New Wine in Old Bottle: Crown Ether-Functionalized Digital Polymer toward Efficient MALDI-TOF MS/MS Decoding via a Classical Supramolecular Interaction

Digital polymers (DPs), which serve as promising molecular-level storage media, have increasingly garnered interest. Their application significantly depends on the efficiency of the information writing (synthesis) and reading processes (sequencing). For reading, rational incorporation of weak bonds in the main chain was applied in most cases in order to improve readability of the tandem mass spectra (MS/MS), which would limit the chain length of DPs, thus reducing the information storage capacity. In this study, the introduction of commercially available crown ether (CE) at the terminus of digital oligo(γ-butyrolactone)s (DOBLs) significantly enhances the predictability and fidelity of matrix-assisted laser desorption/ionization time-of-flight tandem mass spectra (MALDI-TOF MS/MS), thus improving the decoding process. The use of crown ether, leveraging a well-established supramolecular interaction with alkali cations known since 1967, offers a strong affinity between ionization agents and CE motifs, to form a selective effect of the desired fragments during the tandem MS. This method is particularly effective for long-chain DPs, extending up to 32-mer, and allows for customizable fragmentation patterns. The incorporation of CE at the DP chain end presents a novel and efficient strategy for enhancing MS/MS readability and amplifying the information storage capacity of polymers.

Recent advances in spirocyclization of maleimides via transition-metal catalyzed C-H activation

In recent years, the maleimide scaffold has received a great deal of attention in C-H activation. Several types of products can be constructed using maleimides as a coupling partner. Alkylation, alkenylation, annulation, dehydrogenative annulation and spirocyclization are various reactions shown by maleimides in C-H activation. Thus, the maleimide scaffold has been extensively studied in the last few years in C-H activation owing to its unique reactivity. Among the diverse class of reactions of maleimides, spirocyclization is a less explored reaction. The spirocycles, in particular the spirosuccinimides are interesting candidates in drug discovery and materials chemistry. Therefore the method of spirocyclization of maleimides via C-H activation becomes an important strategy for the synthesis of a diverse array of spirosuccinimides. This review summarizes the reports available in this field from 2015-2023 and also highlights the scopes and prospects of this method.

Using Nitroxides To Model the Ion Mobility Behavior of Nitroxide-Ended Oligomers: A Bottom-up Approach To Predict Mobility Separation

Block-truncated poly(phosphodiester)s are digital macromolecules storing binary information that can be decoded by MS/MS sequencing of individual blocks released as primary fragments of the entire polymer. As such, they are ideal species for the serial sequencing methodology enabled by MS-(CID)-IMS-(CID)-MS coupling, where two activation stages are combined in-line with ion mobility spectrometry (IMS) separation. Yet, implementation of this coupling still requires efforts to achieve IMS resolution of inner blocks, that can be considered as small oligomers with α termination composed of one nitroxide decorated with a different tag. As shown by molecular dynamics simulation, these oligomers adopt a conformation where the tag points out of the coil formed by the chain. Accordingly, the sole nitroxide termination was investigated here as a model to reduce the cost of calculation aimed at predicting the shift of collision cross-section (CCS) induced by new tag candidates and extrapolate this effect to nitroxide-terminated oligomers. A library of 10 nitroxides and 7 oligomers was used to validate our calculation methods by comparison with experimental IMS data as well as our working assumption. Based on conformation predicted by theoretical calculation, three new tag candidates could be proposed to achieve the +40 Å2 CCS shift required to ensure IMS separation of oligomers regardless of their coded sequence.

Precision Sequence-Defined Polymers: From Sequencing to Biological Functions

Precise sequence-defined polymers (SDPs) with uniform chain-to-chain structure including chain length, unit sequence, and end functionalities represent the pinnacle of sophistication in the realm of polymer science. For example, the absolute control over the unit sequence of SDPs allows for the bottom-up design of polymers with hierarchical microstructures and functions. Accompanied with the development of synthetic techniques towards precision SDPs, the decoding of SDP sequences and construction of advanced functions irreplaceable by other synthetic materials is of central importance. In this Minireview, we focus on recent advances in SDP sequencing techniques including tandem mass spectrometry (MS), chemically assisted primary MS, as well as other non-destructive sequencing methods such as nuclear magnetic resonance (NMR) spectroscopy, circular dichroism (CD), and nanopore sequencing. Additionally, we delve into the promising prospects of SDP functions in the area of cutting-edge biological research. Topics of exploration include gene delivery systems, the development of hybrid materials combining SDPs and nucleic acids, protein recognition and regulation, as well as the interplay between chirality and biological functions. A brief outlook towards the future directions of SDPs is also presented.

