Super-capacity information-carrying systems encoded with spontaneous Raman scattering

Bead-based spontaneous Raman codes for multiplex immunoassay

In the immunoassay process, for fulfilling the need to identify multiple analytes in a small amount of complex sample matrix, it is desirable to develop highly efficient and specific multiplex suspension array technology. Raman coding strategy offers an attractive solution to code the suspension arrays by simply combing narrow spectral bands with stable signal intensities through solid-phase synthesis on the resin beads. Based on this strategy, we report the bead-based spontaneous Raman codes for multiplex immunoassay. The study resulted in superior selectivity of the Raman-encoded beads for binding with single and multiple analytes, respectively. With the use of mixed types of Raman-encoded immunoassay beads, multiple targets in small amounts of samples were identified rapidly and accurately. By confirming the feasibility of bead-based spontaneous Raman codes for multiplex immunoassay, we anticipate this novel technology to be widely applied in the near future.

Imaging immune checkpoint networks in cancer tissues with supermultiplexed SERS nanoprobes

Combined immune checkpoint (ICP) inhibitors maximize immune response rates of patients compared to the single-drug treatment strategy in cancer immunotherapy, and prediction of such optimal combinations requires high-throughput imaging techniques and suitable data analysis. In this work, we report a rational strategy for predicting combined drugs of ICP inhibitors based on supermultiplexed surface-enhanced Raman scattering (SERS) imaging and correlation network analysis. To this end, we first built an ultrasensitive and supermultiplexed volume-active SERS (VASERS) nanoprobe platform, where Raman molecules are randomly arranged in 3D volumetric electromagnetic hotspots. By examining various bio-orthogonal Raman molecules with different electronic properties, we developed frequency modulation guidelines and achieved 32 resolvable colors in the Raman-silent region, the largest number of resolvable SERS colors demonstrated to date. We then demonstrated one-shot ten-color imaging of ICPs with high spectral resolution in clinical biopsies of breast cancer tissues, suggesting highly heterogeneous expression patterns of ICPs across tumor subtypes. Through correlation network analysis of these high-throughput Raman data, we investigated co-expression relationships among these ten-panel ICPs in cancer tissues and finally identified a variety of possible ICP combinations for synergistic immunotherapy of breast cancers, which may lead to novel therapeutical insights.

Molecular data storage using direct analysis in real time (DART) ionization mass spectrometry for decoding

Molecular data storage is becoming a viable alternative to traditional information storage systems. Here, we propose a method where the presence or absence of a given molecule in a mixture of compounds represents a bit of information. As a novel approach, direct analysis in real time (DART) ionization mass spectrometry is used to recover and decode the information stored at the molecular level. Nicotinic acid derivatives were synthesized and used as the 'bit compounds'. Their volatility and ease of ionization make these molecules especially suitable for DART-MS detection. The application of DART-MS as a method with an ambient ionization technique, enables the re-reading of digital chemical codes embedded in the material of ordinary objects. Our method is designed to store and read back short pieces of digital information, up to several hundred bits. These codes can have the function of barcodes or QR codes, as shown in our proof-of-principle applications. First, modelling a QR code as a link to our university's website, three solutions were prepared, each representing 22 bits. Proceeding further, the bit compounds were incorporated into a polymer matrix that is suitable for 3D printing, and a toy ship was created with a hidden barcode. In addition, decoding software was developed to process the DART-MS spectra. The nicotinic acid components representing the bits dominated the DART-MS spectra and error-free decoding was achieved.

Orthogonal Combinatorial Raman Codes Enable Rapid High-Throughput-Out Library Screening of Cell-Targeting Ligands

High-throughput assays play an important role in the fields of drug discovery, genetic analysis, and clinical diagnostics. Although super-capacity coding strategies may facilitate labeling and detecting large numbers of targets in a single assay, practically, the constructed large-capacity codes have to be decoded with complicated procedures or are lack of survivability under the required reaction conditions. This challenge results in either inaccurate or insufficient decoding outputs. Here, we identified chemical-resistant Raman compounds to build a combinatorial coding system for the high-throughput screening of cell-targeting ligands from a focused 8-mer cyclic peptide library. The accurate in situ decoding results proved the signal, synthetic, and functional orthogonality for this Raman coding strategy. The orthogonal Raman codes allowed for a rapid identification of 63 positive hits at one time, evidencing a high-throughput-out capability in the screening process. We anticipate this orthogonal Raman coding strategy being generalized to enable efficient high-throughput-out screening of more useful ligands for cell targeting and drug discovery.

