Logic-Gated Plasmonic Nanodevices Based on DNA-Templated Assembly

Open AccessCCS ChemistryCOMMUNICATION1 Mar 2021Logic-Gated Plasmonic Nanodevices Based on DNA-Templated Assembly Fengsong Liu†, Qiao Jiang†, Qing Liu, Na Li, Zihong Han, Chao Zhaoran Wang, Yunfei Jiao, Jiashu Sun and Baoquan Ding Liu† CAS Key Laboratory of Nanosystem Hierarchical Fabrication, Center for Excellence in Nanoscience, National Nanoscience Technology, Beijing 100190 University Chinese Academy Sciences, 100049 †F. Liu Q. Jiang contributed equally to this work.Google Scholar More articles by author , Jiang† Google Li Han Wang Jiao *Corresponding author: E-mail Address: [email protected] School Materials Science Engineering, Zhengzhou University, 450001 https://doi.org/10.31635/ccschem.020.202000300 SectionsSupplemental MaterialAboutAbstractPDF ToolsAdd favoritesTrack Citations ShareFacebookTwitterLinked InEmail Life has evolved numerous elegant molecular machines that recognize biological signals affect mechanical changes precisely achieve specific versatile biofunctions. Inspired nature, synthetic could be designed rationally realize nanomechanical operations autonomous computing. We constructed logic-gated plasmonic nanodevices through coassembly two gold nanorods (AuNRs) computing elements a tweezer-shaped DNA origami template. After recognition various inputs, such as strands, glutathione, or adenosine, the geometry circular dichroism (CD) AuNR–origami produced corresponding changes. Then we characterized set modular Boolean (YES, NOT, AND, OR) proceeded construct complicated 3-input circuit capable performing OR-NOT-AND operations. Our logic devices transduced external inputs into conformational near-infrared (NIR) chiral outputs. This DNA-based self-assembly strategy holds great potential applications programmable optical modulators, information processing, bioanalysis. Download figure PowerPoint Introduction Nature respond stimuli produce movements perform intricate functions. substantial research effort focused development artificial with controllable nanostructures environmental responsiveness.1–4 An important step is creation predetermined functions possess processing features.5–7 In recent decades, several systems supramolecular complexes small molecules,8 nanoparticles,9,10 enzymatic cascade networks,11 DNA/RNA aptamers,12 DNAzymes,13 have been employed gates circuits chemical stimuli,8 temperature,14 signals,15 others. Nucleic acid assemblies, which exhibit sequence-specific ease modification, provide intriguing platforms construction multilevel networks.12,16–24 These are computation, regulation. Various computational rationally, usually driven toehold-mediated strand-displacement reactions.25–27 displacement mechanism allows control presence appropriate nucleic other able trigger constructs. responding these operations, gate generate outputs measured via UV–visible absorbance fluorescence emission readout signals.10,20,25 The output affected biochemical environment, might limit efficiency signal-translating reaction variety applications. A nanoassemblies well-defined geometries, precise spatial addressability, reconfigurable structures can intelligently based DNA. fact, dynamic nanoparticle–DNA coassemblies,28–31 crossed (AuNRs),32 AuNR walker,33 tripod,34 among others, constructed. Triggered signals, display robust tunable responses, allowing design reporting. Herein, describe nanodevice nanostructure. used tweezers assembly templates. Two AuNRs were organized an asymmetric configuration each template (Figure 1) create nanoarchitectures signals. Multiple folding strands assembled hinge motifs different input stimuli. Logic from coassembled AuNR–DNA nanoarchitectures. transformation triggered single molecular-input combination CD near IR range Figure 1 | Construction coassemblies. (a) Schematic illustration showing nanodevices. (b c) Representative TEM images show open (b) closed (c) conformation. Scale bar, 100 nm. Experimental Methods All oligonucleotides purchased Sangon Biotech (Shanghai, China). Auric (HAuCl4·3H2O), cetyltrimethylammonium bromide (CTAB), sodium borohydride (NaBH4), silver nitrate (AgNO3), tris (carboxyethyl) phosphine hydrochloride (TCEP), reduced glutathione (GSH) Sigma-Aldrich (St. Louis, MO, USA). Adenosine was Solarbio (Beijing, Preparation scaffold p7249 ssDNA M13mp18 single-stranded (7249 nt) prepared following method: JM109 Escherichia coli cultured overnight lysogeny broth (LB) medium then 2 × YT microbial growth (containing 5 mM MgCl2) at 37 °C 12 h. M13 phages (p7249) inoculated bacteria when OD600 E. coli–containing reached 0.5, mixture further incubated shaker. h incubation, culture collected centrifuged 6000g 30 min remove pellets. phage-containing supernatant mixed NaCl (30 g/L) polyethylene glycol (PEG; 40 ice bath centrifugation 10,000g, phage pellet resuspended Tris-Cl (10 mM, pH 8.5), NaOH (0.2 M) SDS (1%) added, followed incubation solution 25 3 min. Next, after adding potassium acetate (3 M, 5.5) neutralization, gently 10 min, it 12,000g nt)-containing precipitated precooled ethanol (70%) kept –20 centrifuging washed (70%), resuspension 8.5). concentration 260 nm using Ultraviolet–visible (UV–vis) spectrometer (Shimadzu, Shanghai, Self-assembly slowly annealing genome multiple short 95 room temperature (RT). long (M13mp18 DNA) nM. Staple capture times excess scaffold; excess. scaffold, staple, capture, annealed TAE Mg2+ buffer (Tris, mM; acetic acid, 20 EDTANa2, magnesium acetate, 12.5 8.0) thermocycler (Bio-Rad). program follows: 70 °C, rate 1°C/5 min; 70°C 60 1°C/10 60°C 1°C /20 raw products finally 4 °C. removed purification, employing Amicon centrifugal filtration device (100 kDa MWCO Millipore Sigma, Synthesis modification synthesized seed-mediated method modified thiolated low-pH 4.0. UV–Vis spectrophotometer UV-2600 (SHIMADZU, Kyoto, Japan) measure absorption AuNRs. morphology imaged transmission electron microscopy (TEM; HT7700; HITACHI, Tokyo Japan). Modified purified ratio 4∶1. 45 over course 6 cycles. Purification performed ethidium (EtBr)-free agarose gel. running TBE (tris base 5.4 g/L, boric 2.75 EDTA-Na2 0.1M) MgCl2, loading 50% glycerol. characterization μL deposited carbon-coated grids RT. For clear observation origami, sample negatively stained 2% uranylacetate imaging obtained Hitachi HT-7700, operated 80 kV dark-field mode. Conformational trigged (N-Linker) hinges added molar 2∶1. RT (buffer: MgCl2). Glutathione (GSH)-induced signal switching containing disulfide bonds GSH Signal adenosine–aptamer interaction Purified adenosine-responsive adenosine Tris-HCl 150 8.2) Optical spectra JASCO J-1500 (Tokyo, instrument flushed nitrogen throughout experiment. measurements 0.5 mm length cells scanning carried out 500–900 nm, 200 nm/min. Results Discussion Design Rothemund’s method,35 tweezer-like structure consisting arms ( Supporting Information S1). short-staple nanostructure contained rigid, 15 helix-bundle (15HB) arms, connected flexible portions scaffold. Hinge connecting adjusting distance between 1a). When conformation 1a, Loop B), nanotweezers tended remain state, due static repulsion structural tension black strands) strand mixture, folded compact conformation, leading state. strands. Agarose gel electrophoresis (AGE) analysis S2) results S3) demonstrated successful fabrication both nanotweezers. groups pink green) extended tweezer function binding sites attachment. Different sequences S4) functionalized DNA, complementary previously reported.36 ssDNA-modified combined 1∶4 decreasing time course/6 Through hybridization, arranged intended resolved 1% AGE S5). target bands S5) cut extracted filter columns. Figures 1b 1c S6 present representative hybrid highly yield achieved open- closed-state Operation exhibited responses utilized operation. states assayed exploited devices. As shown 2a, maintained