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

Amalian, J.-A.; Ouahabi, A. Al; Cavallo, Guglielmo; König, N. F.; Poyer, S.; Lutz, Jonas; Charles, L.

doi:10.1002/jms.3880

Cited by 6 publications

(9 citation statements)

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“…Besides the investigation of enhanced synthetic approaches, which further increase the degree of control, the potential applications of such defined structures gain increasing attention 16 . Particularly, the application in the field of data storage has been discussed in detail 2,31,32,[36][37][38][39][40] . The data storage capacity of DNA serves as prototype as it carries the genetic code 18,19 .…”

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

et al. 2020

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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.

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

et al. 2020

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“…In contrast, an additional MS‐active group was introduced into the end‐group of sequence‐controlled polyurethanes to improve their ionization yield, another key requirement for reliable sequencing by MS/MS 14 . In order to capitalize on the robustness of the phosphoramidite used in the automated synthesis of long poly(phosphodiester)s, specific reagents were prepared to include alkoxyamine linkages in the final chains, the low bond dissociation energy of which makes all phosphate bonds MS/MS‐silent, lowering the number of product ion series from eight to two and hence ensuring full sequence coverage of long chains 15 . Similarly, Zhang and co‐workers recently showed that controlling the oxidation degree of sulfur atoms in the backbone of poly(succinimide thioester)s drastically enhances dissociation selectivity 16 .…”

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confidence: 99%

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

Charles

Mondal

Greff

et al. 2020

Rapid Comm Mass Spectrometry

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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.

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“…Beside the nature of coding moiety, two main strategies can be envisaged to design the polymeric skeleton. One can first focus on developing synthesis protocols for production of highly monodisperse samples of long polymeric chains, which molecular structure can be further optimized to ensure their MS/MS readability [11]. For example, this approach was successfully implemented for sequence-defined poly(phosphodiester)s. These species were first synthesized as defect-free chains with degrees of polymerization (DP) above 100 using an automated synthesis protocol to implement phosphoramidite chemistry [12].…”

Section: Introductionmentioning

confidence: 99%

Promoting carboxylate salts in the ESI source to simplify positive mode MS/MS sequencing of acid-terminated encoded polyurethanes

Poyer

Petit

Telitel

et al. 2020

International Journal of Mass Spectrometry

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Synthetic polymers prepared by solid-phase processes are often released from the solid support by hydrolysis, leading to an acidic α chain-end which can usefully be employed to perform mass spectrometry experiments in the negative ion mode. This is the case for sequence-defined polyurethanes, which exhibit very simple MS/MS pattern as deprotonated species in great contrast to data obtained in the positive ion mode. Indeed, after deprotonation of their acidic end-group, collision induced dissociation (CID) of these polymers proceeds via competitive cleavages of all carbamate bonds. This leads to a unique series of anionic fragments spaced by the mass of one of the other coding co-monomer, enabling their sequence to be readily deciphered. However, as their size increases, polyurethanes are best ionized in the positive mode but their dissociation pattern is far more complicated, with four to five fragmentation routes depending on the adducted cation. This spectral complexity could however be highly reduced when selecting precursor ions that have experienced H/Na (or any other alkali) exchange in their acidic α end-group: in these conditions, only one reaction is observed and yields pairs of complementary products. Mechanisms could be proposed to explain how, although part of an end-group, the acidic proton had a key role in the dissociation processes of polyurethane chains. Exchange of this proton was then further optimized by proper selection of the Xanion in the NaX salt supplemented to the electrosprayed solution. By allowing simplification of MS/MS data while avoiding signal dilution over multiple ion series, CID of these [M -H + zNa] (z-1)+ permitted to envisage reliable decoding of sequence-defined polyurethanes storing large amount of information.

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

Cited by 6 publications

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

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

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

Promoting carboxylate salts in the ESI source to simplify positive mode MS/MS sequencing of acid-terminated encoded polyurethanes

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