# Selective and Precise Editing of Digital Polymers Through Parallel or Series Toehold-Mediated Strand Displacement

Jakub Ossowski, Cyril Antheaume, Jean-françois Lutz, Maria Nerantzaki

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Jakub Ossowski, Cyril Antheaume, Jean-françois Lutz, Maria Nerantzaki. Selective and Precise Editing of Digital Polymers Through Parallel or Series Toehold-Mediated Strand Displacement. Advanced Functional Materials, 2025, pp.e11868. 10.1002/adfm.202511868. hal-05406191

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# Selective and Precise Editing of Digital Polymers Through Parallel or Series Toehold-Mediated Strand Displacement

Jakub Ossowski, Cyril Antheaume, Jean-François Lutz,* and Maria Nerantzaki*

Two toehold-mediated strand displacement mechanisms—parallel (PTMSD) and series (STMSD)—are explored as strategies for editing digital information stored in synthetic bio-hybrid polymers. To demonstrate their potential, uniform DNA-poly(phosphodiester) (PPDE) conjugates are synthesized using automated phosphoramidite chemistry and characterized by HPLC and mass spectrometry. In these macromolecules, binary information is encoded exclusively in the synthetic polymer segment, while the DNA single strands (ssDNA) serve as programmable motifs for orthogonal self-assembly. DNA sequences are optimized using nucleic acid design software, and the synthetic domains are encoded with a previously reported binary alphabet. These bio-hybrid precursors are then assembled into linear supramolecular architectures via DNA-directed self-assembly. The resulting structures incorporated both digitally encoded polymer segments and double-stranded DNA connectors, as well as accessible ssDNA toeholds that enabled PTMSD and STMSD. Polyacrylamide gel electrophoresis (PAGE) is used to monitor the strand displacement reactions, confirming that PTMSD enables the selective release or erasure of encoded information through dual-toehold accessibility. Furthermore, STMSD is shown to facilitate stepwise rewriting of information. As a proof-of-concept, an English word encoded in the system is successfully edited into its French translation.

## 1. Introduction

Serving as the foundation for modern technologies, data has become essential for advancements in sectors like artificial intelligence, digital health, and the internet of things. The global data generation is expanding exponentially, with estimates suggesting that the global memory demand will surpass the silicon supply by 2040.[1] Taking these limitations into consideration, synthetic digital polymers have emerged as a possible alternative

to current data storage technologies.[2] The main advantage of digital polymers lies in the flexibility of monomers' selection,[3] which allows for the design of macromolecules with high information density,[4] controllable stability,[5] or specific functional properties.[6] This flexibility could also help overcome difficulties in the synthesis[7] and sequencing processes,[8] which are major obstacles for DNA-based data storage.[9] Still, research on polymer data storage has only recently begun, and important properties such as the ability to selectively edit digital polymers – through erasing, repairing, or rewriting data – remain largely underexplored. Despite that, several promising strategies have been proposed,[5,10] many of them still struggle with issues of specificity and selectivity.

Hybrid DNA-polymer bioconjugates present a promising solution to the aforementioned challenges by combining the advantages of both synthetic polymers and DNA.[11] On one hand, the synthetic component provides tunability; on the other hand, DNA's base pairing enables programmed self-assembly and molecular information processing. Such bioconjugates can be easily synthesized using phosphoramidite chemistry,[12] a method widely used today for the synthesis of both DNA[13] and synthetic poly(phosphodiester)s (PPDEs). Moreover, they can be self-assembled through orthogonal DNA hybridization.[14] For instance, a previous study has shown that it is possible to prepare a large digital assembly containing as many as 720 coded bits.[15]

DNA can also provide structural reconfiguration to these systems using dynamical processes such as branch migration and strand displacement.[16] Toehold-mediated strand displacement (TMSD) is a thermodynamically controlled reaction in which two complementary strands (substrate and input) hybridize, displacing an existing strand (output) in the process.[17] This reaction is initiated and facilitated by a short single-stranded region, known as the “toehold”, which binds to the input strand and drives the branch migration process. TMSD serves as a key mechanism for DNA nanotechnology and DNA computing[18] which was first introduced by Adleman.[19] Our recent work demonstrated that it can also be used to control the information content of DNA-PPDE bio-hybrid assemblies.[20] In this prior work, the substrate and the input macromolecules contained non-coded PPDE homopolymers, whereas the output macromolecule contained a

