Time-traceable micro-taggants for anti-counterfeiting and secure distribution of food and medicines

This study presents an innovative solution for the enhanced tracking and security of pharmaceuticals through the development of microstructures incorporating environmentally responsive, coded microparticles. Utilizing maskless photolithography, we engineered these microparticles with a degradable masking layer with 30 μm thickness that undergoes controlled dissolution. Quantitative analysis revealed that the protective layer's degradation, monitored by red fluorescence intensity, diminishes predictably over 144 h in phosphate-buffered saline under physiological conditions. This degradation not only confirms the microparticles' integrity but also allows the extraction of encoded information, which can serve as a robust indicator of medicinal shelf life and a deterrent to tampering. These findings indicate the potential for applying this technology in real-time monitoring of pharmaceuticals, ensuring quality and authenticity in the supply chain.

Highly Accurate Sequence- and Position-Independent Error Profiling of DNA Synthesis and Sequencing

A comprehensive error analysis of DNA-stored data during processing, such as DNA synthesis and sequencing, is crucial for reliable DNA data storage. Both synthesis and sequencing errors depend on the sequence and the transition of bases of nucleotides; ignoring either one of the error sources leads to technical challenges in minimizing the error rate. Here, we present a methodology and toolkit that utilizes an oligonucleotide library generated from a 10-base-shifted sequence array, which is individually labeled with unique molecular identifiers, to delineate and profile DNA synthesis and sequencing errors simultaneously. This methodology enables position- and sequence-independent error profiling of both DNA synthesis and sequencing. Using this toolkit, we report base transitional errors in both synthesis and sequencing in general DNA data storage as well as degenerate-base-augmented DNA data storage. The methodology and data presented will contribute to the development of DNA sequence designs with minimal error.

Barcoded multiple displacement amplification for high coverage sequencing in spatial genomics

Determining mutational landscapes in a spatial context is essential for understanding genetically heterogeneous cell microniches. Current approaches, such as Multiple Displacement Amplification (MDA), offer high genome coverage but limited multiplexing, which hinders large-scale spatial genomic studies. Here, we introduce barcoded MDA (bMDA), a technique that achieves high-coverage genomic analysis of low-input DNA while enhancing the multiplexing capabilities. By incorporating cell barcodes during MDA, bMDA streamlines library preparation in one pot, thereby overcoming a key bottleneck in spatial genomics. We apply bMDA to the integrative spatial analysis of triple-negative breast cancer tissues by examining copy number alterations, single nucleotide variations, structural variations, and kataegis signatures for each spatial microniche. This enables the assessment of subclonal evolutionary relationships within a spatial context. Therefore, bMDA has emerged as a scalable technology with the potential to advance the field of spatial genomics significantly.

Pen-drawn Marangoni swimmer

Pen-drawing is an intuitive, convenient, and creative fabrication method for delivering emergent and adaptive design to real devices. To demonstrate the application of pen-drawing to robot construction, we developed pen-drawn Marangoni swimmers that perform complex programmed tasks using a simple and accessible manufacturing process. By simply drawing on substrates using ink-based Marangoni fuel, the swimmers demonstrate advanced robotic motions such as polygon and star-shaped trajectories, and navigate through maze. The versatility of pen-drawing allows the integration of the swimmers with time-varying substrates, enabling multi-step motion tasks such as cargo delivery and return to the original place. We believe that our pen-based approach will significantly expand the potential applications of miniaturized swimming robots and provide new opportunities for simple robotic implementations.

I-LIFT (image-based laser-induced forward transfer) platform for manipulating encoded microparticles

Encoded microparticles have great potential in small-volume multiplexed assays. It is important to link the micro-level assays to the macro-level by indexing and manipulating the microparticles to enhance their versatility. There are technologies to actively manipulate the encoded microparticles, but none is capable of directly manipulating the encoded microparticles with homogeneous physical properties. Here, we report the image-based laser-induced forward transfer system for active manipulation of the graphically encoded microparticles. By demonstrating the direct retrieval of the microparticles of interest, we show that this system has the potential to expand the usage of encoded microparticles.

