Rapid Silicification of a DNA Origami with Shape Fidelity.

High-fidelity patterning of DNA origami nanostructures on various interfaces holds great potential for nanoelectronics and nanophotonics. However, distortion of a DNA origami often occurs due to the strong interface interactions, e.g., on two-dimensional (2D) materials. In this study, we discovered that the adsorption of silica precursors in rapid silicification can prevent the distortion caused by graphene and generates a high shape-fidelity DNA origami-silica composite on a graphene interface. We found that an incubation time of 1 min and silicification time of 16 h resulted in the formation of DNA origami-silica composites with the highest shape fidelity of 99%. By comparing the distortion of the DNA origami on the graphene interface with and without silicification, we observed that rapid silicification effectively preserved the integrity of the DNA origami. Statistical analysis of scanning electron microscopy data indicates that compared to bare DNA origami, the DNA origami-silica composite has an increased shape fidelity by more than two folds. Furthermore, molecular dynamics simulations revealed that rapid silicification effectively suppresses the distortion of the DNA origami through the interhelical insertion of silica precursors. Our strategy provides a simple yet effective solution to maintain the shape-fidelity DNA origami on interfaces that have strong interaction with DNA molecules, expanding the applicable interfaces for patterning 2D DNA origamis.

Isolation, purification, and structural characterization of polysaccharides from Codonopsis pilosula and its therapeutic effects on non-alcoholic fatty liver disease in vitro and in vivo.

Codonopsis pilosula is a famous edible and medicinal plants, in which polysaccharides are recognized as one of the important active ingredients. A neutral polysaccharide (CPP-1) was purified from C. pilosula. The structure was characterized by HPSEC-MALLS-RID, UV, FT-IR, GC-MS, methylation analysis, and NMR. The results showed that CPP-1 was a homogeneous pure polysaccharide, mainly containing fructose and glucose, and a small amount of arabinose. Methylation analysis showed that CPP-1 composed of →1)-Fruf-(2→, Fruf-(1→ and Glcp-(1→ residues. Combined the NMR results the structure of CPP-1 was confirmed as α-D-Glcp-(1 â†’ [2)-ß-D-Fruf-(1 â†’ 2)-ß-D-Fruf-(1]26 â†’ 2)-ß-D-Fruf with the molecular weight of 4.890 × 103 Da. The model of AML12 hepatocyte fat damage was established in vitro. The results showed that CPP-1 could increase the activity of SOD and CAT antioxidant enzymes and reduce the content of MDA, thus protecting cells from oxidative damage. Subsequently, the liver protective effect of CPP-1 was studied in the mouse model of nonalcoholic fatty liver disease (NAFLD) induced by the high-fat diet. The results showed that CPP-1 significantly reduced the body weight, liver index, and body fat index of NAFLD mice, and significantly improved liver function. Therefore, CPP-1 should be a potential candidate for the treatment of NAFLD.

Quantitative Analysis of Resistance to Deformation of the DNA Origami Framework Supported by Struts.

Nanostructures with controlled shapes are of particular interest due to their consistent physical and chemical properties and their potential for assembly into complex superstructures. The use of supporting struts has proven to be effective in the construction of precise DNA polyhedra. However, the influence of struts on the structure of DNA origami frameworks on the nanoscale remains unclear. In this study, we developed a flexible square DNA origami (SDO) framework and enhanced its structural stability by incorporating interarm supporting struts (SDO-s). Comparing the framework with and without such struts, we found that SDO-s demonstrated a significantly improved resistance to deformation. We assessed the deformability of these two DNA origami structures through the statistical analysis of interior angles of polygons based on atomic force microscopy and transmission electron microscopy data. Our results showed that SDO-s exhibited more centralized interior angle distributions compared to SDO, reducing from 30-150° to 60-120°. Furthermore, molecular dynamics simulations indicated that supporting struts significantly decreased the thermodynamic fluctuations of the SDO-s, as described by the root-mean-square fluctuation parameter. Finally, we experimentally demonstrated that the 2D arrays assembled from SDO-s exhibited significantly higher quality than those assembled from SDO. These quantitative analyses provide an understanding of how supporting struts can enhance the structural integrity of DNA origami frameworks.

Spacer-Programmed Two-Dimensional DNA Origami Assembly.

