ABSTRACT A zero‐knowledge proof lets one party convince another that a claim is true while withholding everything that would explain why it is true. We move that idea off conventional hardware and into chemistry, encoding a proof of graph isomorphism directly in synthetic DNA. Each node of a graph is given its own deliberately orthogonal DNA strand; an edge is confirmed only when a short complementary half‐linker meets its matching pair and forms a stable duplex. The verifier watches which bindings occur, but the pattern of binding never reveals how the two graphs line up, so the isomorphism stays hidden. Whether such a construction stays secure at the molecular level turns on two things: how distinguishable the sequences are, and how stable the duplexes they form turn out to be. We probe both. A seeded Monte Carlo study of orthogonal 20‐m libraries, built with balanced GC content and a minimum Hamming separation of , places the chance that an off‐target strand passes for a genuine linker on the order of : empirically at a binding threshold of mismatches, and under once the threshold is tightened to , each value reported with a Wilson confidence interval. This molecular error never becomes the bottleneck. A cheating prover already passes a round with probability one‐half from the isomorphism challenge alone, so the biochemical term enters soundness only as an additive correction, over the edges examined, rather than racing the decay across rounds. Read this way, DNA strands behave as cryptographic witnesses whose noise is small enough to bound and to account for, which lets a proof run at molecular scale without surrendering the hidden mapping.
DNA-encoded chemical libraries (DECLs/DELs) enable the pooled synthesis and selection of millions to billions of DNA-barcoded small molecules, providing an efficient route to discover binders and early leads against diverse biological targets. As DEL-derived programs advance toward identifying clinical candidates, the asset surface of a DEL platform expands from a small set of optimized hits to include library designs, building-block combinations, DNA tags, selection data, and physical library stocks, thus creating new challenges in registration, traceability, and scalable ownership in transfer practices. Non-fungible tokens (NFTs) are unique blockchain-native tokens that can represent digital assets that can be coupled to smart contracts to enable traceable transactions and programmable rights management, which inspire proposals to tokenize intellectual-property (IP) assets such as patents. Here, we review (i) the scientific and commercial value of DEL in modern drug discovery, (ii) NFT/blockchain concepts, specifically in reported biomedical-IP and supply-chain use cases, and (iii) a conceptual architecture for NFT-enabled registration and controlled transfer of DEL libraries or sublibraries using on-chain identifiers with off-chain encrypted metadata and legal agreements.
Open access
Chemical Synthesis and Analysis
Innovative Microfluidic and Catalytic Techniques Innovation
Marxel S. Abogado, Worasait Suwannik, Geoffrey A. Solano, Somchoke Ruengittinun
Consensus sequences are reconstructed representations of original DNA strands, generated by aligning and combining multiple fragmented reads. This paper presents zkConsensus, a privacy-preserving system that verifies the generation of consensus sequences without revealing sensitive genetic information with the use of Zero-Knowledge Proofs (ZKPs). Implemented in Circom language, the circuit validates three validation parts: the consistency between original and aligned reads, the correctness of alignment scores across all read pairs, and the support for the consensus bases through majority voting. The system takes as public inputs the original reads, their lengths, and an expected score, while treating the alignments, reverse complement indications, start positions, and final consensus as private.
Anne M. Luescher, Andreas L. Gimpel, Wendelin J. Stark, Reinhard Heckel · 5 authors
Abstract Physical unclonable functions (PUFs) based on unique tokens generated by random manufacturing processes have been proposed as an alternative to mathematical one-way algorithms. However, these tokens are not distributable, which is a disadvantage for decentralized applications. Finding unclonable, yet distributable functions would help bridge this gap and expand the applications of object-bound cryptography. Here we show that large random DNA pools with a segmented structure of alternating constant and randomly generated portions are able to calculate distinct outputs from millions of inputs in a specific and reproducible manner, in analogy to physical unclonable functions. Our experimental data with pools comprising up to >10 10 unique sequences and encompassing >750 comparisons of resulting outputs demonstrate that the proposed chemical unclonable function (CUF) system is robust, distributable, and scalable. Based on this proof of concept, CUF-based anti-counterfeiting systems, non-fungible objects and decentralized multi-user authentication are conceivable.
Open access
DNA and Biological Computing
Physical Unclonable Functions (PUFs) and Hardware Security
Slim Bettaieb, Loïc Bidoux, Olivier Blazy, Philippe Gaborit
Designing code-based signatures is both an important and challenging problem. A standard way to tackle it consists to use the Fiat-Shamir heuristic along with an identification scheme that is required to be zero-knowledge. The authors of [1] have highlighted an issue within the zero-knowledge proof of the Veron identification scheme [2]. It turns out that the zero-knowledge proof of the AGS protocol [3] is impacted in a similar way. In this paper, we present a masking technique that solves the aforementioned issue without inducing any performance penalty. We introduce the Masked Veron and Masked AGS protocols that both leverage this masking technique and provide their zero-knowledge proofs. In addition, we present a new technique improving the performances of signatures built from code-based identification schemes subject to the attack described in [4]. The Masked Veron and Masked AGS protocols feature all the existing performance improvements from the literature.