Spatial epitranscriptomics reveals A-to-I editome specific to cancer stem cell microniches

Epitranscriptomic features, such as single-base RNA editing, are sources of transcript diversity in cancer, but little is understood in terms of their spatial context in the tumour microenvironment. Here, we introduce spatial-histopathological examination-linked epitranscriptomics converged to transcriptomics with sequencing (Select-seq), which isolates regions of interest from immunofluorescence-stained tissue and obtains transcriptomic and epitranscriptomic data. With Select-seq, we analyse the cancer stem cell-like microniches in relation to the tumour microenvironment of triple-negative breast cancer patients. We identify alternative splice variants, perform complementarity-determining region analysis of infiltrating T cells and B cells, and assess adenosine-to-inosine base editing in tumour tissue sections. Especially, in triple-negative breast cancer microniches, adenosine-to-inosine editome specific to different microniche groups is identified.

The spatial context of epitranscriptomic features in the tumour microenvironment remains poorly understood. Here, a method for transcriptomic and epitranscriptomic analysis of immunofluorescence-stained tissue, Select-seq, is applied to stem cell-like microniches in triple negative breast cancer.

Purification of multiplex oligonucleotide libraries by synthesis and selection

Complex oligonucleotide (oligo) libraries are essential materials for diverse applications in synthetic biology, pharmaceutical production, nanotechnology and DNA-based data storage. However, the error rates in synthesizing complex oligo libraries can be substantial, leading to increment in cost and labor for the applications. As most synthesis errors arise from faulty insertions and deletions, we developed a length-based method with single-base resolution for purification of complex libraries containing oligos of identical or different lengths. Our method-purification of multiplex oligonucleotide libraries by synthesis and selection-can be performed either step-by-step manually or using a next-generation sequencer. When applied to a digital data-encoded library containing oligos of identical length, the method increased the purity of full-length oligos from 83% to 97%. We also show that libraries encoding the complementarity-determining region H3 with three different lengths (with an empirically achieved diversity >10⁶) can be simultaneously purified in one pot, increasing the in-frame oligo fraction from 49.6% to 83.5%.

Cell-Free Bacteriophage Genome Synthesis Using Low-Cost Sequence-Verified Array-Synthesized Oligonucleotides

Synthesizing engineered bacteriophages (phages) for human use has potential in various applications ranging from drug screening using a phage display to clinical use using phage therapy. However, the engineering of phages conventionally involves the use of an in vivo system that has low production efficiency because of high virulence against the host and low transformation efficiency. To circumvent these issues, de novo phage genome synthesis using chemically synthesized oligonucleotides (oligos) has increased the potential for engineering phages in a cell-free system. Here, we present a cell-free, low-cost, de novo gene synthesis technology called Sniper assembly for phage genome construction. With massively parallel sequencing of microarray-synthesized oligos, we generated and identified approximately 100 000 clonal DNA clusters in vitro and 5000 error-free ones in a cell-free environment. To demonstrate its practical application, we synthesized the Acinetobacter phage AP205 genome (4268 bp) using 65 sequence-verified DNA clones. Compared to previous reports, Sniper assembly lowered the genome synthesis cost ($0.0137/bp) by producing low-cost sequence-verified DNA.

OPENchip: an on-chip in situ molecular profiling platform for gene expression analysis and oncogenic mutation detection in single circulating tumour cells

Liquid biopsy holds promise towards practical implementation of personalized theranostics of cancer. In particular, circulating tumour cells (CTCs) can provide clinically actionable information that can be directly linked to prognosis or therapy decisions. In this study, gene expression patterns and genetic mutations in single CTCs are simultaneously analysed by strategically combining microfluidic technology and in situ molecular profiling technique. Towards this, the development and demonstration of the OPENchip (On-chip Post-processing ENabling chip) platform for single CTC analysis by epithelial CTC enrichment and subsequent in situ molecular profiling is reported. For in situ molecular profiling, padlock probes that identify specific desired targets to examine biomarkers of clinical relevance in cancer diagnostics were designed and used to create libraries of rolling circle amplification products. We characterize the OPENchip in terms of its capture efficiency and capture purity, and validate the probe design using different cell lines. By integrating the obtained results, molecular analyses of CTCs from metastatic breast cancer (HER2 (ERBB2) gene expression and PIK3CA mutations) and metastatic pancreatic cancer (KRAS gene mutations) patients were demonstrated without any off-chip processes. The results substantiate the potential implementation of early molecular detection of cancer through sequencing-free liquid biopsy.