Two-dimensional (2D) DNA origami assembly represents a powerful approach to the programmable design and construction of advanced 2D materials. Within the context of hybridization-mediated 2D DNA origami assembly, DNA spacers play a pivotal role as essential connectors between sticky-end regions and DNA origami units. Here, we demonstrated that programming the spacer length, which determines the binding radius of DNA origami units, could effectively tune sticky-end hybridization reactions to produce distinct 2D DNA origami arrays. Using DNA-PAINT super-resolution imaging, we unveiled the significant impact of spacer length on the hybridization efficiency of sticky ends for assembling square DNA origami (SDO) units. We also found that the assembly efficiency and pattern diversity of 2D DNA origami assemblies were critically dependent on the spacer length. Remarkably, we realized a near-unity yield of ∼98% for the assembly of SDO trimers and tetramers via this spacer-programmed strategy. At last, we revealed that spacer lengths and thermodynamic fluctuations of SDO are positively correlated, using molecular dynamics simulations. Our study thus paves the way for the precision assembly of DNA nanostructures toward higher complexity.

Optimization of Three Extraction Methods and Their Effect on the Structure and Antioxidant Activity of Polysaccharides in Dendrobium huoshanense.

Dendrobium huoshanense is a famous edible and medicinal herb, and polysaccharides are the main bioactive component in it. In this study, response surface methodology (RSM) combined with a Box-Behnken design (BBD) was used to optimize the enzyme-assisted extraction (EAE), ultrasound-microwave-assisted extraction (UMAE), and hot water extraction (HWE) conditions and obtain the polysaccharides named DHP-E, DHP-UM, and DHP-H. The effects of different extraction methods on the physicochemical properties, structure characteristics, and bioactivity of polysaccharides were compared. The differential thermogravimetric curves indicated that DHP-E showed a broader temperature range during thermal degradation compared with DHP-UM and DHP-H. The SEM results showed that DHP-E displayed an irregular granular structure, but DHP-UM and DHP-H were sponge-like. The results of absolute molecular weight indicated that polysaccharides with higher molecular weight detected in DHP-H and DHP-UM did not appear in DHP-E due to enzymatic degradation. The monosaccharide composition showed that DHPs were all composed of Man, Glc, and Gal but with different proportions. Finally, the glycosidic bond types, which have a significant effect on bioactivity, were decoded with methylation analysis. The results showed that DHPs contained four glycosidic bond types, including Glcp-(1→, →4)-Manp-(1→, →4)-Glcp-(1→, and →4,6)-Manp-(1→ with different ratios. Furthermore, DHP-E exhibited better DPPH and ABTS radical scavenging activities. These findings could provide scientific foundations for selecting appropriate extraction methods to obtain desired bioactivities for applications in the pharmaceutical and functional food industries.

Meta-DNA Strand Displacement for Sub-Micron-Scale Autonomous Reconfiguration.

Dynamic molecular interactions in chemical reaction networks lead to complex behaviors in living systems. Whereas recent advances in programming DNA molecular reactions have reached a high level of complexity at molecular and nanometer scales, achieving programmable autonomous behavior at submicron or even larger scales remains challenging. Here, we present a mechanism of meta-DNA strand displacement reactions (M-SDRs) that is mediated solely by meta-toehold (M-toehold) using versatile submicron building blocks of meta-DNA (M-DNA). M-SDR emulates the toehold binding and branch migration processes of conventional strand displacement. Importantly, the kinetics of M-SDR can be modulated over a range of five orders of magnitude reaching a maximum rate of about 1.62 × 105 M-1 s-1. Further, we demonstrate the use of M-SDR to program autonomous reconfiguration in information transmission and logical computation systems. We envision that M-SDR serves as a versatile mechanism for emulating autonomous behavior approaching the cellular level.

Plasmonic Nanodiamonds.

While nitrogen-vacancy (NV) centers in diamonds have emerged as promising solid-state quantum emitters for sensing applications, the tantalizing possibility of coupling them with photonic or broadband plasmonic nanostructures to create ultrasensitive biolabels has not been fully realized. Indeed, it remains technologically challenging to create free-standing hybrid diamond-based imaging nanoprobes with enhanced brightness and high temporal resolution. Herein, we leverage the bottom-up DNA self-assembly to develop hybrid free-standing plasmonic nanodiamonds, which feature a closed plasmonic nanocavity completely encapsulating a single nanodiamond. Correlated single nanoparticle spectroscopical characterizations suggest that the plasmonic nanodiamond displays dramatically and simultaneously enhanced brightness and emission rate. We believe that they hold huge potential to serve as a stable solid-state single-photon source and could serve as a versatile platform to study nontrivial quantum effects in biological systems with enhanced spatial and temporal resolution.