J. Ossowski, C. Antheaume, J.-F. Lutz, M. Nerantzaki

CNRS

ISIS

Université de Strasbourg

8 allée Gaspard Monge, Strasbourg 67000, France

E-mail: jflutz@unistra.fr; nerantzaki@unistra.fr

<figure><img src="image_3.png" /></figure>

The ORCID identification number(s) for the author(s) of this article can be found under https://doi.org/10.1002/adfm.202511868

© 2025 The Author(s). Advanced Functional Materials published by Wiley-VCH GmbH. This is an open access article under the terms of the Creative Commons Attribution License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited.

DOI: 10.1002/adfm.202511868
<figure><img src="image_4.png" /><figcaption>Bio-hybrid Complex C1 (P1+P2+P3)</figcaption></figure>

**Scheme 1.** Schematic illustration of the designed information-containing supramolecular complex C1 containing two accessible toeholds ($t_1$ and $t_2$) enabling PTMSD and STMSD reactions. The red cylinders represent digitally-encoded synthetic segments. The letters written inside them are portions of ASCII-encoded text.

digitally-encoded segment. After hybridization of the substrate with the output, incubation in the presence of the input led to efficient TMSD and release of the digital segment. However, this recent study was limited to a simplified model system featuring a single toehold, limiting its applicability to more advanced functions. For applications in data storage, more sophisticated architectures incorporating multiple accessible toeholds are required.

We examine the applicability of parallel toehold-mediated strand displacement (PTMSD) and series toehold-mediated strand displacement (STMSD) for the controlled editing of digital bio-hybrid assemblies. These mechanisms, which employ two distinct toeholds, have already demonstrated efficiency in DNA-based computation.[21] Herein, we extend these approaches to the design and manipulation of diblock and triblock DNA-PPDE bio-hybrids.

## 2. Results and Discussion

### 2.1. Design of the Bio-Hybrid Polymers

To investigate the potential to achieve programmed output signals through PTMSD and STMSD, we envisioned a linear supramolecular construct (C1) composed of three digital PPDE segments, self-assembled via covalently bonded complementary ssDNA extremities. As shown in **Scheme 1**, the design involves different types of bio-hybrid macromolecules: two 5'-PPDE-b-DNA-3' diblocks (P1 and P3) and a central 5'-DNA-b-PPDE-b-DNA-3' triblock (P2). The sequences of the ssDNA binding sites were programmed to allow orthogonal hybridization. Each binding site, though, contains a unique toehold domain of 10 nucleotides (nt) ($t_1$ and $t_2$) enabling precise control over the system's disassembly into its constituent segments, through either PTMSD or STMSD. The binary sequences of PPDE segments in polymers P1-P3 were designed to encode ASCII letters, forming the word "Storage" when hybridized into complex C1. The rules of encryption for encoding PPDE segments were established in previous works.[22] In brief, a binary code is implemented in the synthetic macromolecules using two comonomers