Microcavity- and Microlaser-Based Optical Barcoding: A Review of Encoding Techniques and Applications

Optical microbarcodes have recently received a great deal of interest because of their suitability for a wide range of applications, such as multiplexed assays, cell tagging and tracking, anticounterfeiting, and product labeling. Spectral barcodes are especially promising because they are robust and have a simple readout. In addition, microcavity- and microlaser-based barcodes have very narrow spectra and therefore have the potential to generate millions of unique barcodes. This review begins with a discussion of the different types of barcodes and then focuses specifically on microcavity-based barcodes. While almost any kind of optical microcavity can be used for barcoding, currently whispering-gallery microcavities (in the form of spheres and disks), nanowire lasers, Fabry-Pérot lasers, random lasers, and distributed feedback lasers are the most frequently employed for this purpose. In microcavity-based barcodes, the information is encoded in various ways in the properties of the emitted light, most frequently in the spectrum. The barcode is dependent on the properties of the microcavity, such as the size, shape, and the gain materials. Various applications of these barcodes, including cell tracking, anticounterfeiting, and product labeling are described. Finally, the future prospects for microcavity- and microlaser-based barcodes are discussed.

Exploring the generality of ligands for Silica-Encapsulated nanoclusters as SERS labels

The surface enhanced Raman scattering (SERS) reporters are rather limited, and the Raman peaks still overlap in varying degrees, making SERS multiplex coding a critical bottleneck in the exploration of SERS nanotechnology. Herein, we design a general strategy to expand the SERS probe scope to 26 probes of six types, which can be further expanded within a limited range, with stable performance and structure. By constructing (Au-aggregate)@Ag@silica and (Au-aggregate)@silica nanocomposites, we develop optimal enhancement strategies for each Raman molecules. Mixed signal-ligand SERS probes improve the complexity of Raman spectra and expand the coding capacity. By integrating the strategies, SERS inks are produced and applied in anti-counterfeiting. With these improvements, this work breaks the constrains of probe selection, bringing SERS one step closer to the sensor or anti-counterfeiting application.

Silent region barcode particle arrays for ultrasensitive multiplexed SERS detection

Suspension arrays are a critical components of next generation multiplexed detection technologies. Current fluorescence suspension arrays are limited by a multiplexed coding ceiling and difficulties with ultrasensitive detection. Raman mode is a promising substitute, but the complex spectral peak distributions and extremely weak intrinsic signal intensity severely diminish Raman signal performance in suspension arrays. To address these limitations, we constructed a Raman suspension array system using plasmonic microbeads as barcode substrates and Au nanoflowers as reporter carriers. The well-designed shell morphology and plasmonic microbead composition enabled significant surface enhancement Raman scattering (SERS) such that we were able to adjust silent region Raman-coding intensity levels. Due to synergistic SERS effects from the plasmonic shell and the multi-branched Au nanoflower nanostructure, the reporting signal was greatly improved, enabling ultrasensitive detection of 5-plexed lung cancer markers. Detection in patient serum samples demonstrated good consistency with the standard electrochemiluminescence method. Thus, this silent region SERS barcode-based suspension array is a developmental advance for modern multiplexed biodetection, potentially providing a powerful early disease screening and diagnosis tool.

Molecular data storage with zero synthetic effort and simple read-out

Compound mixtures represent an alternative, additional approach to DNA and synthetic sequence-defined macromolecules in the field of non-conventional molecular data storage, which may be useful depending on the target application. Here, we report a fast and efficient method for information storage in molecular mixtures by the direct use of commercially available chemicals and thus, zero synthetic steps need to be performed. As a proof of principle, a binary coding language is used for encoding words in ASCII or black and white pixels of a bitmap. This way, we stored a 25 × 25-pixel QR code (625 bits) and a picture of the same size. Decoding of the written information is achieved via spectroscopic (1H NMR) or chromatographic (gas chromatography) analysis. In addition, for a faster and automated read-out of the data, we developed a decoding software, which also orders the data sets according to an internal "ordering" standard. Molecular keys or anticounterfeiting are possible areas of application for information-containing compound mixtures.

