Molecular access to multi-dimensionally encoded information

Shotgun Sequencing of 512-mer Copolyester Allows Random Access to Stored Information

Digital information encoded in polymers has been exclusively decoded by mass spectrometry. However, the size limit of analytes in mass spectrometry restricts the storage capacity per chain. In addition, sequential decoding hinders random access to the bits of interest without full-chain sequencing. Here we report the shotgun sequencing of a 512-mer sequence-defined polymer whose molecular weight (57.3 kDa) far exceeds the analytical limit of mass spectrometry. A 4-bit fragmentation code was implemented at aperiodic positions during the synthetic encoding of 512-bit information without affecting storage capacity per chain. Upon activating the fragmentation code, the polymer chain splits into 18 oligomers, which could be individually decoded by tandem-mass sequencing. These sequences were computationally reconstructed into a full sequence using an error-detection method. The proposed sequencing method eliminates the storage limit of a single polymer chain and allows random access to the bits of interest without full-chain sequencing.

Complex Sequence-Defined Heteropolymers Enable Controlled Film Growth in Layer-By-Layer Assembly

Digitally-encoded poly(phosphodiesters) (d-PPDE) with highly complex primary structures are evaluated for layer-by-layer (LbL) assembly. To be easily decoded by mass spectrometry (MS), these digital polymers contain many different monomers: 2 coding units allowing binary encryption, 1 cleavable spacer allowing controlled MS fragmentation, and 3 mass tags allowing fragment identification. These complex heteropolymers are therefore composed of 6 different motifs. Despite this strong sequence heterogeneity, it is found that they enable a highly controlled LbL film formation. For instance, a regular growth is observed when alternating the deposition of negatively-charged d-PPDE and positively-charged poly(allyl amine hydrochloride) (PAH). Yet, in this approach, the interdistance between consecutive coded d-PPDE layers remains relatively small, which may be an issue for data storage applications, especially for the selective decoding of the stored information. Using poly(sodium 4-styrene sulfonate) (PSS) as an intermediate non-coded polyanion, it is shown that a controlled interdistance between d-PPDE layers can be easily achieved, while still maintaining a regular LbL growth. Last but not least, it is found in this work that d-PPDE of relatively small molecular weight (i.e., significantly smaller than those of PAH and PSS) still enables a controlled LbL assembly.

Exchanging and Releasing Information in Synthetic Digital Polymers Using a Strand-Displacement Strategy

Toehold-mediated strand displacement (TMSD) was tested as a tool to edit information in synthetic digital polymers. Uniform DNA-polymer biohybrid macromolecules were first synthesized by automated phosphoramidite chemistry and characterized by HPLC, mass spectrometry, and polyacrylamide gel electrophoresis (PAGE). These precursors were diblock structures containing a synthetic poly(phosphodiester) (PPDE) segment covalently attached to a single-stranded DNA sequence. Three types of biohybrids were prepared herein: a substrate containing an accessible toehold as well as input and output macromolecules. The substrate and the input macromolecules contained noncoded PPDE homopolymers, whereas the output macromolecule contained a digitally encoded segment. After hybridization of the substrate with the output, incubation in the presence of the input led to efficient TMSD and the release of the digital segment. TMSD can therefore be used to erase or rewrite information in self-assembled biohybrid superstructures. Furthermore, it was found in this work that the conjugation of DNA single strands to synthetic segments of chosen lengths greatly facilitates the characterization and PAGE visualization of the TMSD process.

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.

Design of Microstructure-Engineered Polymers for Energy and Environmental Conservation

With the ever-growing demand for sustainability, designing polymeric materials using readily accessible feedstocks provides potential solutions to address the challenges in energy and environmental conservation. Complementing the prevailing strategy of varying chemical composition, engineering microstructures of polymer chains by precisely controlling their chain length distribution, main chain regio-/stereoregularity, monomer or segment sequence, and architecture creates a powerful toolbox to rapidly access diversified material properties. In this Perspective, we lay out recent advances in utilizing appropriately designed polymers in a wide range of applications such as plastic recycling, water purification, and solar energy storage and conversion. With decoupled structural parameters, these studies have established various microstructure-function relationships. Given the progress outlined here, we envision that the microstructure-engineering strategy will accelerate the design and optimization of polymeric materials to meet sustainability criteria.

Research Progress in Construction and Application of Enzyme-Based DNA Logic Gates

As a research hotspot in the field of information processing, DNA computing exhibits several important underlying characteristics-from parallel computing and low energy consumption to high-performance storage capabilities-thereby enabling its wide application in nanomachines, molecular encryption, biological detection, medical diagnosis, etc. Based on DNA computing, the most rapidly developed field focuses on DNA molecular logic-gates computing. In particular, the recent advances in enzyme-based DNA logic gates has emerged as ideal materials for constructing DNA logic gates. In this review, we explore protein enzymes that can manipulate DNA, especially, nicking enzymes and polymerases with high efficiency and specificity, which are widely used in constructing DNA logic gates, as well as ribozyme that can construct DNA logic gates following various mechanism with distinct biomaterials. Accordingly, the review highlights the characteristics and applications of various types of DNAzyme-based logic gates models, considering their future developments in information, biomedicine, chemistry, and computers.

