a stepwise address afterwards added activate strands at added locations. Releasing the old activate strands and abacus new ones can transform the adjustment aback to its antecedent conformation—a capricious action that can be again assorted rounds. In addition, we were able to ascendancy the advancement alleyway to chase assigned routes, as able-bodied as to stop and again resume advancement by mechanically decoupling the antijunctions or introducing “block strands.” The kinetics of adjustment transformation can be added by animated temperature or formamide. These accumulation and transformations were advised mainly by diminutive force microscopy and built-in agarose gel electrophoresis.
Our assignment demonstrates controlled, multistep, all-embracing transformation in DNA nanoarrays, accumulated by commutual modular activating units that can alteration their structural advice to neighbors. The array’s activating behavior can be adapted by alien factors, the shapes and sizes of arrays, the admission of transformation at alleged units, and the engineered advice advancement pathways. We apprehend that the DNA broadcast arrays will afford new ablaze on how to accumulate nanostructures with accretion admeasurement and circuitous activating behaviors, and may accredit a ambit of applications, such as the architecture of diminutive accessories to ascertain and construe diminutive interactions to conformational changes in DNA structures, to accidentally activate consecutive diminutive events.
In a address agnate to that of domino arrays (top), the diminutive DNA nanoarray transforms in a step-by-step broadcast process, able by the admixture of a activate fiber to a distinct assemblage (middle). Adapted stages of nanoarray transformation were accepted by AFM (bottom). Scale bar, 50 nm.
Information broadcast at the diminutive akin is an capital abnormality in abundant actinic and biological processes, such as intricate signaling cascades. One key claiming in complete diminutive self-assembly is to accumulate bogus structures that imitate these circuitous behaviors in controllable systems. We approved prescribed, all-embracing advice broadcast in an bogus diminutive adjustment accumulated from modular DNA structural units. The activating DNA diminutive adjustment exhibits transformations with programmable initiation, propagation, and regulation. The transformation of the adjustment can be able at alleged units and again propagated, afterwards accession of added triggers, to adjoining units and eventually the absolute array. The specific advice pathways by which this transformation occurs can be controlled by altering the architecture of alone units and the arrays.
Molecular self-assembly has played a acute role in bottom-up artifact of abstracts beyond abounding breadth scales. Structural DNA nanotechnology (1) has accepted to be a almighty access for the architecture and architecture of arbitrarily shaped bogus nanostructures, including changeless and activating structures, abundantly because of the programmability of this able biomolecule. The acreage has produced diverse, custom-shaped DNA nanostructures, including apparent (1D) ribbons (2–4) and tubes (2, 4–10), 2D lattices (5, 10–16), and bound 2D and 3D altar with assigned shapes (14, 17–30).
The basal acceptance of DNA nanostructure architecture is to architect structural advice into the DNA sequences by programming complementarity amid basic DNA strands (1). The present approaches for amalgam DNA nanostructures abundantly abatement into two aloft categories: DNA origami and DNA tiles. DNA origami is a “folding” method, in which a continued “scaffold” fiber (often M13 viral genomic DNA) is bankrupt into a assigned appearance via interactions with hundreds of short, complete “staple” strands (20). The DNA asphalt adjustment assembles DNA structures by abutting baby structural units, about consisting of a baby cardinal of strands (11). The DNA origami access has produced absolutely addressable structures up to several bags of abject pairs (bp) (7). Similar-sized, absolutely addressable structures accept additionally been bogus with appropriate types of DNA tiles, such as single-stranded tiles (4, 26) or DNA artery (27).
Besides engineering intricate changeless structures, DNA has additionally been acclimated to accumulate activating structures with tailored postassembly transformations—another important advantage of self-assembly from information-rich biomolecules. Abounding activating DNA accessories accept been demonstrated, including tweezers (31–34), walkers (35–40), reconfigurable arrays accumulated from simple DNA asphalt units (41), and added circuitous accessories (14, 42, 43). These accessories can faculty a ambit of concrete or actinic cues. Nonetheless, the activating behaviors of massive, circuitous DNA structures are still limited. The absolute systems about display almost simple activating behaviors that absorb a distinct footfall or a few accomplish of transformation. Moreover, admitting their massive size, abounding activating DNA origami structures were advised to board mainly changeless segments abutting by a few baby activating regions (14, 42, 43).
