Controlling the structure of sequence-defined poly(phosphodiester)s for optimal MS/MS reading of digital information

Using ion mobility spectrometry to understand signal dilution during tandem mass spectrometry sequencing of digital polymers: Experimental evidence of intramolecular cyclization

RATIONALE

Optimizing the structure of digital polymers is an efficient strategy to ensure their tandem mass spectrometry (MS/MS) readability. In block-truncated poly(phosphodiester)s, homolysis of C-ON bonds in long chains permits the release of smaller blocks amenable to sequencing. Yet the dissociation behavior of diradical blocks was observed to strongly depend on their charge state.

METHODS

Polymers were ionized in negative mode electrospray and activated in-source so that blocks released as primary fragments can be investigated using ion mobility spectrometry (IMS) or sequenced in the post-IMS collision cell. Collision cross sections (CCS) were derived from arrival times using a calibration procedure developed for polyanions using the IMSCal software. A multistep protocol based on quantum methods and classical molecular dynamics was implemented for molecular modeling and calculation of theoretical CCS.

RESULTS

Unlike their triply charged homologues, dissociation of diradical blocks at the 2- charge state produces additional fragments, with +1 m/z shift for those holding the nitroxide α-termination and -1 m/z for those containing the carbon-centered radical ω-end. These results suggest cyclization of these diradical species, followed by H• transfer on activated reopening of this cycle. This assumption was validated using IMS resolution of the cyclic/linear isomers and supported by molecular modeling.

CONCLUSIONS

Combining IMS with molecular modeling provided new insights into how the charge state of digital blocks influences their dissociation. These results permit to define new guidelines to improve either ionization conditions or the structural design of these digital polymers for best MS/MS readability.

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.

Conception and Evaluation of a Library of Cleavable Mass Tags for Digital Polymers Sequencing

A library of phosphoramidite monomers containing a main-chain cleavable alkoxyamine and a side-chain substituent of variable molar mass (i.e. mass tag) was prepared in this work. These monomers can be used in automated solid-phase phosphoramidite chemistry and therefore incorporated periodically as spacers inside digitally-encoded poly(phosphodiester) chains. Consequently, the formed polymers contain tagged cleavable sites that guide their fragmentation in mass spectrometry sequencing and enhance their digital readability. The spacers were all prepared via a seven steps synthetic procedure. They were afterwards tested for the synthesis and sequencing of model digital polymers. Uniform digitally-encoded polymers were obtained as major species in all cases, even though some minor defects were sometimes detected. Furthermore, the polymers were decoded in pseudo-MS3 conditions, thus confirming the reliability and versatility of the spacers library.

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.

Design, Synthesis and Actual Applications of the Polymers Containing Acidic P-OH Fragments: Part 1. Polyphosphodiesters

Among natural and synthetic polymers, main-chain phosphorus-containing polyacids (PCPAs) (polyphosphodiesters), stand in a unique position at the intersection of chemistry, physics, biology and medicine. The structural similarity of polyphosphodiesters PCPAs to natural nucleic and teichoic acids, their biocompatibility, mimicking to biomolecules providing the 'stealth effect', high bone mineral affinity of polyphosphodiesters resulting in biomineralization at physiological conditions, and adjustable hydrolytic stability of polyphosphodiesters are the basis for various biomedical, industrial and household applications of this type of polymers. In the present review, we discuss the synthesis, properties and actual applications of polyphosphodiesters.

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.

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.

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.

Dual sequence definition increases the data storage capacity of sequence-defined macromolecules

Sequence-defined macromolecules offer applications in the field of data storage. Challenges include synthesising precise and pure sequences, reading stored information and increasing data storage capacity. Herein, the synthesis of dual sequence-defined oligomers and their application for data storage is demonstrated. While applying the well-established Passerini three-component reaction, the degree of definition of the prepared monodisperse macromolecules is improved compared to previous reports by utilising nine specifically designed isocyanide monomers to introduce backbone definition. The monomers are combined with various aldehyde components to synthesise dual-sequence defined oligomers. Thus, the side chains and the backbones of these macromolecules can be varied independently, exhibiting increased molecular diversity and hence data storage capacity per repeat unit. In case of a dual sequence-defined pentamer, 33 bits are achieved in a single molecule. The oligomers are obtained in multigram scale and excellent purity. Sequential read-out by tandem ESI-MS/MS verifies the high data storage capacity of the prepared oligomers per repeat unit in comparison to other sequence defined macromolecules.

Revealing Data Encrypted in Sequence-Controlled Poly(Alkoxyamine Phosphodiester)s by Combining Ion Mobility with Tandem Mass Spectrometry

The defined sequence of two comonomers in sequence-controlled macromolecules can be used to store binary information which is further decoded by MS/MS sequencing. In order to achieve the full sequence coverage requested for reliable decoding, the structure of these polymers can be optimized to minimize their dissociation extent, as shown for poly(alkoxyamine phosphodiester)s (PAPs) where weak alkoxyamine bonds were introduced in each repeating unit to make all phosphate groups MS/MS silent. However, for secret communications, a too high MS/MS readability could be a drawback. In this context, the design of PAPs was further optimized in this work to also include a decrypting key based on slight variation of a fragment collision cross section. This was achieved by employing two different nitroxides to build the alkoxyamine moiety, each containing a coding alkyl segment of the same mass but different architectures. As a result, the digital sequence determined from primary fragments observed in MS/MS had to be decrypted according to appropriate rules that depend on the drift times measured by ion mobility spectrometry for repeating units released as secondary product ions.

Collision-induced dissociation of stable nitroxides: A combined tandem mass spectrometry and computational study of TEMPO• and SG1•

The dissociation behavior of two stable nitroxides, namely 2,2,6,6-tetramethylpiperidine-1-oxyl (TEMPO^•) and N-tert-butyl-1-diethylphosphono-2,2-dimethylpropyl nitroxide (SG1^•), subjected as protonated molecules to collisional activation was investigated using a combination of different mass spectrometry experiments and theoretical calculations. Elemental composition of reaction products was derived from accurate mass data measured in high resolution tandem mass spectrometry experiments, primary fragments were distinguished from secondary ions based on both breakdown curves and MS³ data, and H/D exchange experiments were performed to support proposed structures. Postulated fragmentation pathways were then studied in terms of energetic, using the standard B3LYP/6-31G(d) method. While protonation of TEMPO^• mainly occurred on the oxygen atom of the nitroxyl function, a series of protomers were found for SG1^• with the adducted proton preferentially located onto the P=O group of this phosphorylated species. For both protonated nitroxides, major product ions measured in tandem mass spectrometry arose from reactions occurring at low energy costs via elimination of radical species. Formation of secondary fragments that were detected with low abundance when raising the activation level of both precursor ions could be rationalized with pathways proceeding via high energy transition states.

High definition polyphosphoesters: between nucleic acids and plastics

Nucleic acids and synthetic polyphosphoester materials have been distinct fields – this review shows how these areas now comprise a continuum.