DNA nanotechnology (1–4) enables the bottom-up self-assembly of detached three-dimensional (3D) altar with subnanometer absolute actualization and all-embracing ambit alignment from the nanometer to the micrometer calibration (5–16) and with atomic weights up to the gigadalton calibration (17, 18). The consistent altar may be site-specifically functionalized and adapted with actinic groups and biomolecules (19–21), and altar can be complete that may additionally accommodate mechanisms to crop machine-like behavior (22–24). Custom DNA altar accept been developed and auspiciously acclimated in assorted applications in basal research, thereby carrying new accurate insights and underlining the accommodation of DNA nanotechnology to crop altar with utility. Examples ambit from structural appraisal (25–27) to biophysics (28–33), to photonics (34–37), to plasmonics (38–42), and to atomic electronics (19, 43–45). Aboriginal accomplish accept additionally been taken to assay uses of advised DNA altar as programmable agents in medical appraisal (24, 46). Scalable biotechnological approaches for bearing single-stranded DNA advice pave the way to accumulate DNA altar at the quantities appropriate for abstracts and bloom affliction applications (47).
To accretion use in altered contexts, advised DNA altar charge abide abiding at the ambition altitude for acceptable time so that the adapted appliance furnishings can be achieved. Commonly, applications in low ionic courage solutions such as in physiological fluids, in added solvents, in air or vacuum, and at animated temperatures aloft 50°C are not accessible. Researchers accept accordingly approved for means to aggrandize the ambit of altitude beneath which advised DNA altar abide stable. Added covalent bonds accept been alien in admirable structures amid appropriately adapted fiber termini via actinic (48, 49) or enzymatic articulation (50). DNA nanostructures may additionally be added counterbalanced by the accretion of cofactors such as 8-methoxypsoralen (51) or oligolysine and oligolysine–polyethylene glycol (PEG) copolymers (52, 53).
Despite these advances, it charcoal adorable to authorize complementary, about applicative approaches for the covalent stabilization of DNA nanostructures that do not crave cher chemically adapted strands or the accretion of cofactors. The achievability of creating added covalent access at user-defined sites in DNA nanostructures would accredit the rational stabilization of absolute structures or genitalia of them for uses in a broader ambit of ecology conditions. Moreover, it may accredit the abiding accoutrement of conformational states in mechanisms and in higher-order assemblies. Here, we present a accepted and scalable adjustment for site-selectively introducing added covalent bonds in DNA nanostructures. The ambition bonding sites are defined in the sequences of DNA strands abandoned and do not crave the accretion of actinic modifications. Our adjustment is about applicative to the assorted ambit of DNA nanostructures, and it functions behindhand whether the DNA strands accept been produced via solid-phase actinic amalgam or application a biotechnological action (47).
Pyrimidine dimers are atomic lesions produced by photochemical reactions in DNA (54). Ultraviolet (UV) ablaze induces the accumulation of covalent bonds through reactions at the C=C bifold bonds in thymine (T) or cytosine (C) bases (Fig. 1, left). Common articles are cyclobutane pyrimidine dimers (CPDs), including thymine dimers. Minor by-products, such as (6-4) pyrimidine-pyrimidone and Dewar isomers, may additionally anatomy aloft UV irradiation. These lesions can arrest DNA archetype and archetype and appropriately are cancerogenic and represent targets of the cellular DNA adjustment accouterment (55). In 1982, Lewis and Hanawalt (56) arise that CPDs can additionally anatomy from adjoining terminal thymines in abstracted DNA strands that are brought calm by a templating commutual DNA strand. However, the abeyant of this award for analytic the adherence botheration in DNA nanotechnology has remained anonymous appropriately far. The key abstraction in our assignment is the user-defined adjustment of thymidines in aing adjacency aural DNA nanostructures to rationally actualize sites for introducing covalent CPD bonds via UV irradiation. These added bonds may be acclimated to articulation chargeless fiber termini, to aish fiber breach that action at crossover sites, and to actualize added interhelical access (Fig. 1, right).
(A) Left: Actinic structures of two adjacent thymidines afore UV irradiation. Right: Schematic analogy of a six-helix array DNA nanostructure featuring single-stranded thymidines at fiber termini (1), at half-crossovers (2), at abounding crossovers (3), and thymidine loops (4) afore UV irradiation. (B) As in (A) but afterwards acknowledgment to ablaze with 310-nm wavelength. CPD bonds are adumbrated as red ellipsoids.
The axiological architecture blocks of DNA nanotechnology are double-helical DNA domains. In DNA origami altar (3, 4, 57), these domains anatomy by admixture of a set of abbreviate single-stranded basic oligonucleotides to a continued single-stranded arch molecule. In added types of DNA nanostructures such as DNA tile-brick altar (16), the double-helical domains are formed alone amid single-stranded oligonucleotides. DNA origami and tile-brick altar accommodate hundreds of single-strand breaks, which represent anemic points. This is because chargeless ends accredit not alone the accumulation but additionally the dissolution of plectonemic double-helical domains. To actualize the advantage for removing the single-strand breach afterwards self-assembly of a ambition object, we adapt DNA strands with added thymidines at both fiber termini (Fig. 1A, burden 1). Although the added bases will not be circuitous in basic Watson-Crick abject pairs, the thymidines will arise in aing adjacency at single-strand breach sites in the bankrupt object, which allows CPD bonds to anatomy amid the two thymidines through betterment with ablaze of 310-nm wavelength.
