Data storage using peptide sequences

Chemical and linguistic considerations for encoding Chinese characters: an embodiment using chain-end degradable sequence-defined oligourethanes created by consecutive solid phase click chemistry

Sequence-defined polymers (SDPs) are currently being investigated for use as information storage media. As the number of monomers in the SDPs increases, with a corresponding increase in mathematical base, the use of tandem-MS for de novo sequencing becomes more challenging. In contrast, chain-end degradation routines are truly de novo, potentially allowing very large mathematical bases for encoding. While alphabetic scripts have a few dozen symbols, logographic scripts, such as Chinese, can have several thousand symbols. Using a new in situ consecutive click reaction approach on an oligourethane backbone for writing, and a previously reported chain-end degradation routine for reading, we encoded/decoded a confucius proverb written in Chinese characters using two encoding schemes: Unicode and Zhèng Mă. Unicode is an internationally standardized arbitrary string of hexadecimal (base-16) symbols which efficiently encodes uniquely identifiable symbols but requires complete fidelity of transmission, or context-based inferential strategies to be interpreted. The Zhèng Mă approach encodes with a base-26 system using the visual characteristics and internal composition of Chinese characters themselves, which leads to greater ambiguity of encoded strings, but more robust retrievability of information from partial or corrupted encodings. The application of information-encoded oligourethanes to two different encoding systems allowed us to establish their flexibility and versatility for data storage. We found the oligourethanes immensely adaptable to both encoding schemes for Chinese characters, and we highlight the expected tradeoff between the efficiency and uniqueness of Unicode encoding on the one hand, and the fidelity to a scripts' particular visual characteristics on the other.

Mirror-image trypsin digestion and sequencing of D-proteins

The development of mirror-image biology systems and related applications is hindered by the lack of effective methods to sequence mirror-image (D-) proteins. Although natural-chirality (L-) proteins can be sequenced by bottom-up liquid chromatography-tandem mass spectrometry (LC-MS/MS), the sequencing of long D-peptides and D-proteins with the same strategy requires digestion by a site-specific D-protease before mass analysis. Here we apply solid-phase peptide synthesis and native chemical ligation to chemically synthesize a mirror-image version of trypsin, a widely used protease for site-specific protein digestion. Using mirror-image trypsin digestion and LC-MS/MS, we sequence a mirror-image large subunit ribosomal protein (L25) and a mirror-image Sulfolobus solfataricus P2 DNA polymerase IV (Dpo4), and distinguish between different mutants of D-Dpo4. We also perform writing and reading of digital information in a long D-peptide of 50 amino acids. Thus, mirror-image trypsin digestion in conjunction with LC-MS/MS may facilitate practical applications of D-peptides and D-proteins as potential therapeutic and informational tools.

Peptide-graphene logic sensing system for dual-mode detection of exosomes, molecular information processing and protection

Peptides with highly sequence-dependent recognition, assembly, and encoding abilities can perform functions similar to DNA or even better, such as biosensing, molecular information processing, coding, or storage. However, the combination of versatile peptides and 2D materials are rarely used for multipurpose integrated applications, including biosensing, information processing and security. Herein, peptide-graphene sensing system was comprehensively used for dual-signal sensing of tumor-derived exosomes (TDEs), logic computing, and information protection. The system used fluorescent-labeled CD63-binding peptide CP05 and graphene oxide (GO) to selectively detect CD63 and TDEs by fluorescence and resonance light scattering. From three levels such as matter, energy, and information analysis, the matter and energy changes in GO-CP05 peptide sensing system were transformed into valuable information, which achieve the dual-mode quantitative detection of TDEs and its marker CD63, and the actual serum analysis. This matter-energy interaction network was also informationized, and utilized for parallel and batch logic computing, two kinds of molecular crypto-steganography (based on peptide sequence and Boolean logic relationships), which facilitates development of intelligent sensing and advanced information technology. This work not only provides a new method for sensitive detection of important disease markers, but also provides ideas for integrating molecular sensing and informatization to open molecular digitization.

How to make DNA data storage more applicable

The storage of digital data is becoming a worldwide problem. DNA has been recognized as a biological solution due to its ability to store genetic information without alteration over long periods. The first demonstrations of high-capacity long-lasting DNA digital data storage have been shown. However, high storage costs and slow retrieval of the data must be overcome to make DNA data storage more applicable and marketable. Herein, we discuss the issues and recent advances in DNA data storage methods and highlight pathways to make this technology more applicable to real-world digital data storage. We envision that a combination of molecular biology, nanotechnology, novel polymers, electronics, and automation with systematic development will allow DNA data storage sufficient for everyday use.

Algorithms for de-novo sequencing of peptides by tandem mass spectrometry: A review

Peptide sequencing is of great significance to fundamental and applied research in the fields such as chemical, biological, medicinal and pharmaceutical sciences. With the rapid development of mass spectrometry and sequencing algorithms, de-novo peptide sequencing using tandem mass spectrometry (MS/MS) has become the main method for determining amino acid sequences of novel and unknown peptides. Advanced algorithms allow the amino acid sequence information to be accurately obtained from MS/MS spectra in short time. In this review, algorithms from exhaustive search to the state-of-art machine learning and neural network for high-throughput and automated de-novo sequencing are introduced and compared. Impacts of datasets on algorithm performance are highlighted. The current limitations and promising direction of de-novo peptide sequencing are also discussed in this review.