High-throughput construction of multiple cas9 gene variants via assembly of high-depth tiled and sequence-verified oligonucleotides

Selective retrieval of sequence-verified oligonucleotides (oligos) from next-generation sequencing (NGS) flow cells, termed megacloning, promises accurate and reliable gene synthesis. However, gene assembly requires a complete collection of overlapping sense and nonsense oligos, and megacloning does not typically guarantee the complete production of sequence-verified oligos. Therefore, missing oligos must be provided via repetitive rounds of megacloning, which introduces a bottleneck for scaled-up efforts at gene assembly. Here, we introduce the concept of high-depth tiled oligo design to successfully utilize megacloned oligos for gene synthesis. Using acquired oligos from a single round of the megacloning process, we assembled 72 of 81 target Cas9-coding gene variants. We further validated 62 of these cas9 constructs, and deposited the plasmids to Addgene for subsequent functional characterization by the scientific community. This study demonstrates the utility of using sequence-verified oligos for DNA assembly and provides a practical and reliable optimized method for high-throughput gene synthesis.

Barcode-free next-generation sequencing error validation for ultra-rare variant detection

The advent of next-generation sequencing (NGS) has accelerated biomedical research by enabling the high-throughput analysis of DNA sequences at a very low cost. However, NGS has limitations in detecting rare-frequency variants (< 1%) because of high sequencing errors (> 0.1~1%). NGS errors could be filtered out using molecular barcodes, by comparing read replicates among those with the same barcodes. Accordingly, these barcoding methods require redundant reads of non-target sequences, resulting in high sequencing cost. Here, we present a cost-effective NGS error validation method in a barcode-free manner. By physically extracting and individually amplifying the DNA clones of erroneous reads, we distinguish true variants of frequency > 0.003% from the systematic NGS error and selectively validate NGS error after NGS. We achieve a PCR-induced error rate of 2.5×10⁻⁶ per base per doubling event, using 10 times less sequencing reads compared to those from previous studies.

Next generation sequencing has difficulty in detecting rare-frequency variants due to high sequencing errors. Here the authors present a barcode-free error validation method that physically extracts erroneous reads to identify true variants.

The metal binding properties of the zinc site of yeast copper-zinc superoxide dismutase: implications for amyotrophic lateral sclerosis

We have investigated factors that influence the properties of the zinc binding site in yeast copper-zinc superoxide dismutase (CuZnSOD). The properties of yeast CuZnSOD are essentially invariant from pH 5 to pH 9. However, below this pH range there is a change in the nature of the zinc binding site which can be interpreted as either (1) a change in metal binding affinity from strong to weak, (2) the expulsion of the metal bound at this site, or (3) a transition from a normal distorted tetrahedral ligand orientation to a more symmetric arrangement of ligands. This change is strongly reminiscent of a similar pH-induced transition seen for the bovine protein and, based on the data presented herein, is proposed to be a property that is conserved among CuZnSODs. The transition demonstrated for the yeast protein is not only sensitive to the pH of the buffering solution but also to the occupancy and redox status of the adjacent copper binding site. Furthermore, we have investigated the effect of single site mutations on the pH- and redox-sensitivity of Co2+ binding at the zinc site. Each of the mutants H46R, H48Q, H63A, H63E, H80C, G85R, and D83H is capable of binding Co2+ to a zinc site with a distorted tetrahedral geometry similar to that of wild-type. However, they do so only if Cu+ is bound at the copper site or if the pH in raised to near physiological levels, indicating that the change at the zinc binding site seen in the wild-type is conserved in the mutants, albeit with an altered pKa. The mutants H71C and D83A did not bind Co2+ in a wild-type-like fashion under any of the conditions tested. This study reveals that the zinc binding site is exquisitely sensitive to changes in the protein environment. Since three of the mutant yeast proteins investigated here contain mutations analogous to those that cause ALS (amyotrophic lateral sclerosis) in humans, this finding implicates improper metal binding as a mechanism by which CuZnSOD mutants exert their toxic gain of function.