In DNA objects, double-helical domains are affiliated to adjoining double-helical domains by interhelical access about formed by antiparallel single-strand crossovers including both half-crossovers and bifold crossovers (Fig. 1A, burden 2 adjoin burden 3). For example, DNA tile-brick altar are about alone affiliated via half-crossovers, while in DNA origami objects, both types of interhelical access may occur. The crossover positions additionally represent anemic credibility in DNA nanostructures due to the disconnected courage bonds in the circling direction. To actualize the advantage for closing the anemic links afterwards self-assembly, we may add added unpaired thymidine bases in the basic strands at crossover positions, as adumbrated in Fig. 1A (motifs 2 and 3). Through proximity, betterment with 310-nm ablaze afresh may abet the accumulation of CPD bonds that covalently affix the strands forth the circling administration (Fig. 1B, motifs 2 and 3), thereby creating accretion topological albatross for circling unwinding.
When designing DNA objects, fiber crossovers are about placed amid adjoining double-helical domains at positions area the circling backbones arise aing together. Commutual to fiber crossovers, we may additionally accomplishment the light-induced CPD dimer bonds to actualize added interhelical linkages afterwards self-assembly of an object. To this end, we abode single-stranded thymidine loops (T loops) at positions area the backbones of adjoining DNA helices almost adjust (Fig. 1A, burden 4). Betterment at 310 nm can afresh abet the conception of covalent interhelical linkages (Fig. 1B, burden 4).
To appraisal our method, we implemented the architecture alterations apparent in Fig. 1 in several variants of multilayer DNA origami objects. We activated the adherence of the consistent altar afterwards betterment with ablaze of 310-nm amicableness in melting abstracts (Fig. 2, left) and in abstracts in which we removed cations from band-aid (Fig. 2, right). We adapted a brick-like multilayer DNA origami (58) commodity in honeycomb-packing geometry (fig. S1) by inserting added thymidines both at all fiber termini and at all fiber crossover positions. We begin that the nonirradiated ascendancy sample disassembled (“unfolded”) about 50°C, as apparent in gel electrophoresis by dematerialization of the bandage advertence bankrupt objects, and actualization of chargeless basic strands (Fig. 2A, larboard gel). By contrast, the ablaze sample preserved its all-around appearance up to 90°C, anticipation by the actuality that the electrophoretic advancement of the bankrupt breed charcoal abundantly unaltered. A slight apply at aerial electrophoretic mobilities shows that some strands still abstracted from the bankrupt altar at aerial temperatures. However, the strands that afar had abundant lower electrophoretic mobilities and appropriately college accumulation than the basic strands that emerged from the aqueous nonirradiated ascendancy sample. The high-temperature attrition of the ablaze commodity and the actualization of higher-mass strands accommodate affirmation for the acknowledged accretion of covalent cross-links at the advised thymidine sites aloft UV irradiation.
(A) From larboard to right: Archetypal of the brick-like DNA origami commodity featuring added thymidines at all fiber termini and at all fiber crossover positions; laser-scanned beaming images of 2.0% agarose gels decrepit with ethidium bromide. Ablaze (135 min at 310 nm) and nonirradiated samples were either incubated for 30 min at altered temperatures or incubated for 3 hours at allowance temperature in double-distilled baptize (ddH2O) absolute successively lower concentrations of monovalent sodium chloride, respectively. p, pocket; u, abundant species; f, bankrupt species; c, cross-linked basic strands; s, uncross-linked basic strands; L, 1kB ladder; NI and I, nonirradiated and ablaze advertence samples in folding absorber with 5 mM MgCl2, respectively. The images of the gels were autoleveled, and the accent regions were autoleveled twice; boilerplate 2D atom micrograph of the ablaze sample in double-distilled water. (B and C) As in (A) but with the brick-like DNA origami commodity featuring added thymidines at all fiber termini and at all fiber crossover positions and with 5-T loops and the arrow commodity featuring added thymidines at all fiber termini and at all fiber crossover positions, respectively. See fig. S9 for globally autoleveled gel images.
We additionally activated the adherence of the ablaze adjoin nonirradiated sample back removing cations from solution. Application filtration, we exchanged buffers and attenuated the samples in double-distilled baptize absolute successively lower concentrations of monovalent sodium chloride (Fig. 2A, right). The ablaze sample remained bankrupt alike in double-distilled baptize absolute aught added cations, admitting the nonirradiated ascendancy disassembled amid 300 and 150 mM sodium chloride (NaCl), as apparent by able advancement accouterment and the actualization of distinct strands with aerial mobility. Manual electron microscopy (TEM) imaging of the ablaze sample attenuated in authentic baptize arise particles with the accepted appearance (fig. S2). The bulk of adverse of the sample in authentic baptize was college than at high-salt conditions. Electrophoretic appraisal afterwards up to 1 day of accumulator in authentic baptize showed no changes in electrophoretic mobility, and we could not ascertain any basic strands that afar from the bankrupt altar (fig. S3). Therefore, simple architecture alterations and UV betterment acquiesce the stabilization of the commonly absolutely cation-sensitive multilayer DNA origami for uses beneath physiological (~150 mM NaCl) and alike lower ionic courage conditions. Abounding added acrid environments may additionally be attainable afterwards UV stabilization. As a simple demonstration, we attenuated the cross-linked altar in aqueous mixtures of dimethyl sulfoxide (an amoebic solvent) afterwards added cations (fig. S4).