Here we authenticate programmable diminutive advice cascades formed by DNA arrays, which simulate some of the key aspects of circuitous biological signaling cascades, such as initiation, propagation, and adjustment empiric in signaling cascades able by T corpuscle receptor binding. (44) Our large, scalable DNA adjustment is akin to a diminutive “domino array”: the step-by-step transformation propagates through the commutual DNA units via accurately assigned pathways (fig. S1). We appearance that the capricious transformation of a DNA adjustment can be able at appointed locations, and follows pathways absolutely controlled by programming the appearance of the adjustment or by abacus diminutive switches that block and again resume the advice broadcast amid units.
We acclimated baby activating DNA units alleged “antijunctions” (45) to body large, scalable, reconfigurable DNA structures. An antijunction contains four DNA bifold domains of according breadth and four activating nicking credibility (Fig. 1, A and B; agenda that the fiber in gray contains a changeless nick, which does not change during reconfiguration). This baby accumulate can about-face amid two abiding conformations—“red” and “green,” apprenticed by base-stacking, through an ambiguous accessible (including partially open) conformation—“orange.” Anniversary bifold is 0.5 × n turns (n = 1, 2, 3, 4…) in breadth (fig. S2A). An antijunction is classified by the ambit amid two adverse activating nicking credibility (i.e., a 42-bp antijunction).
(A) A activating DNA antijunction can about-face amid two abiding conformations, through an ambiguous accessible conformation. (B) Adapted diagrams for a DNA antijunction: abiding conformations “red” and “green,” and ambiguous anatomy “orange.” (C) Transformation of an antijunction assemblage can be induced by accession of a activate strand. The advice is anesthetized from the adapted assemblage to its abutting neighbors, causing them to abide consecutive transformation. (D) Fiber diagram of an commutual 2D DNA broadcast adjustment with 4 units by 8 units. Three activate strands (green) are added to three units in the upper-left angle of the adjustment to admit the transformation (E) The advice of transformation propagates forth assigned pathways, causing the units to catechumen sequentially in this diminutive array.
In a affiliated network, the conformational advice of an antijunction can canyon to its abutting neighbors, introducing consecutive conformational change of the adjoining antijunctions (Fig. 1C). The transformation of an alone antijunction assemblage (e.g., from red to green) can be induced by abacus a activate DNA fiber that forms a connected bifold on one angle of the assemblage (fig. S3A). The key architecture affection of activate strands is that anniversary activate fiber removes a adaptable nick point from an antijunction unit. Afterwards the conformational about-face from red to blooming of the triggered unit, the interface amid the two adjoining units becomes a high-energy accessible conformation, arch to a transformation in the adjoining assemblage to the aforementioned anatomy (green) as the already adapted unit. This action is apprenticed by the abridgement of chargeless energy, acquired by the accumulation of an added base-stacking alternation at the affiliation point (see fig. S3B for added details).
We congenital 2D diminutive DNA broadcast adjustment via self-assembly of the antijunctions (Fig. 1D). A broadcast adjustment can transform from one adjustment anatomy (e.g., all antijunctions are in the red conformation) to accession adjustment anatomy (e.g., all antijunctions are in the blooming conformation). The adjustment transformation follows specific pathways, depending on the array’s geometry and bounden locations of activate strands (fig. S4). For instance, if the activate strands were added to the units (Fig. 1, D and E) at a corner, the broadcast would abide a step-by-step about-face from a red adjustment anatomy to a blooming adjustment anatomy via a askew pathway.
DNA broadcast arrays can be complete with both noncanonical DNA artery (single-stranded modular DNA units) and DNA origami (further altercation is in figs. S5 to S8). Attributable to the coercion of the connected scaffold, a DNA-origami antijunction charge be an odd-number-turn antijunction (e.g., 32-bp antijunction; figs. S5 and S7). In comparison, a DNA-brick antijunction can be either an odd-number-turn antijunction (e.g., 32-bp antijunction; figs. S5 and S7) or an even-number-turn antijunction (e.g., 42-bp antijunction; figs. S6 and S8). One of the adjustment conformations of the DNA-brick arrays is arbitrarily assigned as the red adjustment conformation, and the added is assigned as the blooming adjustment anatomy (fig. S5, B and D). For DNA-origami broadcast arrays, the anatomy breadth the arch does not cantankerous amid DNA helices aural the adjustment is assigned as the red adjustment conformation, and the added anatomy is assigned as the blooming anatomy (fig. S5, C and E).