Digital synthetic polymers for information storage

Digital synthetic polymers with uniform chain lengths and defined monomer sequences have recently become intriguing alternatives to traditional silicon-based information devices or natural biomacromolecules for data storage. The structural diversity of information-containing macromolecules endows the digital synthetic polymers with higher stability and storage density but less occupied space. Through subtly designing each unit of coded structure, the information can be readily encoded into digital synthetic polymers in a more economical scheme and more decodable, opening up new avenues for molecular digital data storage with high-level security. This tutorial review summarizes recent advances in salient features of digital synthetic polymers for data storage, including encoding, decoding, editing, erasing, encrypting, and repairing. The current challenges and outlook are finally discussed to offer potential solution guidance and new perspectives for the creation of next-generation digital synthetic polymers and broaden the scope of their applicability.

Reading Information Stored in Synthetic Macromolecules

The storage of information in synthetic (macro)molecules provides an attractive alternative for current archival storage media, and the advancements made within this area have prompted the investigation of such molecules for numerous other applications (e.g., anti-counterfeiting tags, steganography). While different strategies have been described for storing information at the molecular level, this Perspective aims to provide a critical overview of the most prominent approaches that can be utilized for retrieving the encoded information. The major part will focus on the sequence determination of synthetic macromolecules, wherein information is stored by the precise arrangement of constituting monomers, with an emphasis on chemically aided strategies, (tandem) mass spectrometry, and nanopore sensing. In addition, recent progress in utilizing (mixtures of) small molecules for information storage will be discussed. Finally, the closing remarks aim to highlight which strategy we believe is the most suitable for a series of specific applications, and will also touch upon the future research avenues that can be pursued for reading (macro)molecular information.

Molecular Encryption and Steganography Using Mixtures of Simultaneously Sequenced, Sequence-Defined Oligourethanes

Molecular encoding in abiotic sequence-defined polymers (SDPs) has recently emerged as a versatile platform for information and data storage. However, the storage capacity of these sequence-defined polymers remains underwhelming compared to that of the information storing biopolymer DNA. In an effort to increase their information storage capacity, herein we describe the synthesis and simultaneous sequencing of eight sequence-defined 10-mer oligourethanes. Importantly, we demonstrate the use of different isotope labels, such as halogen tags, as a tool to deconvolute the complex sequence information found within a heterogeneous mixture of at least 96 unique molecules, with as little as four micromoles of total material. In doing so, relatively high-capacity data storage was achieved: 256 bits in this example, the most information stored in a single sample of abiotic SDPs without the use of long strands. Within the sequence information, a 256-bit cipher key was stored and retrieved. The key was used to encrypt and decrypt a plain text document containing The Wonderful Wizard of Oz. To validate this platform as a medium of molecular steganography and cryptography, the cipher key was hidden in the ink of a personal letter, mailed to a third party, extracted, sequenced, and deciphered successfully in the first try, thereby revealing the encrypted document.

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.

Sequencing of Uniform Multifunctional Oligoesters via Random Chain Cleavages

Sequence-defined polymers have been the object of many fascinating studies that focus on their implementation in both material and life science applications. In parallel, iterative synthetic methodologies have become more efficient, whereas the structure elucidation of these molecules is generally dependent on MS/MS analysis. Here, we report an alternative, simple strategy for the determination of the monomer order of uniform oligo(thioether ester)s. This approach, which relies on random cleavages of ester units within the macromolecular backbone via a basic treatment, enables the swift characterization of these macromolecules without the need for MS/MS. Consequently, this method can be used for decoding any information stored within the primary structure of oligoesters by means of ESI- or LC-MS. Finally, we speculate that a range of structurally diverse backbones could be susceptible towards this approach, which could promptly expand the library of chemically sequenceable macromolecules.