Rapid ultrasensitive detection of hexavalent chromium in soil and groundwater by a microProbing imaging platform

Rapid detection methods are needed to investigate the environmental quality risk of soil and groundwater in contaminated lands. Currently there is lack of rapid detection methods to sensitively and accurately analyze contaminations of hexavalent chromium in soil due to the challenge of complex sample pretreatment or expensive instrumentation. Here we report a rapid accurate detection platform for quantifying hexavalent chromium in soil and groundwater with ultrasensitivity. The platform consists of a novel sensor of microProbing beads and a portable microscope. Each microProbing bead was a nanoliter reactor to selectively sequestrate Cr (VI) with the enrichment factor up to 150 ×. The microProbing beads presented the signal uniformity of ~97% for the statistical colorimetric imaging analysis. Combined with a miniaturized microscope, the microProbing beads allowed for detecting aqueous Cr (VI) and soluble Cr (VI) in soil within 45 min. The platform achieved high sensitivity with the detection limits of 0.003 ppb for aqueous Cr (VI) and 0.07 ppm for soil Cr (VI). It accurately detected soil and groundwater samples from a chromium contaminated land in Yangtze River Basin of China. The consistency to the laboratory standard methods was achieved with the low cost of ~0.20 US dollar per test. The microProbing imaging platform with the operational simplicity and device portability is highly promising for the field analysis of Cr (VI) in contaminated lands.

Continuously Multiplexed Ultrastrong Raman Probes by Precise Isotopic Polymer Backbone Doping for Multidimensional Information Storage and Encryption

Raman-based super multiplexing has attracted great interest in imaging, biological analysis, identity security, and information storage. It still remains a great challenge to synthesize a large number of different Raman-active molecules to fulfill the Raman color palette. Here, we report a facile and systematic strategy to construct continuously multiplexed ultrastrong Raman probes. By precisely incorporating different ratios of ¹³C isotope into the backbone of poly(deca-4,6-diynedioic acid) (PDDA), we can obtain a library of PDDAs with tunable double-bond Raman frequencies and adjustable intensity ratios of two triple-bond (¹³C≡¹³C and ¹²C≡¹²C) Raman peaks, while retaining the ultrastrong Raman signals and physicochemical properties of the polymer. We also demonstrate the successful application of ¹³C-doped PDDAs as security inks to generate a novel 3D matrix barcode system for information encryption and high-density data storage. The isotopically doped PDDA series herein pave a new way to advance Raman-based super multiplexing for diverse applications.

Raman inks based on triple-bond-containing polymeric nanoparticles for security

Developing security inks with spectral outputs/multiple colors, which have unique identification characteristics, is of great importance in enhancing the anti-counterfeiting strength of ink anti-counterfeiting technology. Herein, a print-driven triple-bond coding mode is proposed for the first time. Two kinds of triple-bond-containing polymeric nanoparticles (NPs) with Raman shifts at 2227 and 2241 cm^-1 have been designed into printable ink, and the decimal coding output can be easily obtained by reasonably adjusting the proportions of the two polymeric NPs. Single Raman scattering inks can be used as invisible inks to print monochromatic patterns and words that the decoder can read out. According to the two-dimensional pixels of the graphics decoder, invisible colorful graphics can be printed with mixed inks under different polymer proportions. More interestingly, three-dimensional invisible patterns with stronger anti-counterfeiting strength can also be obtained in the double-layer anti-counterfeiting patterns with different proportions of ink by the spatial complementary coding mode. It is predicted that more security inks associated with triple-bond Raman signals will spur the application of the anti-counterfeiting field.

Super-multiplexed vibrational probes: Being colorful makes a difference

Biological systems with intrinsic complexity require multiplexing techniques to comprehensively describe the phenotype, interaction, and heterogeneity. Recent years have witnessed the development of super-multiplexed vibrational microscopy, overcoming the 'color barrier' of fluorescence-based optical techniques. Here, we will review the recent progress in the design and applications of super-multiplexed vibrational probes. We hope to illustrate how rainbow-like vibrational colors can be generated from systematic studies on structure-spectroscopy relationships and how being colorful makes a difference to various biomedical applications.