Resonance Raman studies of cytochrome P450BM3 and its complexes with exogenous ligands

Resonance Raman spectra are reported for both the heme domain and holoenzyme of cytochrome P450BM3 in the resting state and for the ferric NO, ferrous CO, and ferrous NO adducts in the absence and presence of the substrate, palmitate. Comparison of the spectrum of the palmitate-bound form of the heme domain with that of the holoenzyme indicates that the presence of the flavin reductase domain alters the structure of the heme domain in such a way that water accessibility to the distal pocket is greater for the holoenzyme, a result that is consistent with analogous studies of cytochrome P450cam. The data for the exogenous ligand adducts are compared to those previously reported for corresponding derivatives of cytochrome P450cam and document significant and important differences for the two proteins. Specifically, while the binding of substrate induces relatively dramatic changes in the nu(Fe-XY) modes of the ferrous CO, ferric NO, and ferrous NO derivatives of cytochrome P450cam, no significant changes are observed for the corresponding derivatives of cytochrome P450BM3 upon binding of palmitate. In fact, the spectral data for substrate-free cytochrome P450BM3 provide evidence for distortion of the Fe-XY fragment, even in the absence of substrate. This apparent distortion, which is nonexistent in the case of substrate-free cytochrome P450cam, is most reasonably attributed to interaction of the Fe-XY fragment with the F87 phenylalanine side chain. This residue is known to lie very close to the heme iron in the substrate-free derivative of cytochrome P450BM3 and has been suggested to prevent hydroxylation of the terminal, omega, position of long-chain fatty acids.

Structure-related inhibition of human hepatic caffeine N3-demethylation by naturally occurring flavonoids

The effects of flavonoids on caffeine N3-demethylation, a marker activity of CYP1A2, in human liver microsomes were investigated to elucidate the inhibition mechanism and the structure-activity relationship. Caffeine N3-demethylase activity was inhibited by the presence of various flavonoids, whose structures seem to be closely related to the degree of inhibition. Among twenty-one compounds tested, the most active was chrysin with an IC50 value of 0.2 microM. Others had IC50 values ranging from 1 to more than 500 microM. Kinetic analysis revealed that the mechanism of inhibition varied among the flavonoids. The inhibitory effect was postulated to be governed by factors such as the number of hydroxyl groups and glycosylation of these free hydroxyl groups. An increase in the number of free hydroxyl groups reduced the inhibitory effect on P450 activity. Analysis of the quantitative structure-activity relationship (QSAR) showed that the volume to surface area ratio was the most effective factor on the inhibition of caffeine N3-demethylation, and the electron densities on the C3 and C4' atoms exercised significant influence on the inhibitory effect. The calculated inhibitory effect of flavonoids on CYP1A2 activity was highly correlated with the antimutagenicity of flavonoids in 2-amino-3,4-dimethylimidazo[4,5-flquinoline (MelQ)-induced umu response.

Decreased substrate affinity upon alteration of the substrate-docking region in cytochrome P450(BM-3)

A mutation at the surface of the substrate access channel which dramatically decreases the affinity for some fatty acids in P450(BM-3) was discovered by random mutagenesis. The mutation introduced, proline-25 to glutamine, is in close proximity to the arginine-47 residue thought to be responsible for the initial docking of fatty acid substrates. The P25Q mutant displays an affinity for palmitate which is approximately 100-fold weaker than the wild-type enzyme. In addition to its altered substrate affinity, P25Q also exhibits altered hydroxylation specificity and carbon monoxide recombination kinetics in the substrate-free form.