<table><caption>**Table 1.** ESI-HRMS analysis results and yields of the bio-hybrid PPDEs and model ssDNAs synthesized in this work.</caption><thead><tr><th></th><th><i>m</i>/z<sub>th</sub><sup>a)</sup></th><th><i>m</i>/z<sub>exp</sub></th><th>Yield [%]</th><th>Phosphate units<sup>1)</sup></th></tr></thead><tbody><tr><td>P1</td><td>1029.1740</td><td>1029.175<sup>1b)</sup></td><td>70</td><td>15 nt + 24 mer</td></tr><tr><td>P2</td><td>1127.5673</td><td>1127.5717<sup>c)</sup></td><td>47</td><td>40 nt + 16 mer</td></tr><tr><td>P3</td><td>1055.9692</td><td>1055.9700<sup>d)</sup></td><td>74</td><td>26 nt + 16 mer</td></tr><tr><td>P2'</td><td>930.5037</td><td>930.5065<sup>e)</sup></td><td>54</td><td>40 nt + 24 mer</td></tr><tr><td>I1</td><td>1077.7491</td><td>1077.7514<sup>f)</sup></td><td>74</td><td>25 nt</td></tr><tr><td>I2</td><td>1072.7556</td><td>1072.7577<sup>f)</sup></td><td>75</td><td>25 nt</td></tr><tr><td>ssDNA1</td><td>754.9614</td><td>754.9627<sup>g)</sup></td><td>76</td><td>15 nt</td></tr><tr><td>ssDNA2</td><td>1114.0942</td><td>1114.0979<sup>h)</sup></td><td>59</td><td>40 nt</td></tr><tr><td>ssDNA3</td><td>708.4748</td><td>708.4762<sup>h)</sup></td><td>68</td><td>25 nt</td></tr></tbody></table>

defined as 0 and 1 bits. The DNA sequences were designed using the multi-objective optimization functions of NUPACK.[23] The studied reaction pathway was the parallel strand displacement on the model DNA nanostructure (D1) composed of three duplex forming oligonucleotides: ssDNA1, ssDNA2 (recombined by ssDNA2a and ssDNA2b), and ssDNA3 (Scheme S1, Supporting Information). Key software design objectives included minimizing intramolecular secondary structures and preventing binding between unrelated domains.[24] The GC content of each domain was constrained to 30-70% to achieve a balanced distribution of weak (A/T) and strong (G/C) bases. Additional constraints involved avoiding G-quadruplex-forming patterns (consecutive GGGG sequences) and reducing strand breathing at helix ends by designing all branch migration and complement domains to begin and end with G or C nucleotides. To further minimize non-specific hybridization, restricted nucleotide alphabets were

<table><caption>**Table 2.** Different TMSD experiments studied herein as a mechanism for selective erasing of information.</caption><thead><tr><th></th><th>Initial duplex</th><th>I1 (Eq.)<sup>a)</sup></th><th>I2 (Eq.)<sup>a)</sup></th><th>Output</th><th>Formed duplexes</th></tr></thead><tbody><tr><td>T1</td><td>D1</td><td>1</td><td>1</td><td>ssDNA1</td><td>D2, D3</td></tr><tr><td>T2</td><td>D1</td><td>1.5</td><td>1</td><td>ssDNA1</td><td>D2, D3</td></tr><tr><td>T3</td><td>D1</td><td>1</td><td>1.5</td><td>ssDNA1</td><td>D2, D3</td></tr><tr><td>T4</td><td>D1</td><td>1</td><td></td><td>ssDNA1</td><td>D4</td></tr><tr><td>T5</td><td>D1</td><td>1.5</td><td></td><td>ssDNA1</td><td>D4</td></tr><tr><td>T6</td><td>D1</td><td></td><td>1</td><td>D3</td><td>D5</td></tr><tr><td>T7</td><td>D1</td><td></td><td>1.5</td><td>D3</td><td>D5</td></tr><tr><td>T8</td><td>C1</td><td>1</td><td>1</td><td>P1</td><td>C2, C3</td></tr><tr><td>T9</td><td>C1</td><td>1.5</td><td>1</td><td>P1</td><td>C2, C3</td></tr><tr><td>T10</td><td>C1</td><td>1</td><td>1.5</td><td>P1</td><td>C2, C3</td></tr><tr><td>T11</td><td>C1</td><td>1</td><td></td><td>P1</td><td>C4</td></tr><tr><td>T12</td><td>C1</td><td>1.5</td><td></td><td>P1</td><td>C4</td></tr><tr><td>T13</td><td>C1</td><td></td><td>1</td><td>C3</td><td>C5</td></tr><tr><td>T14</td><td>C1</td><td></td><td>1.5</td><td>C3</td><td>C5</td></tr></tbody></table>