As a added example, we able and activated a alternative of the brick-like commodity in which we additionally amid single-stranded T loops (motif 4 in Fig. 1), in accretion to added thymidines at all fiber termini and at all crossover positions (fig. S5). The admeasurement of thermal and cationic stabilization afterwards betterment (Fig. 2B) was agnate compared to the architecture alternative defective the single-stranded T loops. We activated loops absolute one, three, and bristles thymidines. The alternative with 5-T loops showed incrementally greater stabilization at aerial temperatures (80°C), anticipation by gel electrophoretic bandage acuteness (fig. S6). We agenda that the betterment of the brick alternative with added 5-T loops for interhelical bonds additionally leads to a slight electrophoretic advancement access compared to the nonirradiated ascendancy (Fig. 2B, lane R2 adjoin lane R1), which suggests that the added interhelical bonds may advance to some bulk of compaction or automatic stabilization.
As a third example, we chose the ahead declared “pointer” commodity (13), which is a multilayer DNA origami in aboveboard filigree packing geometry, and added added thymidines at all fiber termini and at all crossover positions (fig. S7). As for the brick variants, betterment with UV ablaze counterbalanced this commodity adjoin acknowledgment of temperatures up to 90°C, and the arrow commodity may now be attenuated in authentic baptize afterwards any cations (Fig. 2C). The nonirradiated ascendancy arrow sample already disassembled amid 45° and 50°C and appropriate added than 300 mM NaCl in band-aid to abide folded, as apparent by electrophoretic advancement appraisal (Fig. 2C) and TEM imaging (fig. S8).
In the advance of establishing our method, we activated several ambit such as time of acknowledgment to UV irradiation. In addition, we performed a birthmark appraisal application the de Bruijn appraisal (59) to appraise the structural candor of double-helical domains in DNA altar aloft UV irradiation. About 2 hours of acknowledgment at our UV bureaucracy advance to best able stabilization for all structures activated (figs. S10 and S11) afterwards signs of structural abasement (fig. S12). For beneath betterment times, the cross-linking was not complete, acceptation that structures did not survive acknowledgment to temperatures essentially aloft the melting temperatures afore UV treatment. For betterment times best than the optimal, structural radiation amercement accumulated, as reflected in successively lower electrophoretic mobilities of the objects. Therefore, the acknowledgment to UV betterment follows a Goldilocks principle. Because the optimal betterment time will depend on capacity of the UV ablaze antecedent and added parameters, our optimal betterment times will not necessarily authority up in added contexts. However, users can assay the optimum betterment time by application screens agnate to those we performed.
As categorical in Introduction, our adjustment relies on CPDs, which could anatomy amid T-T but additionally between, for example, T-C contacts. We compared the ability of cross-linking for brick variants able with T-T adjoin T-C at all fiber termini and at all fiber crossover positions (fig. S13). On the abject of the bulk of structures that survive acknowledgment to aerial temperatures afterwards UV exposure, T-T bonds anatomy decidedly added calmly than the T-C contacts and advance to complete stabilization. The cross-linking formed auspiciously through acknowledgment to 310-nm light. Best wavelengths, such as 365 nm, did not advance to stabilization in our easily (fig. S14), although it has been arise that CPD bonds may additionally anatomy through acknowledgment to 365-nm UVA ablaze (60).
Our UV cross-linking adjustment may be acclimated to essentially enhance the adherence of DNA nanostructures, and in accurate multilayer DNA origami objects, for applications beneath physiological conditions. As a demonstration, we attenuated the brick-like multilayer DNA origami object, which absolute added Ts at all basic termini and at all crossover positions in physiological phosphate-buffered acrid (PBS) solution, and incubated the altar at the physiological temperature of 37°C. Alike afterwards 2 canicule of accumulator in PBS at 37°C, there was no apparent abasement of the ablaze and covalently cross-linked sample (Fig. 3A). By contrast, the nonirradiated ascendancy disassembled aural account afterwards acknowledgment to these conditions. Anticipation by the admeasurement to which ablaze architecture variants of the brick sample remained abiding at physiological temperature and ionic strength, the stabilization appeared complete for the architecture alternative that had added T bases to all fiber termini and at all half-crossover and abounding crossover positions. Ligating alone the chargeless fiber termini and a subset of crossovers was not abundantly able in attention the abounding anatomy (fig. S15). In 10% fetal bovine serum (FBS) at 37°C, the ablaze brick sample survived for several hours and essentially best than a nonirradiated ascendancy (Fig. 3B). In serum, apparently the accident of bankrupt structures was acquired by agitator action rather than the low ionic courage of the solution.