Abiotic peptides as carriers of information for the encoding of small-molecule library synthesis

Encoding small-molecule information in DNA has been leveraged to accelerate the discovery of ligands for therapeutic targets such as proteins. However, oligonucleotide-based encoding is hampered by inherent limitations of information stability and density. In this study, we establish abiotic peptides for next-generation information storage and apply them for the encoding of diverse small-molecule synthesis. The chemical stability of the peptide-based tag allows the use of palladium-mediated reactions to efficiently synthesize peptide-encoded libraries (PELs) with broad chemical diversity and high purity. We demonstrate the successful de novo discovery of small-molecule protein ligands from PELs by affinity selection against carbonic anhydrase IX and the oncogenic protein targets BRD4(1) and MDM2. Collectively, this work establishes abiotic peptides as carriers of information for the encoding of small-molecule synthesis, leveraged herein for the discovery of protein ligands.

Emerging Approaches to DNA Data Storage: Challenges and Prospects

With the total amount of worldwide data skyrocketing, the global data storage demand is predicted to grow to 1.75 × 10¹⁴ GB by 2025. Traditional storage methods have difficulties keeping pace given that current storage media have a maximum density of 10³ GB/mm³. As such, data production will far exceed the capacity of currently available storage methods. The costs of maintaining and transferring data, as well as the limited lifespans and significant data losses associated with current technologies also demand advanced solutions for information storage. Nature offers a powerful alternative through the storage of information that defines living organisms in unique orders of four bases (A, T, C, G) located in molecules called deoxyribonucleic acid (DNA). DNA molecules as information carriers have many advantages over traditional storage media. Their high storage density, potentially low maintenance cost, ease of synthesis, and chemical modification make them an ideal alternative for information storage. To this end, rapid progress has been made over the past decade by exploiting user-defined DNA materials to encode information. In this review, we discuss the most recent advances of DNA-based data storage with a major focus on the challenges that remain in this promising field, including the current intrinsic low speed in data writing and reading and the high cost per byte stored. Alternatively, data storage relying on DNA nanostructures (as opposed to DNA sequence) as well as on other combinations of nanomaterials and biomolecules are proposed with promising technological and economic advantages. In summarizing the advances that have been made and underlining the challenges that remain, we provide a roadmap for the ongoing research in this rapidly growing field, which will enable the development of technological solutions to the global demand for superior storage methodologies.

Isotope Ratio Encoding of Sequence-Defined Oligomers

Information storage at the molecular level commonly entails encoding in the form of ordered sequences of different monomers and subsequent fragmentation and tandem mass spectrometry analysis to read this information. Recent approaches also include the use of mixtures of distinct molecules noncovalently bonded to one another. Here, we present an alternate isotope ratio encoding approach utilizing deuterium-labeled monomers to produce hundreds of oligomers endowed with unique isotope distribution patterns. Mass spectrometric recognition of these patterns then allowed us to directly readout encoded information with high fidelity. Specifically, we show that all 256 tetramers composed of four different monomers of identical constitution can be distinguished by their mass fingerprint using mono-, di-, tri-, and tetradeuterated building blocks. The method is robust to experimental errors and does not require the most sophisticated mass spectrometry instrumentation. Such isotope ratio-encoded oligomers may serve as tags that carry information, but the method mainly opens up the capability to write information, for example, about molecular identity, directly into a pure compound via its isotopologue distribution obviating the need for additional tagging and avoiding the use of mixtures of different molecules.

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.

Preservation and Encryption in DNA Digital Data Storage

The exponential growth of the total amount of global data presents a huge challenge to mainstream storage media. The emergence of molecular digital storage inspires the development of the new-generation higher-density digital data storage. In particular, DNA with high storage density, reproducibility, and long recoverable lifetime behaves the ideal representative of molecular digital storage media. With the development of DNA synthesis and sequencing technologies and the reduction of cost, DNA digital storage has attracted more and more attention and achieved significant breakthroughs. Herein, this Review briefly describes the workflow of DNA storage, and highlights the storage step of DNA digital data storage. Then, according to different information storage forms, the current DNA information encryption methods are emphatically expounded. Finally, the brief perspectives on the current challenges and optimizing proposals in DNA information preservation and encryption are presented.

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.

Peptide-Based Sensing, Logic Computing, and Information Security on the Antimonene Platform

Peptides have higher information density than DNA and equivalent molecular recognition ability and durability. However, there are currently no reports on the comprehensive use of peptides' recognition ability and structural diversity for sensing, logic computing, information coding, and protection. Herein, we, for the first time, demonstrate peptide-based sensing, logic computing, and information security on the antimonene platform. The molecular recognition capability and structural diversity (amino acid sequence) of peptides (Pb²⁺-binding peptide DHHTQQHD as a model) adsorbed on the antimonene universal fluorescence quenching platform were comprehensively utilized to sense targets (Pb²⁺) and give a response (fluorescence turn-on) and then to encode, encrypt, and hide information. Fluorescently labeled peptides used as the recognition probe and the information carrier were quenched and hidden by the large-plane two-dimensional material antimonene and specifically bound by Pb²⁺ as the stego key, resulting in fluorescence recovery. The above interaction and signal change can be considered as a peptide-based sensing and steganographic process to further implement quantitative detection of Pb²⁺, complex logic operation, information coding, encrypting, and hiding using a peptide sequence and the binary conversion of its selectivity. This research provides a basic paradigm for the construction of a molecular sensing and informatization platform and will inspire the development of biopolymer-based molecular information technology (processing, communication, control, security).