<footnote>a) Theoretical monoisotopic mass-to-charge ratio. Measured at isotopic maximum by ESI-HRMS in negative ion mode as; b) [M-8H]; c) [M-13H]; d) [M-10H]; e) [M-17H]; f) [M-7H]; g) [M-6H]; h) [M-11H]. The notations nt and mer denote unpaired nucleotides and synthetic PPDE monomers, respectively.</footnote>

<footnote>a) The molar equivalents of I1 and I2 are calculated based on the starting duplex/comlpex.</footnote>
<table><caption>**Table 3.** DNA duplexes and bio-hybrid complexes were formed in this work.</caption><thead><tr><th></th><th>Precursors</th><th>Phosphate units<sup>a)</sup></th></tr></thead><tbody><tr><td>D1</td><td>ssDNA1, ssDNA2, ssDNA3</td><td>30 bp + 20 nt</td></tr><tr><td>D2</td><td>I1, ssDNA2</td><td>15 bp + 25 nt</td></tr><tr><td>D3</td><td>I2, ssDNA3</td><td>25 bp</td></tr><tr><td>D4</td><td>I1, ssDNA2, ssDNA3</td><td>40 bp + 10 nt</td></tr><tr><td>D5</td><td>ssDNA1, ssDNA2</td><td>15 bp + 25 nt</td></tr><tr><td>C1</td><td>P1, P2, P3</td><td>30 bp + 21 nt + 56 mer</td></tr><tr><td>C1'</td><td>P1, P2', P3</td><td>40 bp + 1 nt + 64 mer</td></tr><tr><td>C2</td><td>I1, P2</td><td>15 bp + 25 nt + 24 mer</td></tr><tr><td>C3</td><td>I2, P3</td><td>25 bp + 1 nt + 16 mer</td></tr><tr><td>C4</td><td>I1, P2, P3</td><td>40 bp + 11 nt + 32 mer</td></tr><tr><td>C5</td><td>P1, P2</td><td>15 bp + 25 nt + 40 mer</td></tr></tbody></table>

employed: branch migration and toehold domains consisted primarily of C, A, and T, while complement and toehold-binding domains were mostly limited to G, A, and T.

## 2.2. Synthesis of Model ssDNA and DNA-PPDE Bio-Hybrids

After sequence design, the three bio-hybrid polymers P1-P3 (Table 1, entries 1–3) and two input ssDNA strands I1 and I2 (Table 1, entries 5–6) were synthesized by automated phosphoramidite chemistry, following previously described protocols.[15] Scheme S2 (Supporting Information) shows the biological and synthetic monomers used in this work to construct the ssDNA segments and the digital PPDE segments of these macromolecules. Three model ssDNA oligonucleotides (ssDNA1-3) were also prepared for comparison purposes (Table 1, entries 7–9). A detailed summary of the sequences for all bio-hybrid polymers and ssDNA strands studied in this work is provided in Table S1 (Supporting Information). After synthesis, all samples were purified using a reverse-phase column, characterized by ion-exchange high-performance liquid chromatography (IE-HPLC), followed by a separate fast injection electrospray ionization high resolution mass spectrometry (ESI-HRMS) step. The desired bio-hybrid macromolecules were obtained in yields ranging from 47 to 76% (Table 1). Yields were calculated from the CPG loading (1 µmol column). Monodispersity was confirmed by the observation of a single peak on the HPLC spectra (Figures S3 and S4, Supporting Information) and further validated by ESI-HRMS spectrometry (Table 1 and Figures S5–S13, Supporting Information).

## 2.3. PTMSD Experiments Using Model ssDNA Strands

Table 2 outlines all the PTMSD experiments studied in this work. To evaluate the feasibility of the proposed system and verify the designed sequences, preliminary PTMSD reactions were initially performed using the DNA nanostructure D1 as substrate and the ssDNA strands I1 and I2 as inputs (Scheme S3, Supporting Information). In brief, first, the starting duplex D1 containing two accessible toeholds ($t_1$ and $t_2$) was prepared by annealing three