Fabrication and Decryption of a Microarray of Digital Dithiosuccinimide Oligomers

Digital polymer with precisely arranged binary units provides an important option for information storage. This is especially true if the digital polymers are assembled in a device, as it would be of great benefit to data writing and reading in practice. Herein, inspired by DNA microarray technique, the programmable information storing and reading on a mass spectrometry target plate is proposed. First, an array of 4-bit sequence-coded dithiosuccinimide oligomers was efficiently built through sequential thiol-maleimide Michael couplings with good sequence readability by tandem mass spectrometry (MS/MS). Then, toward engineering microarray for information storage, a programmed robotic arm was specifically designed for precisely loading sequence-coded oligomers onto the target plate, and a decoding software was developed for efficient readout of the data from MS/MS sequencing. Notably, short sequence-coded oligomers chains can be used to write long strings of information, and extra error-correction codes are not required as usual due to the inherent concomitant fragmentation signals. Not only text but also bitimages can be automatically stored and decoded with excellent accuracy. This work provides a promising platform of digital polymers for programmable information storing and reading. This article is protected by copyright. All rights reserved.

Rewritable Macromolecular Data Storage with Automated Read-out

Rewriting data stored on synthetic macromolecules is an interesting feature, even though it is considered as being quite challenging within the area of digital macromolecules. In this context, we initially studied a strategy for modifying the position tag of sequence-encoded macromolecules in a reversible manner. The efficiency of this method, which relies on the orthogonal cleavage of a thioester moiety via aminolysis, was demonstrated by modifying parts of an exemplary sentence. Simultaneously, a novel algorithm was developed to ease the read-out of macromolecular information by means of MS/MS techniques. This program, Oligoreader, can identify potential information-containing macromolecules from a series of MS¹ spectra, analyze the corresponding MS² spectra, and finally decode the data. Consequently, the algorithm simplifies the entire read-out process by avoiding any interference from the operator, which increases the potential for blind sequencing of uniform macromolecules.

Discrete, self-immolative N-substituted oligourethanes and their use as molecular tags

The depolymerization of N-substituted oligourethanes via an intramolecular cyclization event was studied in-depth, while the applicability of these macromolecules as anti-counterfeiting tags was demonstrated by labeling a polyurethane material.

Polymers Strive for Accuracy: From Sequence-Defined Polymers to mRNA Vaccines against COVID-19 and Polymers in Nucleic Acid Therapeutics

Unquestionably, polymers have influenced the world over the past 100 years. They are now more crucial than ever since the COVID-19 pandemic outbreak. The pandemic paved the way for certain polymers to be in the spotlight, namely sequence-defined polymers such as messenger ribonucleic acid (mRNA), which was the first type of vaccine to be authorized in the U.S. and Europe to protect against the SARS-CoV-2 virus. This rise of mRNA will probably influence scientific research concerning nucleic acids in general and RNA therapeutics in specific. In this Perspective, we highlight the recent trends in sequence-controlled and sequence-defined polymers. Then we discuss mRNA vaccines as an example to illustrate the need of ultimate sequence control to achieve complex functions such as specific activation of the immune system. We briefly present how mRNA vaccines are produced, the importance of modified nucleotides, the characteristic features, and the advantages and challenges associated with this class of vaccines. Finally, we discuss the chances and opportunities for polymer chemistry to provide solutions and contribute to the future progress of RNA-based therapeutics. We highlight two particular roles of polymers in this context. One represents conjugation of polymers to nucleic acids to form biohybrids. The other is concerned with advanced polymer-based carrier systems for nucleic acids. We believe that polymers can help to address present problems of RNA-based therapeutic technologies and impact the field beyond the COVID-19 pandemic.

