Reading and writing data by using self-immolative, sequence-defined oligourethanes

Synthesis of sequence-defined oligourethanes (i.e., writing) followed by chemical self-immolation can yield mass fragments detectable standard liquid chromatography-mass spectrometry (LC/MS) instruments reading). Expanding beyond the traditional binary approach chemically distinct monomers as 1s and 0s, in a recent issue Cell Reports Physical Science, Anslyn co-workers introduce hexadecimal encoding multifunctional oligourethanes. Robert Merrifield’s pioneering demonstration solid-phase syntheses early 1960s1Merrifield B. Solid phase synthesis (Nobel Lecture).Angew. Chem. Int. Ed. 1985; 24: 799-810Crossref Scopus (318) Google Scholar ultimately led to development convenient methods making peptides, proteins, oligo- polynucleotides, all which have found important applications medicine.2Marshall G.R. Solid-phase synthesis: paradigm shift.J. Pept. Sci. 2003; 9: 534-544Crossref PubMed (22) This work Merrifield paved way for chemists greatly expand on library possible polymers, where, example, efforts toward non-biological artificial polymers mostly focused achieving largely purely synthetic milestones—such improved control over sequence, stereochemistry, scalability. Even with more advances one area that remains relatively underexplored is so-called “digital polymers,”3Laurent E. Amalian J.-A. Parmentier M. Oswald L. Al Ouahabi A. Dufour F. Launay K. Clément J.-L. Gigmes D. Delsuc M.-A. et al.High-capacity digital polymers: storing images single molecules.Macromolecules. 2020; 53: 4022-4029Crossref (21) are well-defined macromolecules intended use data-storage platforms that, principle, should provide long-term stability greater total information capacity than hard drives solid-state devices. As an DNA, exists natural source genetic information, was logically first be explored information-storage medium late 1980s.4Dong Y. Sun Ping Z. Ouyang Q. Qian DNA storage: research landscape future prospects.Natl. Rev. 7: 1092-1107Crossref (38) The later DNA-based data storage Church, Goldman, others significantly amount could stored—moving from hundreds kilobytes few hundred megabytes recently form 10+ million oligonucleotides.5Ceze Nivala J. Strauss Molecular using DNA.Nat. Genet. 2019; 20: 456-466Crossref (141) However, current expense issues associated scaling syntheses, well extracting via time-consuming sequencing methods, inherent practical limitations prohibit widespread adoption platforms, situation exacerbated fact unlike also susceptible degradation under mild conditions. On other hand, such has many potential advantages. Chief among them ease synthesis, scalability, diversity available functional used store data. For phosphoramidite chemistry been adapted represents strategy several oligomers produced years.6Roy R.K. Meszynska Laure C. Charles Verchin Lutz J.-F. Design digitally encoded decoded erased.Nat. Commun. 2015; 6: 7237Crossref (194) Regardless type methodology employed, each constitutes “writing” phase. In next step, this usually decoded, or “read,” through series tandem (MS/MS) experiments typically predictable molar decoded. Thus, density traditionally investigated longer oligomeric sequences and/or preparation polymers.7Martens S. Landuyt Espeel P. Devreese Dawyndt Du Prez Multifunctional storage.Nat. 2018; 4451Crossref (84) An alternative decoding involves self-immolative polymers8Sagi Weinstain R. Karton N. Shabat Self-immolative polymers.J. Am. Soc. 2008; 130: 5434-5435Crossref (260) depolymerized manner response heat mildly basic Chemical depolymerization presents advantages MS/MS because process produces simple monomer oligomer fragments, read common instrumentation without additional purification steps. One reported previously co-workers9Dahlhauser S.D. Escamilla P.R. VandeWalle A.N. York J.T. Rapagnani R.M. Shei J.S. Glass S.A. Coronado J.N. Moor S.R. Saunders D.P. E.V. Sequencing controlled self-immolation.J. 142: 2744-2749Crossref (23) composed urethane linkages undergo intramolecular 5-exo-trig cyclizations (Figure 1A) reacting hydroxyl O terminus eliminate small-molecule at time. reaction done conditions, 70°C presence weak base (such cesium carbonate [Cs2CO3]). Published Science,10Dahlhauser Vera M.S. Ngo Boley A.J. Simpson Z.B. Efficient molecular urethanes.Cell Rep. Phys. 2021; 2: 100393Abstract Full Text PDF (7) expanded previous demonstrating time how encode decode They synthesized parallel 18 octamers derived small stereo-defined amino alcohols 1B), some they deuterated during reduction canonical non-canonical acids structural variation into library. were carried out solid resins 96-well plates, where reagents precursors deposited mixed. A representative urethane-based octamer (A1; N-to-O termini 4215475-Pheindex) activated coupling chemistry. Functioning indexing subunit, phenylalaninol (Pheindex) group introduced start A1 sequence 1C), octamers. authors stated served normalize readout stage, helped filter any extraneous masses detected analysis. Similarly, capped N 4-fluoro-7-nitrobenzofuran (NBD-F), acted long-wavelength chromophore monitored step. Heating Cs2CO3 DMSO kickstarted process, required 225 min complete prior resultant MS spectrum 1C, right) obtained after deconstruction step yielded easily identifiable pattern need purification. result significant experiment executed Agilent single-quadrupole spectrometer coupled reverse-phase C18 column PC running Agilent’s ChemStation software. overall broadly accessible labs already employ routine analysis synthesis. With example another (labeled A2) possessing 1376303-Pheindex. Using same deconstructed A2, performed sequencing, recorded its constituent fragments. proof concept, A2 calculating differences between peaks (shown red Figure 1D), starting reading frame Pheindex (177.2 amu). These then assigned number (0–7) octal code (e.g., = 7). Not counting frame, string “57451243036731” converted American Standard Code Information Interchange (ASCII) 1D). back plain text Huffman algorithm, finally giving message, “Hello, world!” After decided larger piece text, whereby selected passage Jane Austen’s Mansfield Park: “If scheme happiness fails, human nature turns another; if calculation wrong, we make second better: find comfort somewhere.” statement 153 characters long, including spaces quotation marks, 632 when process. ASCII conversion code, only 158 characters, 26 unique punctuation accounted for. needed their initial eight-monomer while extending length ten subunits, allowing numeral code. therefore increased alcohol 16 adding alpha methylene monomer. To accurately Austen passage, 18, 17 subunits long six long. speed up input open-source Mol.E-decoder software, symbols sorted hex strings. output remarkably yielding no errors. Although potentially robust high-throughput method compressing, storing, retrieving does (as noted authors). First, ionizability hydrophobic side chains affect corresponding signal intensity. Second, might not separate column. former, envision creating fewer groups, latter, it synthesize rather longer. Third, step) automating deprotection reactions shortening either solutions concentrated heating slightly higher temperatures. Adopting these changes works will hopefully enable address pressing issue, density. Solving problem critical implemented par likes existing nucleic acid technologies. stage new exciting data, key takeaways efficient powerful employs cheap, scalable, oligourethane (“writing”) mechanisms LC/MS (“reading”). Relative less techniques unique. cost-effective analytical shows great promise abiotic-based storage. urethanesDahlhauser al.Cell ScienceApril 21, 2021In BriefDense means society continues produce exponentially. Abiotic (plastics) exceptional platform accessibility limitless modifications. efficient, “reading” still needed. Herein, Dahlhauser al. report (writing) (reading) urethanes. Full-Text Open Access