Enhanced Herbicide Metabolism and Target-Site Mutations Confer Multiple Resistance to Fomesafen and Nicosulfuron in Amaranthus retroflexus L.

Amaranthus retroflexus L. is a highly competitive broadleaf weed of corn-soybean rotation in northeastern China. In recent years, the herbicide(s) resistance evolution has been threatening its effective management in crop fields. One resistant A. retroflexus (HW-01) population that survived the protoporphyrinogen oxidase (PPO) inhibitor fomesafen and acetolactate synthase (ALS) inhibitor nicosulfuron applied at their field-recommended rate was collected from a soybean field in Wudalianchi City, Heilongjiang Province. This study aimed to investigate the resistance mechanisms of fomesafen and nicosulfuron and determine the resistance profile of HW-01 to other herbicides. Whole plant dose-response bioassays revealed that HW-01 had evolved resistance to fomesafen (50.7-fold) and nicosulfuron (5.2-fold). Gene sequencing showed that the HW-01 population has a mutation in PPX2 (Arg-128-Gly) and a rare mutation in ALS (Ala-205-Val, eight/twenty mutations/total plants). In vitro enzyme activity assays showed that ALS extracted from the HW-01 plants was less sensitive to nicosulfuron (3.2-fold) than ST-1 plants. Pre-treatment with the cytochrome P450 inhibitors malathion, piperonyl butoxide (PBO), 3-amino-1,2,4-triazole (amitrole), and the GSTs inhibitor 4-chloro-7-nitrobenzofurazan (NBD-Cl) significantly increased fomesafen and nicosulfuron sensitivity in the HW-01 population compared with that of the sensitive (S) population ST-1. Moreover, the rapid fomesafen and nicosulfuron metabolism in the HW-01 plants was also confirmed via HPLC-MS/MS analysis. Furthermore, the HW-01 population showed multiple resistance (MR) to PPO, ALS, and PSII inhibitors, with resistance index (RI) values ranging from 3.8 to 9.6. This study confirmed MR to PPO-, ALS-, and PSII-inhibiting herbicides in the A. retroflexus population HW-01, as well as confirming that the cytochrome P450- and GST-based herbicide metabolic along with TSR mechanisms contribute to their multiple resistance to fomesafen and nicosulfuron.

Micron-Scale Fabrication of Ultrathin Amorphous Copper Nanosheets Templated by DNA Scaffolds.

Two-dimensional (2D) amorphous materials could outperform their crystalline counterparts toward various applications because they have more defects and reactive sites and thus could exhibit a unique surface chemical state and provide an advanced electron/ion transport path. Nevertheless, it is challenging to fabricate ultrathin and large-sized 2D amorphous metallic nanomaterials in a mild and controllable manner due to the strong metallic bonds between metal atoms. Here, we reported a simple yet fast (10 min) DNA nanosheet (DNS)-templated method to synthesize micron-scale amorphous copper nanosheets (CuNSs) with a thickness of 1.9 ± 0.4 nm in aqueous solution at room temperature. We demonstrated the amorphous feature of the DNS/CuNSs by transmission electron microscopy (TEM) and X-ray diffraction (XRD). Interestingly, we found that they could transform to crystalline forms under continuous electron beam irradiation. Of note, the amorphous DNS/CuNSs exhibited much stronger photoemission (∼62-fold) and photostability than dsDNA-templated discrete Cu nanoclusters due to the elevation of both the conduction band (CB) and valence band (VB). Such ultrathin amorphous DNS/CuNSs hold great potential for practical applications in biosensing, nanodevices, and photodevices.

Targeted Identification of Rice Grain-Associated Gene Allelic Variation Through Mutation Induction, Targeted Sequencing, and Whole Genome Sequencing Combined with a Mixed-Samples Strategy.