anchored close proximity, interactions strong left-handed (intensity > mdeg). separated other, weak < According previous reports,29,37 characteristic bisignate peak-dip shape explained antisymmetric models near-field coupling To more insight nanodevice, numerical calculations commercially available finite-difference time-domain (FDTD) package, Lumerical FDTD Solutions. theoretical calculation S7) good agreement experimental observations. defined “0” value “1.” operational Definition states. Strong intensities mdeg) 0, while 1. (b–d) illustrations, images, operation NOT types YES (c d) nanodevice. addition (N-Linkers), adenosine. bars, modifications hybridize loop responsive positions single-input (NOT YES) response molecules. 2b, upon termed “N-Linker” fold motif blue strands). hybridized sealed form, (output 0). reducing agent, (GSH; 2c), 2d). GSH, ubiquitous tripeptide functions, found relatively high (> millimolar range) cancer cells. GSH-responsive relevant diagnosis, therapy.38 Folding partially Loops B, forming keep quantitative experiments optimize manipulating within S8). cleavage bond resulting separation incorporated 2c, molecules increase substantially decreased YES-type adenosine-specific aptamer39 toehold S9) assemble loops form maintains assess responsiveness S10). (1 mM) nanodevices, region 2d, red highlight) bound molecule, dissociation nanodevice’s arms. reconfiguration state resulted Two-input-based strategies described earlier, fabricated 2-input AND OR either leads triggers gate, one aptamer 3a). input, only switched unfolded leaving position 0 3a S11). However, simultaneously, dissociated Transition increased AuNRs, 2-Input gate. (a b) experimentally observed indicated combinations inputs. integrated (termed “AG-Linker”) switch 3b). expected, achieved, separated. opening elicited decrease intensity 3b S12). system Finally, built 3-input, combining OR, net network and/or N-Linker strand. AG-linker, proximity. B so hybridization 4). eliciting regardless absence N-Linker, AG-Linker, producing tested them three analyzed CD, expected S13). Multilevel gates. representing Conclusion series AuNR/DNA controlling components manipulate conformations origami-based including YES, network. contrast conventional use reporting our monitored readily considered sensitive readouts cellular environment.40.Our range, known transparency window. enrich nanomechnical physical components. instance, pyrene-modified strands41 azobenzene derivative complexed G-quadruplex42 nanosystems, translating light-induced motion reversible chiroptical cleaved UV NIR light15 also introduced units. Light-manipulated, wavelength-sensitive customized expected. developed disease-associated biomarkers environments, thus exhibiting bioanalysis situ. It feasible evaluate label cell identification. logical distinct targeting isolation. envisioned intelligent playing increasingly essential roles studies. available. Conflict Interest There no conflict interest report. Funding made possible result generous grant Natural Foundation China (31700871, 21773044, 51761145044, 21721002), Basic Research Program (2016YFA0201601 2018YFA0208900), Municipal & Technology Commission (Z191100004819008), Frontier CAS, QYZDBSSW-SLH029, Strategic Priority Sciences (XDB36000000), Interdisciplinary Innovation Team, K.C. Wong Education (GJTD-2018-03). Acknowledgments authors thank Regional Instrument related tests. References Aguilar C. A.; Craighead H. G.Micro- Nanoscale Devices Investigation Epigenetics Chromatin Dynamics.Nat. Nanotechnol.2013, 8, 709–718. 2. Surana S.; Shenoy A. R.; Krishnan Y.Designing Compatibility Immune System Higher Organisms.Nat. Nanotechnol.2015, 10, 741–747. 3. J.; Esteban-Fernández de Ávila B.; Gao W.; Zhang L.; J.Micro/Nanorobots Biomedicine: Delivery, Surgery, Sensing, Detoxification.Sci. Robot.2017, 2, eaam6431. 4. Tregubov Nikitin P. I.; M. 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