Sequence-Encoded Macromolecules with Increased Data Storage Capacity through a Thiol-Epoxy Reaction

Sequence-encoded oligo(thioether urethane)s with two different coding monomers per backbone unit were prepared via a solid phase, two-step iterative protocol based on thiolactone chemistry. The first step of the synthetic cycle consists of the thiolactone ring opening with a primary amine, whereby the in situ released thiol is immediately reacted with an epoxide. In the second step, the thiolactone group is reinstalled to initiate the next cycle. This strategy allows to introduce two different coding monomers per synthetic cycle, rendering the resulting macromolecules especially attractive in the area of (macro)molecular data storage because of their increased data storage capacity. Subsequently, the efficiency of the herein reported synthesis route and the applicability of the dual-encoded sequence-defined macromolecules as a potential data storage platform have been demonstrated by unraveling the exact monomer order using tandem mass spectrometry techniques.

Easily Functionalized and Readable Sequence-Defined Polytriazoles

Developing sequence-defined skeletons that could be conveniently characterized and functionalized with diverse side groups is attractive but challenging. Here we report one novel sequence-defined polytriazole structure bearing side groups at its triazole rings. Its construction was facilely accessed by the iterative employments of azidation and iridium-catalyzed cycloaddition of azide with internal 1-thioalkyne (IrAAC) in solution phase. The easy preparation of 1-thioalkyne monomers and the excellent tolerance of IrAAC enable the introduction of diverse functional side chains to this architecture. The obtained sequence was effectively characterized by tandem mass spectrometry owing to the efficient fractures of both of the Csp³-S and Csp³-N bonds in its backbone, indicating its potential utilization in high-capacity digital polymer developments. Further successful application of this structure in building monodisperse macromolecules exhibiting aggregation-induced emission (AIE) characteristics demonstrates its expected application in functional material fabrications.

Efficient molecular encoding in multifunctional self-immolative urethanes

Molecular encoding in sequence-defined polymers shows promise as a new paradigm for data storage. Here, we report what is, to our knowledge, the first use of self-immolative oligourethanes for storing and reading encoded information. As a proof of principle, we describe how a text passage from Jane Austen's Mansfield Park was encoded in sequence-defined oligourethanes and reconstructed via self-immolative sequencing. We develop Mol.E-coder, a software tool that uses a Huffman encoding scheme to convert the character table to hexadecimal. The oligourethanes are then generated by a high-throughput parallel synthesis. Sequencing of the oligourethanes by self-immolation is done concurrently in a parallel fashion, and the liquid chromatography-mass spectrometry (LC-MS) information decoded by our Mol.E-decoder software. The passage is capable of being reproduced wholly intact by a third-party, without any purifications or the use of tandem MS (MS/MS), despite multiple rounds of compression, encoding, and synthesis.

Applications of Discrete Synthetic Macromolecules in Life and Materials Science: Recent and Future Trends

In the last decade, the field of sequence-defined polymers and related ultraprecise, monodisperse synthetic macromolecules has grown exponentially. In the early stage, mainly articles or reviews dedicated to the development of synthetic routes toward their preparation have been published. Nowadays, those synthetic methodologies, combined with the elucidation of the structure-property relationships, allow envisioning many promising applications. Consequently, in the past 3 years, application-oriented papers based on discrete synthetic macromolecules emerged. Hence, material science applications such as macromolecular data storage and encryption, self-assembly of discrete structures and foldamers have been the object of many fascinating studies. Moreover, in the area of life sciences, such structures have also been the focus of numerous research studies. Here, it is aimed to highlight these recent applications and to give the reader a critical overview of the future trends in this area of research.

Synthesis and sequencing of informational poly(amino phosphodiester)s

The inclusion of main-chain tertiary amines in digital poly(phosphodiester)s allows synthesis of molecularly-defined achiral polymers and simplifies tandem mass spectrometry sequencing.

IrAAC-based construction of dual sequence-defined polytriazoles

One novel dual sequence-defined polytriazole structure was facilely achieved through an IrAAC-based iterative sequential growth strategy.