The transformation alleyway of a DNA broadcast adjustment is accepted to be dictated by the abiding conformations agnate to bounded activity minima. To investigate these bounded energy-minimum states, we aboriginal advised the self-assembly of ellipsoidal 42-bp DNA-brick broadcast arrays via one-pot isothermal assembly. The after-effects appear that the best ascendant conformations were the red adjustment anatomy and the blooming adjustment conformation. In accession to the two ascendant conformations, which should accord to the two lowest-energy states, we empiric abounding mixed-conformation arrays that abide of both regions of red antijunctions and regions of blooming antijunctions. We empiric that the red antijunction regions and the blooming antijunction regions were consistently bridged by a askew seam(s) that contains accessible orange antijunctions. These orange antijunctions are ambiguous by themselves, but can abide in an adjustment anatomy aback they are belted by red antijunctions and blooming antijunctions (Fig. 2A). These arrays with alloyed antijunction conformations are alleged “mixed array” conformations, which accord to bounded activity minima in the accumulation (Fig. 2B). Added altercation of these abiding alloyed adjustment conformations is in fig. S9.
(A) Assorted conformations aftereffect from accumulation of a DNA-brick broadcast array: “red array” conformation, “green array” conformation, and “mixed array” conformations, which contains units with red conformation, blooming conformation, and orange conformation. The orange units (corresponding to a higher-energy, ambiguous state) anatomy askew seams that arch calm the red units and the blooming units. (B) Proposed, simplified activity mural of assembly. The units accumulate into the two all-around activity minima agnate to the red adjustment anatomy and the blooming adjustment conformation, and bounded activity minima agnate to the alloyed adjustment conformations. (C) Accumulation of the 20 × 4 42-bp DNA-brick broadcast adjustment after-effects in two (red adjustment and blooming array) ascendant articles in the agarose gel. (D) AFM images of alloyed adjustment conformations of the 20 × 4 42-bp DNA-brick broadcast array. (E) The 20 × 8 42-bp DNA-brick broadcast adjustment is acclimated as a “canvas” to accomplish broadcast arrays of adapted sizes and aspect ratios. (F) Percentages of red adjustment conformation, blooming adjustment conformation, and alloyed adjustment anatomy of m × n broadcast arrays. (G) Numbers (n) of red triggers (Rn) and blooming triggers (Gn) about-face the accumulation aftereffect of the 11 × 4 42-bp DNA-brick broadcast array. (H) Abatement of units from the 11 × 4 42-bp DNA-brick broadcast adjustment alters the accumulation result. (I) A aggregate of assemblage abatement and accession of eight red triggers affects the accumulation result. Scale bars, 50 nm.
Native agarose gel electrophoresis of a ellipsoidal 20 assemblage by 4 assemblage (20 × 4) 42-bp DNA-brick broadcast adjustment appear two artefact bands that accord to the red adjustment anatomy and the blooming adjustment conformation, appropriately (Fig. 2C). The blooming adjustment anatomy showed greater advancement than the red adjustment conformation, acceptable due to its continued geometry. The alloyed adjustment conformations board abounding adapted shapes that do not drift as a distinct band, but were empiric in diminutive force microscopy (AFM) images of chapped samples (Fig. 2D).
An 11 × 4 42-bp DNA-brick broadcast adjustment was acclimated to appraisal optimal accumulation altitude (fig. S10). The best crop was empiric aback the adjustment was accumulated at 51.3°C isothermally, in a Tris-EDTA (TE) absorber absolute 10 mM MgCl2. Accession of single-stranded poly-T extensions about the abuttals of the adjustment added bigger the crop (fig. S11), apparently due to the poly-T’s action of mitigating exceptionable accession (20).
To accept how admeasurement and aspect adjustment affect the accumulation of DNA broadcast array, we activated the one-pot accumulation of a accumulation of ellipsoidal 42-bp DNA-brick broadcast arrays. The bigger anatomy is a 20 × 8 DNA-brick adjustment consisting of about generated ∼14,000 bp (Fig. 2E). In total, 16 DNA-brick broadcast arrays with adapted sizes and aspect ratios were generated by application the 20 × 8 broadcast adjustment as a diminutive canvas (Fig. 2F and fig. S12). Built-in agarose gel electrophoresis and AFM images (figs. S13 and S14) were acclimated to appraisal the percentages of the red adjustment conformation, the blooming adjustment conformation, and the alloyed adjustment anatomy of the 16 structures (Fig. 2F, fig. S15, and table S1). All broadcast arrays produced a ample bulk of both the red arrays and the blooming arrays, except for the n × 2 arrays, whose accumulation appeared to favor the larger–aspect adjustment blooming adjustment conformation, suggesting that aspect ratios comedy a added important role for this accumulation of structures. Our analysis, application a simple adjacency archetypal (fig. S16) that advised alone the activity amid the abutting adjoining helices, showed that the array’s aspect ratios had a beyond aftereffect on the n × 2 arrays, connected with the aloft observation.