Oxygen activation by cytochrome P450BM-3: effects of mutating an active site acidic residue

A highly conserved acid residue is found in the I-helix of most cytochrome P450s and has been suggested to play a critical function in oxygen activation and substrate hydroxylation in these monooxygenases. We have investigated this hypothesis for cytochrome P450BM-3 by replacing the naturally occuring glutamate at position 267 with a glutamine residue. In the case of P450BM-3, mutation of the glutamate to glutamine as position 267 drastically reduces the catalytic activity of the enzyme when palmitate is used as a substrate for hydroxylation. On the other hand, the activity change toward laurate hydroxylation is relatively small. The much slower catalytic turnover by the mutant enzyme in palmitate hydroxylation compared with wild type allows the observation of a new spectral intermediate in the hemoprotein. This intermediate is similar to that observed in the corresponding active site acid-to-amide replacement in cytochrome P450cam (N. C. Gerber and S. G. Sligar (1994) J. Biol. Chem. 269, 4260-4266). Also, in analogy with P450cam, this mutation does not lead to any side oxidation processes which produce hydrogen peroxide. Interestingly, however, the alteration in the active site structure which is implied by the change in regio specificity may also effect substrate packing thus leading to the uncoupling of the enzyme to produce additional water rather than a commitment to substrate oxidation. In addition, the distribution of hydroxylation products is altered by this mutation, suggesting some perturbation of the recognition property in P450BM-3.

Carbon monoxide binding to cytochrome P450BM-3: evidence for a substrate-dependent conformational change

The kinetics of carbon monoxide binding to cytochrome P450BM-3 in the presence and absence of substrate has been investigated using flash photolysis. The second order kinetics for CO association with the substrate-free form of the protein appear biphasic. Deconvolution into two exponentials yields fast and slow rate constants of 11.1 +/- 0.6 x 10(6) M-1 s-1 and 3.5 +/- 0.2 x 10(6) M-1 s-1, respectively with 52% of the signal being attributed to the fast phase. Interestingly, upon binding of a substrate such as laurate, the second order kinetics become monophasic, with a value of 3.5 x 10(6) M-1 s-1, which are similar to the slow rate found in the substrate-free form of the protein. We have also examined the geminate CO rebinding kinetics in the presence and absence of various substrates. In the substrate-free form of the overall geminate yield is 30%, and addition of a substrate increases the geminate yield to roughly 50%. Both the substrate-free and substrate-bound forms exhibit complex geminate kinetics which cannot be described by a simple three-state kinetic model. Extension of this model to include four states is required. The addition of substrate causes an increase in the geminate rate constants resulting in a larger geminate amplitude when compared to the substrate-free form. There is also evidence for a correlation between the volume occupied by the substrate and the geminate rate constants. These results are discussed in terms of substrate-dependent conformational changes in cytochrome P450BM-3 and the overall energy landscape of the hemoprotein which couples to conformer equilibria.

The role of Thr268 in oxygen activation of cytochrome P450BM-3

Cytochrome P450BM-3, a catalytically self-sufficient monooxygenase from Bacillus megaterium, catalyzes the omega-n (n = 1-3) hydroxylation of fatty acids in the presence of O2 and NADPH. Like most other P450s, cytochrome P450BM-3 contains a threonine residue (Thr268) in the distal I helix thought to be important for O2 binding and activation. Thr268 has been converted to alanine and the enzymatic properties and heme domain crystal structure determined. Using sodium laurate as the substrate, the mutant exhibited slower rates of O2 and NADPH consumption. In addition, electron transfer is uncoupled from substrate hydroxylation as evidenced by the greater production of water and peroxide in the mutant compared to the wild-type enzyme. The crystal structure of the mutant reveals that the only changes in structure are confined to the site of mutation. These data indicate an important role for Thr268 in O2 binding and activation in the metabolism of sodium laurate by cytochrome P450BM-3.