Engineering cell-derived nanovesicles with active-targeting ligands is an important strategy to enhance the targeting efficiency. However, the enhanced binding capability to targeting cells also leads to the binding with nontarget cells that share the same biomarkers. DNA-based logic gate is a kind of molecular system that responds to chemical inputs by generating output signals, and the relationship between the input and the output is based on a certain logic. Thus, the DNA-based logic gate could provide a new approach to improve the delivery efficiency of the nanovesicle. In this work, we developed a DNA logic-gated module that coupled two tumor cell-targeting factors (e.g., low pH and a tumor cell biomarker) in a Boolean manner. Immobilization of this module on the surface of the nanovesicle enables the nanovesicle to sense tumor cell-targeting factors and regard these cues as inputs AND logic gate. With the guide of DNA-based logic gate, gold carbon dots (GCDs) encapsulated within nanovesicles were delivered into target cells, and then the intracellular redox status variation was reflected by fluorescence change of GCDs. Overall, we developed DNA logic-gated nanovesicles that contract different targeting factors into a unique tag for target cells. This facile functionalization strategy can pave the way for constructing smart nanovesicles and would broaden their application in the field of precision medicine and personalized treatment.
Shengyan Ji, Yüting Xiong, Wenqi Lu, Minmin Li · 12 authors
Inspired by biological nanochannels, a novel cyclic 3',5'-adenosine monophosphate (cAMP)-regulated artificial nanochannel based on a tripeptide Arg-Thr-Ala (RTA) design is developed. Highly specific binding between the tripeptide and cAMP triggers an obvious conformational transition of a smart polymer chain from a contracted state to a swollen one, which leads to a dynamic modulation of the gating behaviours of the nanochannels.
Salmonella represents one of the major causes of foodborne diseases in humans, in addition to provoking important economic losses in the agri-food sector worldwide. Therefore, the surveillance and control of this human pathogenic bacterium in foodstuffs and biological fluids are necessary in order to prevent and diagnose the disease. Molecular methods based on the detection of DNA sequences specific to pathogenic species are an appealing alternative to traditional culture-based methods that require 5 to 6 days to obtain a definitive result. Among them, and because of its easy miniaturization, electrochemical genosensors are a suitable option for decentralized genetic testing [1-2]; however, they often require a set of sample pretreatment steps before genetic DNA analysis, thus making their implementation at the point of need more difficult. Herein, we report the integration of a nucleic acid-based sensor and an isothermal DNA amplification technique, helicase-dependent amplification or HDA, onto indium tin oxide (ITO) surfaces for the detection of a DNA sequence specific for the typA gene of Salmonella. DNA amplification process occurs at 65 ºC with short oligonucleotides flanking the target sequence, which act as primers. The reversed primer is covalently bound to the ITO surface through a thiol group present at its 5’ terminus, whereas forward fluorescein-tagged primer is incorporated in solution. As a result of the isothermal elongation step, fluorescein-tagged DNA duplexes are attached to the ITO surface and their enzymatic labelling is achieved via Fab fragments directed against fluorescein, conjugated with the redox enzyme alkaline phosphatase. Then, α-naphthyl phosphate is enzymatically dephosphorylated into an electroactive derivate α-naphthol whose amount, directly related to the Salmonella present in the sample, is measured by differential pulse voltammetry. This developed integrated sensing platform allows the detection of Salmonella down to 10 genomes in just over 2 hours [3], the same detection limit as that achieved by real-time PCR but without need of high-end benchtop instrumentation. Furthermore, the sensing layer built onto ITO surfaces maintains its performance even after 9 months storage, and possesses a great potential to be extended to the in-situ, fast and reliable detection of other pathogens. References: [1] D. Mabey, R.W. Peeling, A. Ustianowski and M.D. Perkins, Nat. Rev Microbiol., 2004, 2, 231-240. [2] A.S. Patterson, K. Hsieh, H.T. Soh and K.W. Plaxco, Trends Biotechnol., 2013, 31, 704-712. [3] S. Barreda-García, R. Miranda-Castro, N. de-los-Santos-Álvarez, A.J. Miranda-Ordieres, M.J. Lobo-Castañón, Chem. Comm., 2017, 53, 9721-9724. Acknowledgments: This work has been supported by the Spanish Ministerio de Economía y Competitividad (CTQ2015-63567-R), the Principado de Asturias government (FC-15-GRUPIN14-025), and co-financed by FEDER funds.
Salma Bizid, R. Mlika, A. Haj Saïd, Mejed Chemli · 5 authors
Abstract MWCNTs have been dispersed with modified ferrocene‐poly(para‐phenylene) by π staking interaction to improve dispersion of MWCNTS in organic solution. Such interaction has been demonstrated through electrochemical and chemical characterization of the composite. A layer based on the formed composite (MWCNTs/Fc‐PPP) has been deposited on a gold surface and the electrochemical properties of the redox reaction have been studied through Cyclic Voltammetry (CV) and Electrochemical Impedance Spectroscopy (EIS). We demonstrate that such association of the Fc‐PPP to MWCNTs allows their functionalization and introduction of redox markers which could be used as a platform for a sensing application. The proof of the concept has been demonstrated through DNA immobilization and detection of specific oligonucleotide probe of hepatitis C. The properties of the DNA biosensor construction were followed by redox properties of immobilized redox markers. The nanocomposite (MWCNTs/Fc‐PPP) modified by DNA probes demonstrates a sensitivity to DNA hybridization with a detection limit of 1.6 pM and a wide linear range of detection from 1 fM to 100 pM taking advantage from the large surface of MWCNTs and their electronic properties.