We again advised how the one-pot accumulation of arrays was afflicted by the attendance of activate strands, affiliation patterns amid units, and the DNA sequences. In the aboriginal test, the accession of a few activate strands in the one-pot accumulation acutely adapted the R/G ratios for the 11 × 4 42-bp DNA-brick broadcast adjustment (Fig. 2G and table S2). As expected, the added activate strands were added to the one-pot assembly, the added the accumulation confused against the agnate adjustment conformation.
Changing the connectivity amid antijunction units additionally affects the accumulation of the 11 × 4 42-bp DNA-brick broadcast adjustment (Fig. 2H and fig. S17). Aback antijunction units were removed from the 11 × 4 42-bp DNA-brick broadcast array, the accumulation confused to added blooming adjustment conformations (Fig. 2H), apparently because of the accretion attenuated (1.5 units in width) areas, which favor a blooming adjustment conformation.
In allegory to the after-effects in Fig. 2G, accumulation of the 11×4 42-bp DNA brick broadcast adjustment with missing units in the attendance of eight red activate strands resulted in a added alloyed adjustment conformation, acceptable because the bargain connectivity additionally diminishes the capability of activate strands (Fig. 2I). This aftereffect is decidedly arresting with the 11 × 4 42-bp DNA brick broadcast adjustment with two holes—about bisected of the arrays formed a “mask”-shaped alloyed adjustment anatomy (fig. S18). Statistics of the 11 × 4 42-bp DNA brick broadcast adjustment with adapted connectivity are apparent in table S3, and added studies on authoritative the one-pot accumulation of DNA-brick broadcast arrays are included in fig. S19.
Considering that the change of abject stacking occurs alone at anniversary four-way junction, the DNA sequences at the junctions may comedy an important role in chargeless the accumulation results. To verify this hypothesis, we activated two versions of the 11 × 4 42-bp DNA-brick broadcast arrays with adapted sequences at the junctions (fig. S20). The two arrays (design I and II) accept the aforementioned sequences, except for the eight DNA bases at anniversary four-way junction. The accumulation after-effects showed a able alternation amid the alliance sequences (and appropriately the abject stacking) and the red/green (R/G) ratios. In acceptable acceding with our estimate, the blooming adjustment was the ascendant anatomy (R/G = 0.24) for architecture I, while the red adjustment was the ascendant anatomy (R/G = 3.0) for architecture II.
To appraisal a acceptable architecture for our abstraction of DNA adjustment transformation, we compared adapted DNA-brick broadcast arrays and DNA-origami broadcast arrays. Overnight room-temperature evolution of red activate strands with a preassembled 11 × 4 42-bp DNA-brick broadcast array, an 8 × 5 52-bp DNA-brick broadcast array, and a 10 × 4 64-bp DNA-brick broadcast adjustment (fig. S21) did not catechumen a apparent allotment of blooming adjustment anatomy to red adjustment conformation. The arrays were again incubated at college temperatures or in solutions absolute college concentrations of formamide to advance the transformation kinetics, but the DNA-brick broadcast adjustment started to appearance accident at 55°C or 40% formamide afore apparent transformation was observed.
We again angry our absorption to DNA-origami broadcast arrays, which may be added airy to denaturing altitude because of the continued arch strand. We accumulated an 11 × 7 32-bp DNA-origami broadcast adjustment (fig. S22) and an 11 × 4 52-bp DNA-origami broadcast adjustment with a p7560 scaffold. Both arrays resulted in alone the red adjustment conformation. It is alien how the arch (about bisected the diminutive weight of the able array) adeptness affect the accumulation and transformation of the DNA-origami broadcast array, and the arch assurance of the DNA-origami broadcast adjustment requires added study. We eventually chose the 52-bp DNA-origami broadcast adjustment for real-time transformation, as consecutive studies appear that this broadcast adjustment is easiest to transform and is acceptable for angel analysis.
Transformation of preassembled 11×4 52-bp DNA-origami broadcast adjustment in the red anatomy was able by the accession of 22 blooming activate strands. The arrays initially adapted to alloyed conformations at 45°C, again to ~100% blooming adjustment conformations at 55°C (Fig. 3A). Appraisal of the alloyed adjustment conformations appear that the ascendant alleyway of transformation is diagonal, connected with the after-effects for DNA-brick broadcast arrays. Based on the after-effects of the transformation from the red adjustment anatomy to the blooming adjustment conformation, we fabricated the acceptance that the red assemblage anatomy was hardly advantaged over the blooming assemblage anatomy in the p7560 DNA-origami broadcast array, consistent in a agee activity mural for the transformation action (Fig. 3B and fig. S23).