BACKGROUND: The mining of new allelic variation and the induction of new genetic variability are the basis for improving breeding efficiency. RESULTS: In this study, in total, 3872 heavy ion-irradiated M2 generation rice seeds and individual leaves were collected. The grain length was between 8 and 10.22 mm. The grain width was between 1.54 and 2.87 mm. The results showed that there was extensive variation in granulotype. The allelic variation in GS3 and GW5 was detected in 484 mixed samples (8:1) using targeted sequencing technology, and 12 mixed samples containing potential mutations and 15 SNPs were obtained; combined with Sanger sequencing and phenotype data, 13 key mutants and their corresponding SNPs were obtained; protein structural and functional analysis of key mutants screened out 6 allelic variants leading to altered grain shape, as well as the corresponding mutants, including long-grain mutants GS3-2 and GS3-7, short-grain mutants GS3-3 and GS3-5, wide-grain mutant GW5-1 and narrow-grain mutant GW5-4; whole genome sequencing identified new grain length gene allelic variants GS3-G1, GS3-G2 and GS3-G3. CONCLUSION: Based on the above studies, we found 6 granulotype mutants and 9 granulotype-related allelic variants, which provided new functional gene loci and a material basis for molecular breeding and genotype mutation and phenotype analysis. We propose a method for targeted identification of allelic variation in rice grain type genes by combining targeted sequencing of mixed samples and whole genome sequencing. The method has the characteristics of low detection cost, short detection period, and flexible detection of traits and genes.

Investigating the Metabolic Mesosulfuron-Methyl Resistance in Aegilops tauschii Coss. By Transcriptome Sequencing Combined with the Reference Genome.

Aegilops tauschii Coss. is a malignant weed in wheat fields in China, its herbicide resistance has been threatening crop production. This study identified one mesosulfuron-methyl-resistant(R) population, JJMHN2018-05 (R), without target resistance mutations. To fully understand the resistance mechanism, non-target site resistance was investigated by using transcriptome sequencing combined with a reference genome. Results showed that the cytochrome P450 monooxygenase (P450) inhibitor malathion significantly increased the mesosulfuron-methyl sensitivity in R plants, and greater herbicide-induced glutathione S-transferase (GST) activity was also confirmed. Liquid chromatography with tandem mass spectrometry analysis further supported the enhanced mesosulfuron-methyl metabolism in R plants. Gene expression data analysis and qRT-PCR validation indicated that eight P450s, six GSTs, two glycosyltransferases (GTs), four peroxidases, and one aldo-keto reductase (AKRs) stably upregulated in R plants. This research demonstrates that the P450s and GSTs involved in enhanced mesosulfuron-methyl metabolism contribute to mesosulfuron-methyl resistance in A. tauschii and identifies potential contributors from metabolic enzyme families.

DNA-POINT: DNA Patterning of Optical Imprint for Nanomaterials Topography.

Engineering well-defined scale-spanning structures through transfer of diverse biomolecules and materials to a surface is of tremendous interest in life sciences research yet remains profoundly challenging. Here, we report a novel method, termed as DNA patterning of optical imprint for nanomaterials topography (DNA-POINT), for rapid photopatterning of large area, geometrically complex surfaces via light-responsive DNA. Our method employs top-down multiphoton-driven patterning of azobenzene-modified DNA strands, offering precise position control of molecules and nanoparticles along the axial plane and a template for bottom-up self-assembly of multiple layers of different chemical composition along the vertical plane. We demonstrate the surface patterning of plasmonic gold nanoparticles, fluorophore-labeled oligonucleotides, and multiple layers consisting of molecule-nanoparticle hybrid patterns into preconceived shapes without compromising on the functionality of the biomolecules. Furthermore, we exhibit scanning mode operation of DNA-POINT, thereby paving the way for maskless and cleanroom-free fast fabrication of biochips for high-throughput diagnostics and biosensing applications.

Resistance to ALS inhibitors conferred by non-target-site resistance mechanisms in Myosoton aquaticum L.

Myosoton aquaticum L. is a competitive broadleaf weed commonly found in wheat fields in China and has become challenging due to its evolving herbicide resistance. In this study, one subpopulation, RF1 (derived from the tribenuron-methyl-resistant population HN10), with none of the known acetolactate synthase (ALS) resistance mutations was confirmed to exhibit resistance to tribenuron-methyl (SU), pyrithiobac­sodium (PTB), florasulam (TP), flucarbazone-Na (SCT), and diflufenican (PDS). In vitro ALS activity assays showed that the total ALS activity of RF1 was lower than that of the susceptible (S) population. However, there was no difference in ALS gene expression induced by tribenuron-methyl between the two populations. The combination of the cytochrome P450 monooxygenase (P450) inhibitor malathion and tribenuron-methyl resulted in the RF1 population behaving like the S population. The rapid P450-mediated tribenuron-methyl metabolism in RF1 plants was also confirmed by liquid chromatography tandem mass spectrometry (LC-MS/MS) analysis. In addition, approximately equal glutathione S-transferase (GST) activity was observed in RF1 and S plants of untreated and tribenuron-methyl treated groups. This study reported one M. aquaticum L. population without ALS resistance mutations exhibiting resistance to ALS inhibitors and the PDS inhibitor diflufenican, and the non-target-site resistance mechanism played a vital role in herbicide resistance.