Laser-scanned beaming images of 2.0% agarose gels decrepit with ethidium bromide. Cross-linked samples were ablaze for 135 min at 310 nm. (A) The brick-like DNA origami commodity featuring added thymidines at all fiber termini and at all fiber crossover positions was incubated for altered periods of time in PBS band-aid at 37°C. (B) The brick-like DNA origami commodity featuring added thymidines at all fiber termini, at all fiber crossover positions, and 5-T loops was incubated for altered periods of time in 10% FBS at 37°C. (C) The brick-like DNA origami commodity from (A) was apparent to a set of altered nucleases (100 U/ml) for 24 hours at 37°C. Lanes labeled with a “c” announce controls in which the sample was attenuated in the agnate buffers in the absence of nuclease. (D) The brick-like DNA origami commodity from (B) was apparent to DNase I (0.4 U/ml) for altered periods of time at 37°C. (B to D) Nonirradiated and ablaze samples were loaded on the gel alternatingly. All images of the gels were globally autoleved.
Biological fluids, such as serum, accommodate a array of exo- and endonucleases for digesting DNA molecules. To annotate the action of assorted nucleases, we apparent the brick-like multilayer DNA origami commodity featuring Ts at fiber termini, at all crossover positions, and T loops to a console of such enzymes (Fig. 3C). Some enzymes, such as Exo VIII and T7 Exo, by default, arise abeyant on the brick sample whether it was ablaze or not. However, for others (such as Exo I e, Exo T, T7 Endo, and Exo III), accretion of the added covalent bonds through betterment essentially added the lifetime of the cross-linked commodity compared to the nonirradiated ascendancy sample. The best alive DNA-degrading agitator was deoxyribonuclease I (DNase I). A active appraisal of the assimilation of the brick-like commodity application DNase I at claret claret action levels (61) arise that the ablaze and appropriately counterbalanced brick sample was digested abundant added boring than the nonirradiated control. Appraisal of the bandage intensities reveals an about five- to sixfold life-span amplification from 10 to 60 min through cross-linking beneath the altitude activated (Fig. 3D). The brick alternative featuring alone added Ts at fiber termini and at all crossover positions (lacking interhelical T loops) showed somewhat weaker animation adjoin DNase I assimilation (fig. S16).
To annotate the furnishings of UV betterment and CPD bandage accumulation on the anatomy of a DNA object, we exemplarily bent bristles electron anatomy maps application single-particle cryo–electron microscopy (cryo-EM) (Fig. 4, A to C). First, we calm single-particle cryo-EM abstracts on a nonirradiated ascendancy multilayer brick sample absolute added Ts at all fiber termini and all fiber crossover positions (fig. S17). The reconstructed 3D EM anatomy map arise the accepted all-around ellipsoidal brick-like appearance (Fig. 4A). However, the commodity showed additionally a all-around aberration anamorphosis (Fig. 4D), whose admeasurement was added arresting than what was accepted on the abject of a antecedent appraisal of a agnate brick-like commodity defective the added Ts (17). Presumably, the added Ts access the adaptability of crossover sites, which may affect the packing geometry of helices. We bent the chirality of the aberration anamorphosis to be right-handed application a tomographic bend alternation (movie S1).
(A) Cryo-EM anatomy map of the nonirradiated brick-like commodity with TT motifs 1 to 3 (Electron Microscopy Abstracts Bank identifier EMD-4354). (B and C) Cryo-EM anatomy map of the ablaze (135 min at 310 nm) brick-like commodity with TT motifs 1 to 3 in absorber absolute 5 mM MgCl2 or in PBS buffer, respectively. The electron anatomy thresholds are called in such a way that all crossovers in the top bandage are visible, as apparent in the ancillary appearance (Electron Microscopy Abstracts Bank identifier EMD-0027 and EMD-0028, respectively). (D) Slices forth the z administration acquired from the three anatomy maps apparent in (A) to (C) from top to bottom. To actuate the aberration bend basin Theta, the aboriginal and aftermost slices were chosen. (E) Slices assuming the three crossover layers in the reconstructions apparent in (A) to (C). (F) Allegory of the all-around ambit of the uncross-linked alternative in 5 mM MgCl2 absorber and the cross-linked alternative in PBS buffer. Color cipher as apparent in (A) to (C).
Second, we calm single-particle cryo-EM abstracts of the brick-like commodity afterwards acknowledgment to UV betterment (fig. S18). The reconstructed 3D EM anatomy map afresh arise the all-around ellipsoidal brick-like appearance (Fig. 4B). Afterwards irradiation, the right-handed all-around aberration was decidedly beneath (Fig. 4D). We aspect the aberration abridgement to the conception of the added covalent bonds at the crossover sites, which reduces the alliance adaptability and aligns the helices afresh in a geometry afterpiece to the absence honeycomb-packing design. Previously, Chen and coworkers (62) UV-irradiated single-layer DNA origami rectangles to investigate radiation amercement and empiric a twist-reducing flattening effect. However, because the samples of Chen and coworkers were not accurately advised to accommodate thymidine-thymidine cross-linking sites, the apparatus arch to aberration abatement may be altered from our samples. Third, we calm single-particle cryo-EM abstracts of the ablaze brick-like commodity already it had been attenuated in physiological ionic courage PBS absorber (fig. S19). The consistent 3D EM anatomy map afresh arise a all-around ellipsoidal brick-like appearance (Fig. 4C). A slice-by-slice allegory of the three cryo-EM maps indicates that the centralized arrangement of crossovers has been preserved afterwards betterment and acknowledgment to low ionic courage altitude (Fig. 4E, fig. S20, and movies S2 to S4).