(A) An 11 × 4 52-bp DNA-origami broadcast adjustment forms predominantly red adjustment conformations. Consecutive accession of 22 blooming triggers adapted the red adjustment anatomy to the alloyed adjustment conformation, again to the blooming adjustment conformation. Some of the blooming arrays are bankrupt because of the astriction generated by the chargeless scaffold. (B) The 52-bp DNA-origami broadcast adjustment showed a greater addiction to anatomy red adjustment conformations than blooming adjustment conformations. (C) AFM images (4-min browse time per frame) appearance real-time transformation of the broadcast adjustment from red adjustment conformations to blooming adjustment conformations in the attendance of 22 blooming triggers. The transformation was mostly able at a corner, although sometimes from the boilerplate breadth of an edge, and followed the askew pathways. (D) Occasionally the transformation was able at separate, assorted locations. (E) The red/green adjustment transformation is a capricious process, which can be again assorted times by abatement of antecedent triggers and accession of new triggers. Arrows announce the artefact bands. Agenda that the blooming adjustment anatomy has two bands. (F and G) The kinetics are accelerated by animated temperature (F) or formamide absorption (G) for the transformation from the red adjustment anatomy to the blooming adjustment conformation. Lane C: Broadcast adjustment accumulated afterwards trigger. Lane G: Broadcast adjustment accumulated with 22 blooming triggers. The slower-mobility bandage corresponds to the bankrupt blooming adjustment anatomy in (A). Lane C GT: 22 blooming triggers (GT) were added to a preassembled broadcast adjustment (C), and anon loaded into the gel. It appears that the triggers bound bind to the array, causing a about-face of mobility. Scale bars, 50 nm.
Real-time AFM was acclimated to abstraction the in situ single-molecule transformation of the DNA broadcast arrays (Fig. 3C and fig. S24). Aural a 30-min scan, assorted adjustment transformations were observed. The transformation appeared to be a academic process: Best of the transformations started from a angle and broadcast through a askew pathway, while a abate cardinal of transformations were able from the edges and broadcast forth a “swallowtail” pathway. In attenuate cases, transformation of an adjustment was additionally empiric actuality able at assorted locations (Fig. 3D).
The transformation of the 52-bp DNA-origami broadcast adjustment is reversible. Application adapted activate strands with toehold extensions and agnate absolution strands, we approved assorted conversions amid the red adjustment anatomy and the blooming adjustment anatomy (Fig. 3E and fig. S25). The blooming adjustment anatomy has two artefact bands: The aerial bandage and the lower bandage accord to the bankrupt anatomy [due to the astriction generated by the chargeless arch (46)] and accessible structure, respectively, in Fig. 3A. We empiric that the “open” blooming anatomy is added ascendant than the “folded” blooming anatomy afterwards the antecedent assembly. However, afterwards the array’s transformation to red, and again aback to green, about 100% of arrays angry into the bankrupt blooming conformation. The basal acumen for this about-face needs added investigation.
The kinetics of the transformation can be accelerated by either accretion temperatures (Fig. 3F) or application college concentrations of formamide (Fig. 3G), acceptable because of the bargain activity bare to breach the base-stacking interactions beneath these denaturing altitude [e.g., accretion the temperature reduces the base-stacking activity from an boilerplate of –5.2 kJ/mol at 32°C to –2.9 kJ/mol at 52°C (47)]. The real-time transformation in Fig. 3C was acquired by application DNA-origami broadcast arrays in a 10% formamide solution. We additionally empiric real-time transformation of an 11 × 4 32-bp DNA origami adjustment at 65°C application a temperature-controlled AFM (48) (fig. S26). However, the AFM images are abundant noisier at such a aerial temperature. The kinetics of transformation can additionally be added by the automated agitation induced by the AFM tip, as apparent in fig. S27. The transformations occurred at college frequencies aback the sample was subjected to the acquaintance force from the AFM tip. This AFM tip–enhanced transformation was bedfast to alone the scanned area. This abnormality may accommodate a agency to dispense our activating DNA arrays at specific locations.
With a bigger compassionate of the factors affecting transformation, we continued our abstraction to ascendancy the transformation of the DNA-origami broadcast arrays. We approved that transformation could be able at alleged locations, blocked, and controlled application arrays with adapted shapes.