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.

Revealing the Organization of Catalytic Sequence-Defined Oligomers via Combined Molecular Dynamics Simulations and Network Analysis

Similar to biological macromolecules such as DNA and proteins, the precise control over the monomer position in sequence-defined polymers is of paramount importance for tuning their structures and properties toward achieving specific functions. Here, we apply molecular network analysis on three-dimensional structures issued from molecular dynamics simulations to decipher how the chain organization of trifunctional catalytic oligomers is influenced by the oligomer sequence and the length of oligo(ethylene oxide) spacers. Our findings demonstrate that the tuning of their primary structures is crucial for favoring cooperative interactions between the catalytic units and thus higher catalytic activities. This combined approach can assist in establishing structure-property relationships, leading to a more rational design of sequence-defined catalytic oligomers via computational chemistry.

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.

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.

Design of Abiological Digital Poly(phosphodiester)s

In biological systems, the storage and transfer of genetic information rely on sequence-controlled nucleic acids such as DNA and RNA. It has been realized for quite some time that this property is not only crucial for life but could also be very useful in human applications. For instance, DNA has been actively investigated as a digital storage medium over the past decade. Indeed, the "hard-disk of life" is an obvious choice and a highly optimized material for storing data. Through decades of nucleic acids research, technological tools for parallel synthesis and sequencing of DNA have been readily available. Consequently, it has already been demonstrated that different types of documents (e.g., texts, images, videos, and industrial data) can be stored in chemically synthesized DNA libraries. However, DNA is subject to biological constraints, and its molecular structure cannot be easily varied to match technological needs. In fact, DNA is not the only macromolecule that enables data storage. In recent years, it has been demonstrated that a wide variety of synthetic polymers can also be used for such a purpose. Indeed, modern polymer synthesis allows the preparation of synthetic macromolecules with precisely controlled monomer sequences. Altogether, about a dozens of synthetic digital polymers have already been described, and many more can be foreseen. Among them, sequence-defined poly(phosphodiester)s are one of the most promising options. These polymers are prepared by stepwise phosphoramidite chemistry like chemically synthesized oligonucleotides. However, they are constructed with non-natural building blocks and therefore share almost no structural characteristics with nucleic acids, except phosphate repeat units. Still, they contain readable digital messages that can be deciphered by nanopore sequencing or mass spectrometry sequencing. In this Account, we describe our recent research efforts in synthesizing and sequencing optimal abiological digital poly(phosphodiester)s. A major advantage of these polymers over DNA is that their molecular structure can easily be varied to tune their properties. During the last 5 years, we have engineered the molecular structure of these polymers to adjust crucial parameters such as the storage density, storage capacity, erasability, and readability. Consequently, high-capacity PPDE chains, containing hundreds of bits per chains, can now be synthesized and efficiently sequenced using a routine mass spectrometer. Furthermore, sequencing data can be automatically decrypted with the help of decoding software. This new type of coded matter can also be edited using practical physical triggers such as light and organized in space by programmed self-assembly. All of these recent improvements are summarized and discussed herein.

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.

Sequence-defined oligoampholytes using hydrolytically stable vinyl sulfonamides: design and UCST behaviour

Water soluble sequence-defined oligoampholytes with precisely positioned charges were synthesised via an iterative solid-phase synthesis protocol using vinyl sulfonamide and acrylate building blocks.

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.

Analysis of sequence-defined oligomers through Advanced Polymer Chromatography™ - mass spectrometry hyphenation

In recent years, sequence-defined oligomers have attracted increasing interest in the polymer community and the number of new applications such as macromolecular data storage and encryption is increasing. However, techniques allowing sequence differentiation are still lacking. In this study, the focus is put towards a new strategy allowing structural distinction between sequence-defined oligomers with identical molecular weight and composition, but bearing different sequences. This technique relies on the hyphenation of size exclusion chromatography and mass spectrometry, coupled with ion mobility separation. This approach allows for a quick and easy separation and identification of oligomers with different length and/or sequence.

From Sequence-Defined Macromolecules to Macromolecular Pin Codes

Dynamic sequence-defined oligomers carrying a chemically written pin code are obtained through a strategy combining multicomponent reactions with the thermoreversible addition of 1,2,4-triazoline-3,5-diones (TADs) to indole substrates. The precision oligomers are specifically designed to be encrypted upon heating as a result of the random reshuffling of the TAD-indole covalent bonds within the backbone, thereby resulting in the scrambling of the encoded information. The encrypted pin code can eventually be decrypted following a second heating step that enables the macromolecular pin code to be deciphered using 1D electrospray ionization-mass spectrometry (ESI-MS). The herein introduced concept of encryption/decryption represents a key advancement compared with current strategies that typically use uncontrolled degradation to erase and tandem mass spectrometry (MS/MS) to analyze, decipher, and read-out chemically encrypted information. Additionally, the synthesized macromolecules are coated onto a high-value polymer material, which demonstrates their potential application as coded product tags for anti-counterfeiting purposes.