Quantitative Analysis of Compatibility and Dispersibility in Nanocellulose-Reinforced Composites: Hansen Solubility and Raman Mapping

Considering its high specific modulus, nanocellulose, including rigid cellulose nanocrystals (CNCs) and semiflexible cellulose nanofibrils (CNFs), is widely used as a nano-reinforcing filler for polymeric-based composites, which is regarded as the most promising application of these biomass nanoparticles. The quantitative evaluation of the compatibility and dispersion/aggregation state of nanocellulose in polymeric matrices is a critical issue, as it conditions the efficient stress transfer from the matrix to the filler and effective mechanical reinforcement effect. This study reports a comprehensive set of theories and methods to directly evaluate the compatibility and dispersibility of CNCs and CNFs in four polymer matrices with different polarities, where the compatibility was assessing by Hansen solubility and dispersibility by Raman mapping and cluster analysis. Triple-bond modification on the surface of nanocellulose is a promising approach for accurate recognition in composites, exhibiting the individual signal located in the Raman-silent regions of various polymeric matrices. Based on the discussion of the quantitative dispersion factor, a multiscale percolation model is proposed to better predict the mechanical properties of nanocellulose-reinforced composites based on Raman mapping results, in order to update traditional percolation models.

Vibrational Fingerprint Analysis of an Azo-based Resonance Raman Scattering Probe for Imaging Proton Distribution in Cellular Lysosomes

Due to the fundamental mechanism of vibrational state transitions for chemical bonds, the spectra of Raman scattering are narrow-banded and photostable signals capable of probing specific reactions. In the case of protonation/deprotonation reactions, certain chemical bonds are broken and new bonds are formed. Based on the changes of the vibrational modes for the corresponding bonds, fingerprint analysis of multiple Raman bands may allow for the in situ visualization of proton distribution in live cells. However, Raman scattering faces the well-known challenge of low sensitivity. To perform the vibrational fingerprint analysis of Raman scattering by overcoming this challenge, we developed an azo-based resonance Raman pH probe. It was an azobenzene-featured small molecule responsive to protons with the inherent Raman signal ∼10⁴-fold more intense than that of the conventional alkyne-type Raman reporter 5-ethynyl-2'-deoxyuridine. Through the substitution of the electron-donating and -withdrawing entities to the azobenzene group, the effect of resonance Raman scattering and fluorescence quenching was obtained. This effect resulted in a significant Raman enhancement factor of ∼10³ compared to the counterpart molecules without the molecular design. Based on the enhanced Raman sensitivity of the azo-based resonance Raman pH probe, the identification of vibrational fingerprint changes at the azo group was achieved during the protonation/deprotonation reactions, and the vibrational fingerprint analysis resolved a pH difference of less than 0.2 unit. The method enabled sensitive hyperspectral cell imaging that clearly visualized the change of proton distribution in autophagic cells.

Precise Encoding of Triple-Bond Raman Scattering of Single Polymer Nanoparticles for Multiplexed Imaging Application

Stimulated Raman scattering (SRS) microscopy in combination with innovative tagging strategies offers great potential as a universal high-throughput biomedical imaging tool. Here, we report rationally tailored small molecular monomers containing triple-bond units with large Raman scattering cross-sections, which can be polymerized at the nanoscale for enhancement of SRS contrast with smaller but brighter optical nanotags with artificial fingerprint output. From this, a class of triple-bond rich polymer nanoparticles (NPs) was engineered by regulating the relative dosages of three chemically different triple-bond monomers in co-polymerization. The bonding strategy allowed for 15 spectrally distinguishable triple-bond combinations. These accurately structured nano molecular aggregates, rather than long-chain macromolecules, could establish a universal method for generating small-sized biological SRS imaging tags with high sensitivity for high-throughput multi-color biomedical imaging.