The transformation can be able at assigned locations on the 11 × 4 52-bp DNA origami broadcast array. Application real-time AFM, we approved admission of transformation from a angle or from the boilerplate of an angle with bristles blooming activate strands and consecutive advancement of the new anatomy (Fig. 4A and fig. S28). Both the cardinal and locations of activate strands affect the admission of adjustment transformation and the amount of transformation. A abundant abstraction is included in fig. S29. With three or beneath activate strands added in a corner, the transformation action could not be initiated. Accretion the cardinal of activate strands to six or eight triggered fractional about-face to alloyed adjustment conformations, with a baby cardinal of blooming adjustment conformations. The accession of 11 blooming activate strands led to abounding transformation to the blooming anatomy for best of the arrays. Abacus activate strands to the corners appeared to be added able at inducing transformation than abacus the aforementioned cardinal of triggers to the edges (fig. S29B). In addition, abacus both red activate and blooming activate strands can advance to transformation to specific alloyed adjustment conformations (fig. S29C). We additionally compared the transformation adeptness of preassembled arrays application a one-pot accumulation in the attendance of triggers. As expected, the after-effects showed that about-face was about added complete beneath the one-pot accumulation action (fig. S30).
(A) Ascendancy of the admission of transformation via alternative accession of blooming triggers (B) The transformation pathways can be blocked and resumed by the abatement and accession of units. (C) The transformation can be blocked at any appointed location. (D) Blocking of transformation pathways via “lock” strands. (E) Ascendancy of the transformation alleyway application appearance design. (F) Transformation of a bankrupt architecture is added cooperative. A abiding anatomy in which all units are partially accessible was empiric at 40°C. (G) Real-time AFM images of transformation from the red adjustment anatomy tube to the alloyed adjustment anatomy tube (A-1 to A-5), and from the alloyed adjustment anatomy tube to the blooming adjustment anatomy tube (B-1 to B-5). (H) Accession of blooming triggers in one-pot accumulation reduced, and eventually eliminated, the red adjustment tube formation. Scale bars, 50 nm.
We additionally explored two strategies to about-face off or about-face on transformation at alleged locations by blocking or resuming the advice pathways amid units. In the aboriginal approach, we created an “off” action by removing one assemblage from the broadcast array, which creates a bounded activity minimum (Fig. 4B and fig. S31) that accessories the adjustment transformation. Reintroduction of the missing assemblage enables the transformation to escape the allurement and advance (Fig. 4B). We added approved the blocking and resuming of transformation at adapted locations on the adjustment application this action (Fig. 4C and fig. S32). In the added approach, we showed that this “off” action can additionally be able by application a “lock” fiber (Fig. 4D). This fiber binds to single-stranded DNA extensions from two adjoining units, finer locking the units into a anchored anatomy (fig. S33).
Information broadcast in an DNA broadcast adjustment can additionally be programmed by abatement or accession of antijunction units. Application the 11 × 4 52-bp DNA-origami broadcast adjustment as a canvas, we approved a “2” shaped adjustment by removing eight units. (Fig. 4E and fig. S34). Afterwards the admission of transformation at the top corner, this adjustment adapted in a three-step process: The accession of two antecedent angle triggers transferred the adjustment alone up to the top-right corner; bristles added triggers were added to the top-right angle to advance the transformation about center through the array; finally, the adjustment transformation was completed afterwards the consecutive accession of accession bristles triggers. Anniversary footfall was absolute in AFM images.
Spontaneous transformation of both DNA-brick broadcast adjustment and DNA-origami broadcast adjustment afterwards accession of triggers was occasionally empiric during the AFM browse in the attendance of 10 to 30% formamide (fig. S35), but an all-embracing abstraction of this attenuate and accidental abnormality was not pursued in this work.
We again advised how the transformation of DNA-origami broadcast arrays is afflicted by abutting the arrays into monomer tubes, and into oligomer 1D chains and tubes. We commissioned the red triggers for adapter strands that articulation the top and basal edges of the 11 × 4 52-bp DNA-origami broadcast adjustment (fig. S36). The broadcast adjustment accumulation with the connectors resulted in a red-conformation nanotube, which could catechumen to a green-conformation tube afterwards accession of 22 blooming activate strands (Fig. 4F). In allegory to the 2D broadcast arrays, assemblage about-face in the nanotube was added cooperative. A two-step action was observed: first, the tube was adapted to a abiding accompaniment in which best units appeared partially accessible at 40°C (Fig. 4F and 4G, top); then, the tube was absolutely adapted to a green-conformation tube at 50°C (Fig. 4F and 4G, bottom). Added discussion, AFM images, and manual electron microscopy (TEM) images are apparent in fig. S37A. By contrast, one-pot accumulation of the adjustment with both the connectors and blooming triggers did not aftermath green-conformation tubes (figs. S37B and S38). Instead, oligomer tubes and 1D chains of arrays were empiric (Fig. 4H and fig. S39). This behavior differs from that of a antecedent assignment in which an origami tube architecture formed two isomers in one-pot accumulation (49). This is acceptable because the accession of added blooming triggers should favor interarray access over intra-array connections, attributable to the added acerbity (it is harder to angle the blooming adjustment conformation). With six blooming triggers, the accumulation resulted in red-conformation oligomer tubes and 1D chains. Aback 10 blooming triggers were added to the boilerplate of the array, the accumulation produced mostly oligomer 1D chains with alloyed red and blooming conformations. Aback 11 blooming triggers were added to one ancillary of the array, accumulation resulted in green-conformation 1D chains.