Reading mixtures of uniform sequence-defined macromolecules to increase data storage capacity

In recent years, the field of molecular data storage has emerged from a niche to a vibrant research topic. Herein, we describe a simultaneous and automated read-out of data stored in mixtures of sequence-defined oligomers. Therefore, twelve different sequence-defined tetramers and three hexamers with different mass markers and side chains are successfully synthesised via iterative Passerini three-component reactions and subsequent deprotection steps. By programming a straightforward python script for ESI-MS/MS analysis, it is possible to automatically sequence and thus read-out the information stored in these oligomers within one second. Most importantly, we demonstrate that the use of mass-markers as starting compounds eases MS/MS data interpretation and furthermore allows the unambiguous reading of sequences of mixtures of sequence-defined oligomers. Thus, high data storage capacity considering the field of synthetic macromolecules (up to 64.5 bit in our examples) can be obtained without the need of synthesizing long sequences, but by mixing and simultaneously analysing shorter sequence-defined oligomers.

Synthesis and [2+2]-photodimerisation of monothiomaleimide functionalised linear and brush-like polymers

[2+2]-Photodimerisation of monothiomaleimides has been demonstrated on functionalised linear and brush-like polymers. In water/acetonitrile (95 : 5) mixtures the rate of reaction is accelerated significantly by irradiation of the thiomaleimide end group (λmax = 350 nm) with UV light, reaching full conversion within 10 minutes.

Optimal conditions for tandem mass spectrometric sequencing of information-containing nitrogen-substituted polyurethanes

RATIONALE

To prevent solubility issues faced with sequence-defined polyurethanes, a new family of digital polyurethanes was conceived with the alkyl coding chain held by the carbamate nitrogen (N) atom and CH₃ instead of OH as the ϖ termination. This led to different dissociation mechanisms that were explored prior to optimizing tandem mass spectrometric (MS/MS) sequencing.

METHODS

N-Substituted polyurethanes (N-R PUs) were dissolved in methanol and subjected to collision-induced dissociation (CID) as deprotonated chains in the negative ion mode, and as ammonium and sodium adducts in the positive ion mode, using electrospray ionization (ESI) as the ionization technique. Their dissociation behavior was thoroughly investigated using a quadrupole time-of-flight (QTOF) instrument in order to provide accurate mass measurements to support proposed fragmentation mechanisms.

RESULTS

While O-(CO) bonds were broken in N-H PUs, the CH₂ -O linkage between repeating units was cleaved upon CID of N-R PUs. This main process occurred either from deprotonated molecules or from cationized chains but was followed by different rearrangements, producing up to four product ion series. Yet, MS/MS spectra could be drastically simplified for precursor ions having their acidic α group methylated, as was found to spontaneously occur upon storage in methanol.

CONCLUSIONS

Using experimental conditions aimed at avoiding any reactive proton in precursor ions (no acidic end-groups and alkali adduction), full coverage sequence of N-R PUs was successfully achieved with the single ion series observed in MS/MS, opening a promising perspective for reading large amounts of information stored in these dyad-encoded polymers.

Selective Bond Cleavage in Informational Poly(Alkoxyamine Phosphodiester)s

The collision-induced dissociation (CID) of sequence-defined poly(alkoxyamine phosphodiester)s is studied by electrospray ionization mass spectrometry. These informational polymers are synthesized using three different nitroxide building blocks, namely proxyl-, SG1-, and TEMPO-derivatives. For a polymer containing TEMPO- and SG1-based main chain alkoxyamines, it is found that both types of alkoxyamines break in CID tandem mass spectrometry (MS/MS). However, SG1-sites are preferentially cleaved and this predominance can be increased by reducing collision energy, even though selective bond fragmentation is not observed. On the other hand, for a polymer containing proxyl- and SG1-alkoxyamines, selective bond cleavage is observed at all studied collision energies. The SG1-alkoxyamines can be first cleaved in MS/MS conditions and secondly the proxyl-alkoxyamines in pseudo-MS³ conditions. These results open up interesting new avenues for the design of readable, erasable or programmable informational polymers.

Easily readable palindromic sequence-defined polymers built by cascade thiol-maleimide Michael couplings

The rational combination of cascade thiol-maleimide Michael couplings (CTMMC) with iterative exponential chain growth was demonstrated as an efficient way to synthesize palindromic sequence-defined polymers.