<figure><img src="image_5.png" /><figcaption>**Figure 1.** 20% PAGE evaluation of PTMSD reactions using model ssDNA. First, ssDNA1-3 (lanes 2–4) were mixed equimolarly to form duplex D1 (lane 7). Next, the input strands I1 and I2 (lanes 5–6) were added to D1 with a D1/I1/I2 molar ratio of 1:1:1 (T1, lane 10), 1:1.5:1 (T2, lane 11) or 1:1:1.5 (T3, lane 12). Lanes 8 and 9 correspond to control duplexes D2 and D3, respectively. Lane 1 represents 10–300 bp DNA ladder. It shall be noted that this ladder is made for dsDNA analysis and therefore should only be used as guide for the eyes.</figcaption></figure>

complementary oligonucleotides ssDNA1-3 (Table 3). Following the same annealing protocol, two control DNA assemblies (D2 and D3) were also prepared (Table 3). Then, PTMSD reactions were conducted with D1/I1/I2 ratios of 1:1:1 (T1), 1:1.5:1 (T2) and 1:1:1.5 (T3). All strand displacement experiments were incubated at room temperature overnight. For visual monitoring of TMSD experiments, we used a previously described PAGE protocol, that enables the efficient separation and identification of strand displacement precursors and products.[20] This protocol involves an asymmetrical cyanine dye (SYBR Gold), which can be used as a stain for double-stranded DNA (dsDNA) and ssDNA. Figure 1 shows PAGE results obtained for the PTMSD experiments T1-T3. The band of duplex D1 (lane 7) appears fuzzy probably due to low persistence length, while the secondary band of duplex D3 (lane 9) indicates dimeric configurations. In Figure 1 (lanes 10–12) it can also be seen that the simultaneous addition of input strands I1 and I2, resulted in the complete disappearance of starting duplex D1, the formation of duplexes D2 and D3, and the successful release of the output ssDNA1. Moreover, in experiments T2 and T3, the presence of excess input strands is evident in lanes 11–12, highlighting the resolution of the experimental setup. Two distinct TMSD reactions were also investigated by adding different molar ratios of either input strand I1 or I2 to starting duplex D1 (TMSD Experiments T4-T7). Interestingly, PAGE analysis confirmed that strand displacement occurs as long as one of the two inputs exists (Figure S12, Supporting Information).

## 2.4. Selective Release/Erasing of Abiotic Information through PTMSD Reactions

PTMSD was afterward investigated to perform selectively one or more erase operations on information-containing supramolecular construct C1, serving as substrate and the central

<footnote>a) The notations bp denote base pairs.</footnote>
<figure><img src="image_6.png" /><figcaption>**Scheme 2.** Simultaneous or selective TMSD modifications of the bio-hybrid complex C1 that serves as a central information hub of this study. a) PTMSD performed using both input strands I1 and I2 simultaneously. b) Selective modification using I1 only. c) Selective modification using I2 only.</figcaption></figure>

information hub in this study. The ssDNA strands I1 and I2 were used as inputs (Scheme 2). First, the bio-hybrid digital polymers P1-P3 and input strands I1 and I2 were annealed and their electrophoretic mobility was studied by PAGE (Figure 2). When compared with model ssDNA oligonucleotides ssDNA1-3, the covalent conjugation of synthetic PPDE segments reduces the migration rate of the corresponding DNA-PPDE conjugates (P1-P3) (Figure 2a, lanes 2–4). This observation aligns with our previous studies showing that the migration of bio-hybrids is primarily influenced by their molecular weight.[20,25]

Next, DNA-guided self-assembly was used for the fabrication of C1 containing two accessible toeholds ($t_1$ and $t_2$) based on precursors P1–P3. According to the sequence design, the complex C1 contains three synthetic blocks (56 digital monomers) connected by two dsDNA sections of 15 base pairs (bp) each (Table S1, Supporting Information and Scheme 2). C1 was prepared using the same protocol as for DNA assemblies (Table 3). For comparison purposes, four control bio-hybrid complexes C2-C5 were also prepared. Assembly was confirmed by electrophoresis, which evidenced the formation of a superstructure of a much higher molecular weight than the individual precursors P1–P3 (Figure 2a, lanes 2–7). Subsequently, in an attempt to decompose selectively the starting complex C1 into three distinct products carrying different digital synthetic segments, input strands