Growth and site-specific organization of micron-scale biomolecular devices on living mammalian cells.

Mesoscale molecular assemblies on the cell surface, such as cilia and filopodia, integrate information, control transport and amplify signals. Designer cell-surface assemblies could control these cellular functions. Such assemblies could be constructed from synthetic components ex vivo, making it possible to form such structures using modern nanoscale self-assembly and fabrication techniques, and then oriented on the cell surface. Here we integrate synthetic devices, micron-scale DNA nanotubes, with mammalian cells by anchoring them by their ends to specific cell surface receptors. These filaments can measure shear stresses between 0-2 dyn/cm2, a regime important for cell signaling. Nanotubes can also grow while anchored to cells, thus acting as dynamic cell components. This approach to cell surface engineering, in which synthetic biomolecular assemblies are organized with existing cellular architecture, could make it possible to build new types of sensors, machines and scaffolds that can interface with, control and measure properties of cells.

Investigating the Mechanism of Metabolic Resistance to Tribenuron-Methyl in Capsella bursa-pastoris (L.) Medik. by Full-Length Transcriptome Assembly Combined with RNA-Seq.

Capsella bursa-pastoris (L.) Medik. has evolved resistance to ALS-inhibiting herbicides on a large scale. Previous studies primarily focused on the target-site resistance (TSR), and the non-TSR (NTSR) is not well characterized. In this study, pre-treatment with the cytochrome P450 monooxygenase (P450) inhibitor malathion clearly reduced the tribenuron-methyl resistance in the resistant (R) population. After tribenuron-methyl treatment, the glutathione S-transferase (GST) activity of R plants was significantly higher than that of susceptible (S) plants. The higher tribenuron-methyl metabolism in R plants was also confirmed by using LC-MS/MS analysis. Isoform sequencing (Iso-Seq) combined with RNA sequencing (RNA-Seq) was used to identify candidate genes involved in non-target metabolic resistance in this population. A total of 37 differentially expressed genes were identified, 11 of them constitutively upregulated in R plants, including three P450s, one GST, two glycosyltransferases, two ATP-binding cassette transporters, one oxidase, and two peroxidases. This study confirmed the metabolic tribenuron-methyl resistance in C. bursa-pastoris, and the transcriptome data obtained by Iso-Seq combined with RNA-Seq provide gene resources for understanding the molecular mechanism of NTSR in C. bursa-pastoris.

Evaluation of Micronutrient Status Post Laparoscopic Sleeve Gastrectomy: an Australian Perspective.

BACKGROUND: Laparoscopic sleeve gastrectomy (LSG) is a type of bariatric technique that has comparable outcomes to Roux-en-Y gastric bypass, the current gold standard. However, it can be associated with nutritional deficiencies postoperatively. The aim of this study was to evaluate micronutrient status post LSG. METHODS: This is a retrospective study of 565 patients who underwent an LSG from January 2015 to September 2018. Patients lost to follow-up at 3, 6 and 12 months were 6.3%, 18.6% and 32.4%, respectively. Follow-up of the patients included regular dietetic input and micronutrient supplementation. Data that was collected included both anthropometry and nutritional markers. RESULTS: The mean preoperative weight and body mass index (BMI) were 118.13 ± 25.36 kg and 42.40 ± 7.66 kg/m2, respectively. Statistically, significant reductions in anthropometric parameters including weight, BMI (30.50 kg/m2), total weight loss (28.03%), excess weight loss (72.03%) and BMI loss (12.32 kg/m2) were observed at all timepoints up to 12 months follow-up. At 12 months, there were significant increases in 25-OH vitamin D with the incidence of deficiency decreasing from 45.7 to 15.0% compared to baseline. The incidence of hyperparathyroidism also decreased from 32.2 to 18.9% compared to baseline, and incidence of folate deficiency increased from 7.7 to 19.2%. Other nutritional parameters including calcium, iron, ferritin, vitamin B12, holotranscobalamin (active B12) and haemoglobin did not significantly change. CONCLUSIONS: Modest effects on micronutrient status were observed in the 12-month postoperative period. Of clinically significant, de novo folate deficiencies increased, and vitamin D deficiency and hyperparathyroidism decreased. Thus, optimizing postoperative micronutrient status is imperative following LSG.