The all-embracing aspect arrangement of the cryo-EM anatomy map bent for the cross-linked sample at low (physiological) ionic courage was altered compared to the cryo-EM anatomy maps, which were bent at college ionic courage in the attendance of magnesium (Fig. 4, A to C and F). The object’s cantankerous area broadcast beneath physiological altitude by about 15% and shrank in the circling administration by about 8%. The anamorphosis apparently is a aftereffect of the able electrostatic abhorrence in PBS buffer, which pushes the helices abroad from anniversary other. Afterwards UV irradiation, these armament would commonly advance to the disassembly of the object. However, the added covalent CPD bonds afterwards UV ablaze acknowledgment anticipate the double-helical DNA domains from dissociating.
Finally, we additionally calm single-particle cryo-EM abstracts of the brick-like alternative advised with added T loops for interhelical bonds afore and afterwards acknowledgment to UV irradiation, respectively. The consistent 3D EM anatomy maps afresh arise the accepted all-around ellipsoidal brick-like appearance (figs. S21 and S22, respectively). However, the centralized crossover filigree was beneath able-bodied bound than in the architecture variants that lacked the added T loops, which we aspect to the added arresting atomic adverse in these samples that is acquired by the attendance of added adjustable T loops.
The targeted accretion of base-paired thymidines additionally enables us to covalently cross-link DNA-based mechanisms and higher-order assemblies beyond bounden interfaces. We authenticate actuality the achievability of locking conformational states with a ahead declared two-state about-face (fig. S23) (11). The bankrupt accompaniment of the about-face is counterbalanced by abject pair–stacking contacts back the shape-complementary surfaces of its two beams arise in absolute acquaintance (Fig. 5A). The commodity may be switched amid the two states by adopting and blurred the temperature or through accretion of cations such as magnesium chloride. We accepted that in the bankrupt state, terminal thymidines positioned anon at the blunt-ended abject pair–stacking contacts may be in acceptable adjacency to acquiesce the accumulation of CPD dimer bonds aloft UV irradiation. The about-face architecture already absolute several such TT-stacking contacts. A time-resolved appraisal of the furnishings of UV betterment on the about-face in the attendance of 30 mM MgCl2 (which stabilizes the bankrupt state) reveals that, afterwards 30-min exposure, about 80% of the particles were irreversibly trapped in the bankrupt state. We achieve this from the bandage arrangement in gel electrophoresis beneath the low ionic courage conditions, which commonly advance to the aperture of the about-face at 5 mM MgCl2 (Fig. 5, B and C). Hence, the CPD bonds may additionally be formed amid absolutely abstracted double-helical DNA domains that are captivated in proximity.
(A) Schematics of the two-state about-face that consists of two adamant beams flexibly affiliated in the boilerplate by an anchored Holliday junction. Cylinders in the models represent double-helical DNA domains, and shape-complementary apparent actualization are accent in red and blue. Insets appearance blow-ups of the blunt-ended interfaces of bulging (red) and backward (blue) apparent features. Thymidines anon amid at the blunt-end armpit can be cross-linked aloft UV ablaze irradiation. The consistent CPD bandage is adumbrated as a red ellipsoid. (B) Laser-scanned beaming angel of 2.0% agarose gel decrepit with ethidium bromide. About-face samples were ablaze at 310 nm for altered periods of time and loaded on the gel. o and c, breed of particles clearing accessible and bankrupt state, respectively. (C) Plot of the atom of cross-linked about-face particles as a action of time acquired from the gel in (B). The agreement was performed in triplicate; abstracts credibility represent the mean, and absurdity confined represent the SD. (D) Admirable TEM micrographs. Top: Nonirradiated sample with particles clearing the accessible state. Bottom: Ablaze (20 min at 310 nm) sample with particles bound in the bankrupt conformational state. Calibration bars, 100 nm. Inset: Boilerplate 2D atom micrograph of cross-linked particles. Calibration bar, 20 nm. (E) Top left: Archetypal of the multilayer DNA origami brick that polymerizes into beeline filaments. Fields of appearance of TEM micrographs recorded at the adumbrated conditions. Calibration bars, 100 nm.
In addition, we authenticate the achievability of stabilizing higher-order assemblies with a ahead declared multilayer DNA origami brick (fig. S24) that oligomerizes at aerial ionic courage via shape-complementary abject pair–stacking contacts into beeline filaments (11). The filaments, by default, deliquesce back the ionic courage of the band-aid is bargain afresh (Fig. 5E). By agreement TT motifs at the abject pair–stacking contacts, the higher-order filaments may additionally be covalently counterbalanced by simple UV irradiation. As a result, the filaments no best abstract back apparent afresh to low ionic courage conditions, as apparent by TEM imaging (Fig. 5E). The achievability of stabilizing accurate conformational states or higher-order assemblies may be abnormally advantageous to adapt containers or mechanisms congenital from abounding subunits for applications in low ionic courage conditions. Interior design, as apparent in Fig. 1, and interfacial bonding schemes, as illustrated in Fig. 5, could be accumulated to crop subunits and higher-order assemblies that bear a advanced ambit of conditions.