I1 and I2 were introduced either simultaneously (Scheme 2a) or separately (Scheme 2b,c) to C1. Simultaneous PTMSD reactions were conducted with C1/I1/I2 ratios of 1:1:1 (T8), 1:1.5:1 (T9) and 1:1:1.5 (T10) (Table 2). Notably, PAGE analysis (Figure 2a, lanes 10–12) revealed the complete disappearance of starting duplex C1, the successful release of the output P1, and the formation of new complexes C2 and C3. Furthermore, for TMSD experiments T9 and T10 the residual unreacted inputs I1 and I2 were detected as faint single bands. The selectivity of the system was further demonstrated in TMSD experiments T11-T14 where input strands I1 and I2 were introduced separately (Scheme 2b,c). PAGE results shown in Figure 2b,c demonstrate that it is possible to achieve precise release of output signals depending on the input sequence used. In detail, incubation of C1 with I1 results in the displacement of P1 and in the formation of a new complex C4 (Figure 2b, lanes 8–9). Accordingly, the use of C1 and I2 enables the appearance of two new bio-hybrid complexes C3 and C5 (Figure 2c, lanes 9–10).

## 2.5. STMSD as a Rewriting Mechanism

Finally, the STMSD mechanism was investigated (Scheme 3). This stepwise strand displacement process was used herein as
<figure><img src="image_7.png" /><figcaption>**Figure 2.** 20% PAGE evaluation of the modification of **C1** made by (a) PTMSD or (b,c) distinct TMSD reactions. In all cases, lane 1 is a commercial DNA ladder (10bp to 300 bp), lanes 2–4 correspond to **P1**–**P3** and lane 6 to complex **C1**. In panel a, the input strands **I1** and **I2** (lanes 5–6) were added to **C1** with a **C1/I1/I2** molar ratio of either 1:1:1 (experiment **T8**, lane 10), 1:1.5:1 (**T9**, lane 11) or 1:1:1.5 (**T10**, lane 12). Lanes 8 and 9 correspond to preformed control complexes **C2** and **C3**, respectively. In panel b, the input strand **I1** (lane 5) was incubated with **C1/I1** molar ratio of 1:1 (experiment **T11**, lane 8) or 1.5:1 (**T12**, lane 9) molar ratio. Lane 7 shows the expected complex **C4** for comparison purposes. In panel c, the input strand **I2** (lane 5) was added to **C1** with a **C1/I2** molar ratio of 1:1 (experiment **T13**, lane 9) or 1:1.5 (**T14**, lane 10). Lanes 7 and 8 correspond to pre-assembled control complexes **C5** and **C3**, respectively.</figcaption></figure>

<figure><img src="image_8.png" /><figcaption>**Scheme 3.** A two-step STMSD process for rewriting the information content of **C1**. a) A first TMSD reaction between **C1** (substrate) and **I1** (input) allows the formation of intermediate complex **C4** and the release of the digital segment **P1** (output). b) Then, a second TMSD reaction between **C4** (substrate) in the presence of **P1** enables a rewriting mechanism where the digital segment **C2** (output) in the **C4** construct (substrate) is replaced by the digital segment **P2**' (input). This stepwise protocol is necessary since blue domains of **I1** and **P2**' can hybridize with each other.</figcaption></figure>
<figure><img src="image_9.png" /><figcaption>**Figure 3.** 20% PAGE evaluating the STMSD rewriting mechanism. First, three bio-hybrids **P1**, **P2** and **P3** (lanes 2, 3, 5) were mixed equimolarly to form complex **C1** (lane 7). Second, the input strand **I1** (lane 6) was mixed equimolarly with **C1** (experiment **T15i**, lane 11). Finally, the polymer **P2'** (lane 4) was added to the resulting solution (experiment **T15ii**, lane 12). The model targeted complexes **C4** and **C1'** are shown in lanes 8–9 for reference. Lane 1 corresponds to 10–300 bp DNA ladder.</figcaption></figure>