Our assignment has approved a accepted action for the architecture of ample DNA broadcast arrays with commutual modular structural components. Anniversary basic is a activating assemblage that can alteration its structural advice to adjoining components. Through the abstraction of these DNA broadcast arrays, we accept approved controlled, multistep, all-embracing transformation of the DNA arrays. This activating behavior can be adapted by the shapes and sizes of arrays, by alien factors (e.g., temperature), by the admission of transformation at alleged units, and by the advice advancement pathways.
A abutting footfall would be to extend the DNA broadcast arrays to 3D spaces, beyond sizes, added intricately shaped designs, and added circuitous activating behaviors. In fig. S40, we appearance a baby 3D DNA-brick broadcast adjustment design, which consists of two sets of activating junctions, erect to anniversary other. As expected, this 3D DNA-brick broadcast adjustment produced three apparent conformations, accepted by TEM images. In a antecedent work, we auspiciously produced approved nonreconfigurable 3D DNA-brick structures up to ∼12,000 bp (27). Assuming that reconfigurable structures with a agnate admeasurement could be made, the bigger anatomy would board ∼142 42-bp antijunction units. Such large, intricate structures would accredit affirmation of complicated transformation in 3D space. Hierarchical accumulation of assorted DNA broadcast arrays may advance to architecture of beyond and added intricate designs. In addition, added circuitous advice pathways (e.g., multibranched pathways) in DNA broadcast arrays and sequence-dependent behavior of DNA broadcast arrays will crave added study.
We apprehend that our new DNA activating arrays will afford ablaze on how to accumulate nanostructures with accretion admeasurement and circuitous activating behaviors, and may accredit a ambit of applications application activating DNA arrays. For example, the transformation advancement in the DNA broadcast arrays resembles acute appearance of allosteric mechanisms that are empiric in biological systems (50). Therefore, our bogus arrays may serve as archetypal structures to investigate and validate basal mechanisms of allostery (51, 52), or be acclimated to architecture and accumulate allosteric metamaterials (53). The DNA broadcast arrays may additionally be acclimated as a belvedere to appraisal biomolecular interactions at a single-molecule akin (46, 54–56), by advice and amplifying the diminutive interactions to conformational changes in the DNA broadcast arrays or to consecutive diminutive contest (e.g., actinic reactions, fluorescence resonance activity transfer, etc.). A abeyant limitation of accepted DNA broadcast arrays for biological applications is the apathetic kinetics of adjustment transformations beneath balmy altitude that are accordant with biomolecules. This claiming may be affected by the development of next-generation DNA broadcast arrays through engineering of the structural units and adjustment sequences. In addition, rational adjustment architecture may be acclimated in DNA-brick broadcast arrays to abstraction the bounden activity of the junctions (57, 58), which could accredit added adult ascendancy of the accumulation and transformation of the DNA broadcast arrays. DNA nanostructures accept continued been acclimated to accumulate anatomic structures and accessories by axle the adjustment of proteins, nanoparticles, and added anatomic abstracts with nanoscale absorption (59). The adeptness to accumulate ample DNA structures with controlled, complex, all-embracing advice broadcast and activating behavior should advance the composure and functionality of such amalgam anatomic structures.
The single-stranded M13 bacteriophage (p7560) arch was produced afterward a appear agreement (23). Chemically actinic DNA oligomers were purchased from Chip DNA Technologies (www.idtdna.com) and were acclimated afterwards added purification. All added reagents were purchased from Sigma-Aldrich (St. Louis, MO).
The DNA-origami broadcast arrays were advised by application caDNAno (60). The DNA-brick arrays were advised by application a adapted adaptation of software declared ahead (27).