Users of our adjustment can artlessly ascertain sites of covalent bonding in DNA assemblies by creating TT arrangement motifs, area the two Ts charge not be positioned aural double-helical domains. The altar advised actuality featured, by default, several sites for CPD bandage accumulation because the bacteriophage-derived arch fiber itself already absolute assorted TT and AA motifs. To aish the accumulation of causeless CPD dimers aloft betterment and to abstain the added T insertions if so desired, new custom arch sequences may be developed in the future. By design, these sequences could abridgement TT motifs and affection AA motifs in the approved intervals that accord to the centralized alliance agreement rules in honeycomb- or aboveboard lattice–packing geometries. Scaffold-free DNA objects, such as tile-brick structures (15), may additionally be accurately advised with sequences that selectively abode TT motifs at crossovers and at fiber termini to accredit covalent bonding by UV irradiation. Our after-effects appearance that the bald adjacency of thymidines is acceptable to arrangement the accumulation of covalent linkages through UV irradiation. Moreover, the thymidines do not necessarily charge to be placed aural a double-helical ambience to anatomy these linkages.
The cryo-EM maps presented actuality appearance that the DNA altar bottle their all-around appearance afterwards UV treatment. Our maps additionally add to the anatomy of structural abstracts in DNA nanotechnology and advice accept the affiliation amid architecture capacity and consistent shape. For example, we presented a multilayer DNA origami cryo-EM map at physiological ionic strength. Formerly, it was not accessible to assay these structures because the altar would “explode” beneath these conditions. Our cryo-EM map at physiological altitude reveals a abundant abscess behavior, which helps acknowledge the accretion of electrostatics to all-around shape. Approaching designs for physiological altitude will charge to accede the abscess behavior to aftermath shapes according to specifications.
Our adjustment supports a broader account of DNA-based nanotechnology, in accurate for the added structurally circuitous multilayer 3D DNA objects, which arguably action adorable degrees of abandon to designers but tend to be added acute to ecology conditions. Because of the simplicity, arrangement programmability, and scalability, covalent bonding by UV betterment will advice pave the way for applications of DNA nanostructures in a advanced array of altitude for a ambit of fields.
The acknowledgment mixtures absolute arch DNA at a absorption of 20 nM and oligonucleotide strands at 200 nM each. The folding absorber included 5 mM tris, 1 mM EDTA, 5 mM NaCl (pH 8), and 20 mM MgCl2. The acknowledgment mixtures were subjected to a thermal annealing access application Tetrad (MJ Research, now Bio-Rad) thermal cycling devices. Oligonucleotides were purchased from Eurofins MWG. See Table 1 for folding ramps acclimated to accumulate the altar declared in this study.
After the folding reaction, all acknowledgment articles were antiseptic application one annular of PEG precipitation (63). The consistent pellet was attenuated in folding absorber (5 mM tris, 1 mM EDTA, and 5 mM NaCl) including 5 mM MgCl2. The final aggregate was called to get a monomer absorption of 100 nM. The samples were equilibrated at 30°C and 450 rpm brief in a shaker incubator (Thermomix abundance from Eppendorf). All procedures were performed as ahead declared (64).
For UV irradiation, we acclimated a 300-W xenon ablaze antecedent (MAX-303 from Asahi Spectra) with a aerial manual bandpass clarify centered about 310 nm (XAQA310 from Asahi Spectra). We acclimated a ablaze adviser (Asahi Spectra) to brace the ablaze into the sample by agreement it anon on top of a 0.65-ml acknowledgment tube. Unless contrarily indicated, the brick-like samples were ablaze for 135 min, the arrow samples for 120 min, and the polymerizing brick samples for 30 min. Samples were ablaze in folding absorber (5 mM tris, 1 mM EDTA, and 5 mM NaCl) including 30 mM MgCl2, unless contrarily stated.
All samples (cross-linked and uncross-linked) were subjected to three circuit of ultrafiltration (Amicon Ultra 500 μl with 100k cutoff). Ultrafiltration was agitated out at 20°C and 7k about centrifugal force (Eppendorf 5424R). The absorber was replaced by folding absorber (5 mM tris, 1 mM EDTA, and 5 mM NaCl; including 5 mM MgCl2), PBS, or double-distilled baptize supplemented with 300, 150, 100, 50, 25, and 0 mM NaCl. Samples acclimated for cryo-EM were concentrated to 1000 nM.
Samples were electrophoresed on 2.0% agarose gels absolute 0.5× tris-borate- EDTA and 5 mM MgCl2 for about 2 hours at 90-V bent voltage in a gel box absorbed in a baptize or ice bath, unless contrarily stated. Samples were loaded on the gel at a monomer absorption of about 5 nM. The electrophoresed agarose gels were scanned application a Typhoon FLA 9500 laser scanner (GE Healthcare) at a resolution of 25 μm/pixel. The consistent 16-bit tif images were analyzed application ImageJ 1.440.
Samples were adsorbed on glow-discharged, collodion-supported, carbon-coated (10 nm) Cu400 TEM grids (in-house production) and decrepit application a 2% aqueous uranyl formate band-aid absolute 25 mM sodium hydroxide. Samples were incubated for 15 to 300 s depending on the buffer/solvent used. For samples attenuated in solvents including low concentrations of absolutely answerable ions, we acclimated college monomer concentrations (50 nM) and best evolution times. We acclimated magnifications amid ×10,000 and ×30,000 to access the data.
Imaging was performed on altered microscopes (see Table 2). TEM micrographs acclimated in the abstracts were high-pass–filtered to aish all-embracing staining gradients, and the adverse was autoleveled (Adobe Photoshop CS6).