a rewriting mechanism to transform a source word into a target word. As a proof-of-principle, the english word “Storage” was translated into the french word “Stockage”. **Figure 3** shows PAGE results obtained for that experiment. The bio-hybrid polymer **P2'** (Table 1, entry 4) was first synthesized by automated phosphoramidite chemistry, in order to be used as input and replace syntetic segment **P2** in the complex **C1**. The binary sequence of PPDE segment in this polymer was designed to encode ASCII letters, forming the syllable “cka”. Then, the starting complex **C1** together with three control complexes **C1'**, **C2**, and **C4** were prepared through DNA-guided assembly, using equimolar amounts of the respective components, as detailed in Table 3. Assembly was confirmed by electrophoresis, which evidenced the formation of assemblies of much higher molecular weight than the individual precursors (Figure 3, lanes 2–10). Afterward, a STMSD process was initiated by adding sequentially the input strands **I1** and **P2'** in equimolar ratios with respect to starting complexes **C1** and **C4** (Table 4, STMSD experiments **T15i** and **T15ii**). After each strand displacement, no bands associated with the starting complexes or any unexpected species were detected, according to PAGE results presented in Figure 3. Indeed, experiment **T15i** (lane 11) clearly shows the complete disappearance of starting complex **C1** (containing the word “Storage”), the successful release of output **P1**, and the appearance of a new complex **C4**. The subsequent STMSD reaction **T15ii** (lane 12) – incubation of **C4** (substrate) with the bio-hybrid input **P2'** in the presence of

<table><caption>**Table 4.** STMSD reactions studied in this work for rewriting information.</caption><thead><tr><th></th><th>Initial<br>complex</th><th>I1 (Eq.)<sup>a)</sup></th><th>P2' (Eq.)<sup>a)</sup></th><th>Output</th><th>Formed<br>complexes</th></tr></thead><tbody><tr><td><b>T15i</b></td><td>C1</td><td>1</td><td></td><td>P1</td><td>C4</td></tr><tr><td><b>T15ii</b></td><td>C4</td><td></td><td>1</td><td>C2</td><td>C1'</td></tr></tbody></table>

**P1** – allows the formation of new species: the (output) complex **C2** and the new complex **C1'** (containing the word “Stockage”).

### 3. Conclusion

In summary, we have demonstrated that STMSD and STMSD reactions enable precise and selective editing of information stored in synthetic digital polymers. In particular, this study emphasizes the use of DNA as a versatile scaffold enabling both self-assembly and selective information processing of bio-hybrid digital PPDEs. What is more, the PPDE segments, used as data storage units, are not restricted to the monomers employed in this study, offering flexibility for their customization. The presented model design is also potentially scalable and could be extended to larger linear supra-macromolecules with multiple toeholds, following the same assembly principles. Furthermore, the suggested approach is adaptable to create 2D and 3D architectures, enabling precise spatial organization of stored information as well as enhancing storage density. Beyond the demonstrated selective release and precise rewriting of information, the design holds potential for more advanced operations. Ongoing research focuses on strategies that can enable the isolation of the released outputs from bulk solutions for sequencing and decoding.

### Supporting Information

Supporting Information is available from the Wiley Online Library or from the author.

### Acknowledgements

This research was conducted in the frame of the national collaborative network MolecuArXiv. It was supported by a grant of the French government, managed by the Agence Nationale de la Recherche (ANR) under the frame of the France 2030 investment plan (ANR-22-PEXM-0004). J.O. thanks the CSC Graduate School funded by the Agence Nationale de la Recherche (CSC-IGS ANR-17-EURE-0016) for a master fellowship.

### Conflict of Interest

The authors declare no conflict of interest.

### Data Availability Statement

The data that support the findings of this study are available from the corresponding author upon reasonable request.

### Keywords

data storage, digital polymers, DNA self-assembly, sequence-controlled polymers, toehold-mediated strand displacement

Received: May 12, 2025

Revised: June 8, 2025

Published online:

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<footnote>a) The molar equivalents of **I1** and **P2'** are calculated relative to the initial bio-hybrid complex.</footnote>
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