Azo-Enhanced Raman Scattering for Enhancing the Sensitivity and Tuning the Frequency of Molecular Vibrations

Raman scattering provides stable narrow-banded signals that potentially allow for multicolor microscopic imaging. The major obstacle for the applications of Raman spectroscopy and microscopy is the small cross section of Raman scattering that results in low sensitivity. Here, we report a new concept of azo-enhanced Raman scattering (AERS) by designing the intrinsic molecular structures using resonance Raman and concomitant fluorescence quenching strategies. Based on the selection of vibrational modes and the enhancing unit of azobenzenes, we obtained a library of AERS molecules with specific Raman signals in the fingerprint and silent frequency regions. The spectral characterization and molecular simulation revealed that the azobenzene unit conjugated to the vibrational modes significantly enhanced Raman signals due to the mechanism of extending the conjugation system, coupling the electronic-vibrational transitions, and improving the symmetry of vibrational modes. The nonradiative decay of azobenzene from the excited state quenched the commitment fluorescence, thus providing a clean background for identifying Raman scattering. The most sensitive AERS molecules produced Raman signals of more than 4 orders of magnitude compared to 5-ethynyl-2'-deoxyuridine (EdU). In addition, a frequency tunability of 10 distinct Raman bands was achieved by selecting different types of vibrational modes. This methodology of AERS allows for designing small-molecule Raman probes to visualize various entities in complex systems by multicolor spontaneous Raman imaging. It will open new prospects to explore innovative applications of AERS in interdisciplinary research fields.

Zero-Background Surface-Enhanced Raman Scattering Detection of Cymoxanil Based on the Change of the Cyano Group after Ultraviolet Irradiation

A zero-background method based on surface-enhanced Raman scattering (SERS) was developed for the rapid determination of cymoxanil residue in food. Because of the influence of complex matrices, conventional Raman spectroscopy has multiple peaks that overlap with those of target molecules, which makes qualitative and quantitative detection difficult. However, the cyano group (C≡N) of cymoxanil after ultraviolet irradiation has a special characteristic peak in the Raman-silent region (1800-2800 cm^-1), which eliminates the possible background interference. The intensity of the characteristic peak at 2130 cm^-1 exhibited a good linear relationship (R² = 0.9907) with the concentration of cymoxanil in the range of 1.0-50.0 mg/L, whose limit of detection was 0.5 mg/L. The novel method was also applied to the detection of cymoxanil residue in real samples such as cucumber and grape, and the results were in good agreement with those from high-performance liquid chromatography analysis. This revealed that the SERS method has great potential in the detection of cymoxanil in fruits and vegetables. Moreover, ultraperformance liquid chromatography-quadrupole-time-of-flight-mass spectrometry (UPLC-QTOF/MS) was adopted to identify the photoproducts of cymoxanil. The photolysis mechanism was explored by SERS and the UPLC-QTOF/MS technique, which provided basic information on photodegradation of cymoxanil.

A new analytical platform for potential point-of-care testing of circulating tumor cells

It is of significance to detect circulating tumor cells (CTCs) in whole blood using transportable instruments at the point of care to assist evaluating chemotherapeutic efficacy and recurrence risk of cancer patients. However, the current widely used detection methods either require expensive and complex equipments, need complicated enrichment steps, or produce high rates of false positive and/or negative results. Aiming for solving the two critical challenges involved in instrumentation miniaturization and simplification of sample preparation for POCT of CTCs without sacrificing the detection sensitivity and accuracy, this work reports a custom-built, automatic, large field-of-view microscopic CTC cytometer and a novel enrichment strategy based on a synthesized peptide ligand discovered from One-Bead One-Compound library screening. The custom-built microscope has compact size, low weight and efficient cost while still maintaining a detection limit of as low as 5 target objects. The simplified sample preparation utilized a novel peptide LXW7 functionalized to magnetic beads and allows for rapid, highly selective and sensitive detection of CTCs. This analytical platform may fulfill the unmet need for possible point-of-care CTC counting, and provide a new option for early diagnosis of cancers and convenient evaluation of chemotherapeutic efficacy and cancer recurrence.

Organic micro/nanoscale materials for photonic barcodes

This review summarizes recent advances in micro/nanoscale photonic barcodes based on organic materials from the aspects of diverse optical encoding techniques.