For 2D angel processing, libraries of alone atom micrographs were created by atom acrimonious application the RELION-2 acrimonious accepted (65). Generation of boilerplate 2D atom micrographs was performed application RELION-2 (65). Typically, about 2000 alone particles were averaged.
For the brick-like commodity with TT motifs 1 to 3, concentrations amid 700 and 850 nM were used. The samples were activated to C-Flat 1.2/1.3, 1.2/1.3, 2/1, or 2/2 blubbery grids (Protochips). Plunge freezing was performed with an FEI Vitrobot Mark V apparatus with a blemish time of 3 s, a blemish force of −1, and a cesspool time of 0 s beneath 95% clamminess and 22°C.
For the brick-like commodity with TT motifs 1 to 4, concentrations amid 560 and 800 nM were used. The samples were activated to C-Flat 1.2/1.3, 2/1, or 2/2 blubbery grids. Plunge freezing was performed with an FEI Vitrobot Mark V apparatus with a blemish time of 3 s, a blemish force of −1, and a cesspool time of 0 s beneath 95% clamminess and 22°C.
Automated abstracts accumulating was performed on a Titan Krios G2 electron microscope (FEI) operated at 300 kV and able with a Falcon III absolute detector (FEI). We acclimated EPU for distinct atom and FEI tomography for bend alternation acquisition. For all brick-like altar beneath altered conditions, movies absolute 15 frames, 1.5- to 2-s acknowledgment time, and a absolute dosage of 60 e−/Å2 were recorded on a Falcon III (FEI) absolute electron apprehension camera in fractioning approach at a calibrated deepening of ×29,000 with a abstract pixel admeasurement of 2.3 Å. Defocus ethics alignment from −1 to −3 μm were used.
The recorded movies were subjected to motion alteration with MotionCor2 (66), and subsequently, adverse alteration action ambit were estimated with CTFFIND4.1 (67). All consecutive processing accomplish were performed in RELION-2.1 (65, 68). For anniversary abstracts set, references for automatic acrimonious were affected from about 5000 manually called particles. With the best particles, assorted circuit of reference-free 2D allocation were performed. The best 2D chic averages, as advised by beheld inspection, were selected. An antecedent archetypal was produced from a bild book generated by CanDo. Afterwards assorted circuit of 3D classification, the classes assuming the best actualization were called for 3D autorefinement, and subsequently, post-processing for cutting of the aesthetic map was performed with altered manually called B factors.
A cryo-tomogram for validation of the aberration administration was acquired with FEI tomography, with a defocus of −3 μm at a calibrated deepening of ×29,000, agnate to a abstract pixel admeasurement of 2.3 Å. The affair was set up as bidirectional angry in increments of 2° up to 50°, and the dosage per angel was set to ~2 e−/Å2. The consistent bend alternation was candy with the IMOD 4.9 accepted (69).
In Fig. 2, samples were bankrupt and PEG-purified, and the MgCl2 absorption was adapted to 30 mM. Afterwards UV irradiation, the absorber was exchanged to the ambition buffer/solvent by application ultracentrifugation. Afore gel electrophoresis, the samples were incubated for about 2 to 3 hours at allowance temperature. Samples for the temperature awning were incubated for 30 min at the adumbrated temperatures. The samples for negative-stain TEM were able at a monomer absorption of 50 nM, with evolution on the filigree for 3 to 5 min.
In Fig. 3B, the adherence awning in folding absorber (5 mM MgCl2) supplemented with 10 % FBS (not heat-inactivated; Gibco; A3160801, Thermo Fisher Scientific) was performed at a monomer absorption of 20 nM at 37°C for the adumbrated time. The samples were arctic in aqueous nitrogen and analyzed application agarose gel electrophoreses. In Fig. 3C, all nucleases were purchased from New England Biolabs and acclimated at a absorption of 100 U/ml in the supplied manufacturer’s buffer. The samples (10 nM) were incubated at 37°C for 24 hours. In Fig. 3D, the time advance of the adherence adjoin DNase I nuclease assimilation was performed at a monomer absorption of 10 nM in the supplied DNase I absorber at 37°C.
In Fig. 5, the betterment time awning for the about-face was performed in triplicate. The ablaze aggregate was 25 μl at a monomer absorption of 5 nM. For the appraisal of the gel apparent in Fig. 5B, we affected the arrangement amid the bandage including bankrupt particles and the bands including accessible and bankrupt particles. The grayscale ethics for anniversary bandage were acquired by integration. The abstracts credibility in Fig. 5C represent the average, and the absurdity confined represent the SD of the three absolute experiments. For the accumulation of the filaments, monomers were bankrupt and PEG-purified. The pellet was attenuated in folding absorber (5 mM MgCl2) to access a monomer absorption of 100 nM. Afterwards equilibration, the MgCl2 absorption was adapted to 20 mM, and the sample was incubated at 40°C for 3 canicule in the Tetrad to access filaments. One allotment of the sample was ablaze at 310 nm for 30 min. The MgCl2 absorption was decreased to 5 mM by the accretion of EDTA.
Supplementary actual for this commodity is accessible at http://advances.sciencemag.org/cgi/content/full/4/8/eaau1157/DC1
Fig. S1. Architecture diagram of the brick-like (TT motifs 1 to 3) commodity able application caDNAno.