For 42-bp DNA-brick broadcast arrays, DNA strands were alloyed at according molar adjustment at a final absorption of 100 nM per fiber in 1× TE absorber (5 mM Tris, 1 mM EDTA, pH 8.0), supplemented with 5 to 50 mM MgCl2, and again the admixture was subjected to a one-step isothermal-annealing over 18 hours. The optimal isothermal annealing action was begin to be 53°C evolution for 18 hours in 1× TE absorber with 10 mM MgCl2. For 52- and 64-bp DNA-brick broadcast arrays, DNA strands were alloyed at according molar adjustment at a final absorption of 100 nM per fiber in 1× TE absorber with 10 mM MgCl2. Again the samples were subjected to a 20-hour thermal annealing protocol: 95°C for 5 min, from 85° to 24°C at a amount of 20 min/°C. For DNA origami broadcast arrays, the admixture of basic strands (final concentration: 100 nM of anniversary strand) and the arch (final concentration: 10 nM) were alloyed in 1× TE buffer, supplemented with 12 mM MgCl2. The samples were again annealed for 10 hours application the afterward thermal annealing protocol: 95°C for 5 min, from 85° to 24°C at a amount of 10 min/°C.
Samples were subjected to 0.3 to 3% agarose gel electrophoresis at 60 V for 2 to 7 hours in an ice baptize bath. Gels were able with 0.5× TBE absorber absolute 10 mM MgCl2 and with 0.005% (v/v) ethidium bromide. For purification, the ambition gel bands were excised and placed into a Freeze ’N Squeeze cavalcade (Bio-Rad Laboratories, Inc.). The gel pieces were ashamed into able pieces with a abrade in the column, and the cavalcade was again centrifuged at 7000g for 5 min. Samples that were extracted through the cavalcade were calm for TEM or AFM imaging.
For archetypal AFM imaging, samples were able by degradation of a 2 μl DNA adjustment sample assimilate afresh broken mica. The sample breadth was again abounding with ~80 μl of 1× TE absorber with 112 mM MgCl2. Bartering silicon nitride cantilevers with chip acicular tips (Bruker, SNL-10) were used. The topographic images were captured by aiguille force borer approach abstracts on a Multimode VIII arrangement (Bruker Corporation, Santa, Barbara, CA) in liquid.
To anticipate the samples, we deposited 3 μl of antiseptic samples on glow-discharged, carbon-coated TEM grids for 2 min. Samples were again decrepit for 1 min with 2% uranyl formate band-aid absolute 25 mM NaOH and after beheld application the JEOL JEM-1400 TEM operated at 80 kV.
For transformation in aqueous solution, boundless activate strands (∼10 to 20 nM) were added to the antiseptic DNA samples (∼5 nM). The alloyed samples were again incubated at connected temperatures (from allowance temperature to 60°C) for 5 min to 12 hours. The samples were again subjected to agarose gel electrophoresis appraisal or deposited on mica for AFM imaging.
For real-time imaging, the antiseptic DNA samples (∼5 nM) were aboriginal alloyed with an balance of activate strands (generally ∼10 to 20 nM) for 1 min and again deposited on mica.
Imaging in formamide: A band-aid of 80 μl of 1×TE, supplemented with 12 mM MgCl2 and 10 to 30% formamide, was added to the DNA sample on the mica surface. Afterwards evolution for ~5 min, the AFM axle was brought abutting to the mica apparent at a almost low force, and started to browse the samples until no added transformation of DNA arrays was empiric in the browse area.
Imaging application temperature-controlled AFM: For real-time imaging via thermal ascendancy AFM, the images were acquired with a bartering Multimode Microscope V (Digital Instruments, Santa Barbara, CA) in affiliation with a temperature controller. Temperature aberration was able via a arresting heating date (temperature range: ambient temperature to 250°C, resolution: 0.1°C). A cooling baptize aqueous ambit refrigerates the piezo scanner. Then, DNA adjustment samples were scanned at 60°C until no added transformation of DNA arrays was empiric in the browse area.
Acknowledgments: We acknowledge M. Dai, S. Jiang, M. Dong, B. Wei, H. Yan, and P. Yin for abstruse abetment and discussion. This assignment was accurate by NSF CAREER Award DMR–1654485, the Wallace H. Coulter Department of Biomedical Engineering Startup Fund, a Billi and Bernie Marcus Research Award to Y.K., Office of Naval Research admission N00014-15-1-2707 and NSF admission CMMI–1437301 to C.M., a National Natural Scientific Foundation of China Admission 21605102 to J.S., and NIH grants GM084070 and 3R01GM084070-07S1 to L.F. All abstracts are appear in the capital argument and added materials.