Seeding, Plating and Electrical Characterization of Gold Nanowires Formed on Self-Assembled DNA Nanotubes.

Self-assembly nanofabrication is increasingly appealing in complex nanostructures, as it requires fewer materials and has potential to reduce feature sizes. The use of DNA to control nanoscale and microscale features is promising but not fully developed. In this work, we study self-assembled DNA nanotubes to fabricate gold nanowires for use as interconnects in future nanoelectronic devices. We evaluate two approaches for seeding, gold and palladium, both using gold electroless plating to connect the seeds. These gold nanowires are characterized electrically utilizing electron beam induced deposition of tungsten and four-point probe techniques. Measured resistivity values for 15 successfully studied wires are between 9.3 × 10-6 and 1.2 × 10-3 Ωm. Our work yields new insights into reproducible formation and characterization of metal nanowires on DNA nanotubes, making them promising templates for future nanowires in complex electronic circuitry.

Multicomponent DNA Polymerization Motor Gels.

Hydrogels with the ability to change shape in response to biochemical stimuli are important for biosensing, smart medicine, drug delivery, and soft robotics. Here, a family of multicomponent DNA polymerization motor gels with different polymer backbones is created, including acrylamide-co-bis-acrylamide (Am-BIS), poly(ethylene glycol) diacrylate (PEGDA), and gelatin-methacryloyl (GelMA) that swell extensively in response to specific DNA sequences. A common mechanism, a polymerization motor that induces swelling is driven by a cascade of DNA hairpin insertions into hydrogel crosslinks. These multicomponent hydrogels can be photopatterned into distinct shapes, have a broad range of mechanical properties, including tunable shear moduli between 297 and 3888 Pa and enhanced biocompatibility. Human cells adhere to the GelMA-DNA gels and remain viable during ≈70% volumetric swelling of the gel scaffold induced by DNA sequences. The results demonstrate the generality of sequential DNA hairpin insertion as a mechanism for inducing shape change in multicomponent hydrogels, suggesting widespread applicability of polymerization motor gels in biomaterials science and engineering.

Programming DNA origami patterning with non-canonical DNA-based metallization reactions.

The inherent specificity of DNA sequence hybridization has been extensively exploited to develop bioengineering applications. Nevertheless, the structural potential of DNA has been far less explored for creating non-canonical DNA-based reactions. Here we develop a DNA origami-enabled highly localized metallization reaction for intrinsic metallization patterning with 10-nm resolution. Both theoretical and experimental studies reveal that low-valence metal ions (Cu2+ and Ag+) strongly coordinate with DNA bases in protruding clustered DNA (pcDNA) prescribed on two-dimensional DNA origami, which results in effective attraction within flexible pcDNA strands for site-specific pcDNA condensation. We find that the metallization reactions occur selectively on prescribed sites while not on origami substrates. This strategy is generically applicable for free-style metal painting of alphabet letters, digits and geometric shapes on all-DNA substrates with near-unity efficiency. We have further fabricated single- and double-layer nanoscale printed circuit board (nano-PCB) mimics, shedding light on bio-inspired fabrication for nanoelectronic and nanophotonic applications.

Quantizing single-molecule surface-enhanced Raman scattering with DNA origami metamolecules.

Tailored metal nanoclusters have been actively developed to manipulate light at the subwavelength scale for nanophotonic applications. Nevertheless, precise arrangement of molecules in a hot spot with fixed numbers and positions remains challenging. Here, we show that DNA origami metamolecules with Fano resonances (DMFR) can precisely localize single dye molecules and produce quantified surface-enhanced Raman scattering (SERS) responses. To enable tailored plasmonic permutations, we develop a general and programmable method for anchoring a set of large gold nanoparticles (L-AuNPs) on prescribed n-tuple docking sites of super-origami DNA frameworks. A tetrameric nanocluster with four spatially organized 80-nm L-AuNPs exhibits peak-and-dip Fano characteristics. The drastic enhancement at the wavelength of the Fano minimum allows the collection of prominent SERS spectrum for even a single dye molecule. We expect that DMFR provides physical insights into single-molecule SERS and opens new opportunities for developing plasmonic nanodevices for ultrasensitive sensing, nanocircuits, and nanophotonic lasers.