Fig. S2. Admirable negative-stained TEM micrographs of the brick-like commodity (TT motifs 1 to 4) in altered buffers/solvents.
Fig. S3. Laser-scanned beaming angel of a 2.0% agarose gel that was run in an ice-cooled baptize bath.
Fig. S4. Laser-scanned beaming angel of a 2.0% agarose gel that was run in an ambient temperature baptize bath.
Fig. S5. Architecture diagram of the brick-like (TT motifs 1 to 4) commodity able application caDNAno.
Fig. S6. Laser-scanned beaming angel of a 2.0% agarose gel placed in an ice-cooled baptize bath.
Fig. S7. Architecture diagram of the arrow object.
Fig. S8. Admirable negative-stained TEM micrographs of the arrow commodity in altered buffers/solvents.
Fig. S9. Laser-scanned beaming angel of a 2.0% agarose gel placed in a baptize bath.
Fig. S10. Laser-scanned beaming angel of a 2.0% agarose gel placed in a baptize bath.
Fig. S11. Laser-scanned beaming angel of a 2.0% agarose gel placed in a baptize bath.
Fig. S12. Laser-scanned beaming angel of a 2.0% agarose gel placed in an ice-cooled baptize bath.
Fig. S13. Laser-scanned beaming angel of a 2.0% agarose gel placed in a baptize bath.
Fig. S14. Laser-scanned beaming angel of a 2.0% agarose gel placed in a baptize bath.
Fig. S15. Laser-scanned beaming angel of a 2.0% agarose gel placed in a baptize bath.
Fig. S16. Laser-scanned beaming angel of a 2.0% agarose gel placed in a baptize bath.
Fig. S17. Cryo-EM abstracts of the brick-like commodity with TT-motifs (1) – (3) afore crosslinking in folding buffer.
Fig. S18. Cryo-EM abstracts of the brick-like commodity with TT-motifs (1) – (3) afterwards crosslinking in folding buffer.
Fig. S19. Cryo-EM abstracts of the brick-like commodity with TT-motifs (1) – (3) afterwards crosslinking in phosphate-buffered acrid (PBS).
Fig. S20. Slice-by-slice decision of cryo-EM maps bent from brick samples.
Fig. S21. Cryo-EM abstracts of the brick-like commodity with TT-motifs (1) – (4) afore crosslinking in folding buffer.
Fig. S22. Cryo-EM abstracts of the brick-like commodity with TT-motifs (1) – (4) afterwards crosslinking in folding buffer.
Fig. S23. Architecture diagram of the about-face object.
Fig. S24. Architecture diagram of the polymerization brick object.
Table S1. Sequences of basic strands for all DNA altar acclimated in this work.
Movie S1. Tomogram acquired from cryo-EM of the brick-like alternative with thymines at all basic termini and with TT motifs at all crossover sites.
Movie S2. Agnate cine to fig. S20 for the nonirradiated (uncross-linked) sample of the brick-like alternative with thymines at all basic termini and with TT motifs at all crossover sites in folding absorber and in the attendance of 5 mM MgCl2.
Movie S3. Agnate cine to fig. S20 for the ablaze (cross-linked) sample of the brick-like alternative with thymines at all basic termini and with TT motifs at all crossover sites in folding absorber and in the attendance of 5 mM MgCl2.
Movie S4. Agnate cine to fig. S20 for the ablaze (cross-linked) sample of the brick-like alternative with thymines at all basic termini and with TT motifs at all crossover sites in PBS absorber and in the absence of MgCl2.
Movie S5. Agnate cine to fig. S20 for the nonirradiated (uncross-linked) sample of the brick-like alternative with thymines at all basic termini, with TT motifs at all crossover sites and added 5-T loops in folding absorber and in the attendance of 5 mM MgCl2.
Movie S6. Agnate cine to fig. S20 for the ablaze (cross-linked) sample of the brick-like alternative with thymines at all basic termini, with TT motifs at all crossover sites and added 5-T loops in folding absorber and in the attendance of 5 mM MgCl2.
Acknowledgments: We acknowledge F. Praetorius for discussions and F. Engelhardt for abetting experiments. Funding: This assignment was accurate by a European Appraisal Council Consolidator Grant to H.D. (GA no. 724261) and the Deutsche Forschungsgemeinschaft through grants provided aural the Gottfried-Wilhelm-Leibniz Program, the Excellence Clusters CIPSM (Center for Integrated Protein Science Munich), and the Technical University of Munich Institute for Advanced Study. Author contributions: T.G., M.K., and B.K. performed the research. H.D. advised the research. T.G. and H.D. wrote the arrangement and able the figures. All authors commented on the manuscript. Aggressive interests: T.G. and H.D. are inventors on a conditional apparent accompanying to this assignment that has been filed by the Technical University of Munich (“Novel adjustment for stabilizing nucleic acerbic nanostructures,” submitted 5 June 2018). The authors acknowledge no added aggressive interests. Abstracts and abstracts availability: All abstracts bare to appraise the abstracts in the cardboard are present in the cardboard and/or the Supplementary Materials. Cryo-EM abstracts that abutment the allegation of this abstraction accept been deposited in the Electron Microscopy Abstracts Bank (EMDB) with accretion codes EMD-4354, EMD-0027, EMD-0028, EMD-4357, and EMD-0029. Added abstracts accompanying to this cardboard may be requested from the authors.
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