DNA Complexes Research Articles

A Comprehensive Review of Pfu DNA Polymerase: Extraction, Production and Applications

Pfu DNA Polymerase, a thermostable enzyme derived from the hyperthermophilic archaeon Pyrococcus furiosus, is widely recognized for its high fidelity and strong processivity. Its 3'-5' exonuclease activity makes it indispensable for the correct amplification of both short and complex DNA strands. These biochemical properties of Pfu DNA Polymerase have encouraged considerable advancements in its extraction and production methods. This review covers some of the traditional approaches for purification, including protein purification and affinity chromatography, and updates on recent advances in recombinant gene expression, automated systems of production, and membrane-based technologies. New ways of engineering enzymes have recently been developed, such as CRISPR-Cas9-mediated gene optimization, which raised the bar on extraction efficiency to meet emerging demand. Once challenging, Pfu DNA Polymerase production has been significantly streamlined through recombinant expression in E. coli both at a laboratory and commercial scale. The optimization techniques that are involved with IPTG concentration and Response Surface Methodology have increased the yield by up to 30%. Auto-induction means even higher biomass outputs are allowed. Today, applications of Pfu DNA Polymerase span from standard PCR up to advanced clinical diagnostics in the fields of molecular biology, forensic analysis, clinical microbiology, and biotechnology.

In Silico Study of the Potential Inhibitory Effects on Escherichia coli DNA Gyrase of Some Hypothetical Fluoroquinolone–Tetracycline Hybrids

Background/Objectives: Despite the discovery of antibiotics, bacterial infections persist globally, exacerbated by rising antimicrobial resistance that results in millions of cases, increased healthcare costs, and more extended hospital stays. The urgent need for new antibacterial drugs continues as resistance evolves. Fluoroquinolones and tetracyclines are versatile antibiotics that are effective against various bacterial infections. A hybrid antibiotic combines two or more molecules to enhance antimicrobial effectiveness and combat resistance better than monotherapy. Fluoroquinolones are ideal candidates for hybridization due to their potent bactericidal effects, ease of synthesis, and ability to form combinations with other molecules. Methods: This study explored the mechanisms of action for 40 hypothetical fluoroquinolone–tetracycline hybrids, all of which could be obtained using a simple, eco-friendly synthesis method. Their interaction with Escherichia coli DNA Gyrase and similarity to albicidin were evaluated using the FORECASTER platform. Results: Hybrids such as Do-Ba, Mi-Fi, and Te-Ba closely resembled albicidin in physicochemical properties and FITTED Scores, while Te-De surpassed it with a better score. Similar to fluoroquinolones, these hybrids likely inhibit DNA synthesis by binding to enzyme–DNA complexes. Conclusions: These hybrids could offer broad-spectrum activity and help mitigate bacterial resistance, though further in vitro and in vivo studies are needed to validate their potential.

Nucleus-Targeting Photosensitizers Enhance Neutrophil Extracellular Traps for Efficient Eradication of Multidrug-Resistant Bacterial Infections.

Neutrophil extracellular traps (NETs) are web-like complexes of DNA and proteins that are extruded by activated neutrophils and play critical roles as major components of the innate immune response against pathogen invasion. However, some microbes have developed strategies to evade NET attacks, leading to impaired immune defenses and persistent infections. In this study, an engineered neutrophil strategy for enhancing the antibacterial activity of NETs is developed. A nucleus-targeting photosensitizer (NCP) with strong reactive oxygen species production and a strong DNA-binding capacity is synthesized. NCP-loaded neutrophils are subsequently constructed via direct incubation of NCP with neutrophils, and the NCP is closely inserted into the nucleus DNA. Upon activation by bacteria-related toxins, NCP-coupled NETs can be released rapidly, actively trapping bacteria and providing a high local concentration of NCP around them. Both in vitro and in vivo results revealed that NCP-coupled NETs can effectively eradicate various multidrug-resistant bacteria and biofilms through photodynamic therapy, overcome bacterial immune evasion, and promote tissue recovery from severe wound infections. This design can significantly strengthen NET function, providing a non-antibiotic alternative platform for treating bacterial infectious diseases.

Epigenetic Landscape of DNA Methylation in Pancreatic Ductal Adenocarcinoma

Pancreatic ductal adenocarcinoma (PDAC) remains one of the most lethal malignancies, characterized by its aggressive progression and dismal prognosis. Advances in epigenetic profiling, specifically DNA methylation analysis, have significantly deepened our understanding of PDAC pathogenesis. This review synthesizes findings from recent genome-wide DNA methylation studies, which have delineated a complex DNA methylation landscape differentiating between normal and cancerous pancreatic tissues, as well as across various stages and molecular subtypes of PDAC. These studies identified specific differentially methylated regions (DMRs) that not only enhance our grasp of the epigenetic drivers of PDAC but also offer potential biomarkers for early diagnosis and prognosis, enabling the customization of therapeutic approaches. The review further explores how DNA methylation profiling could facilitate the development of subtype-tailored therapies, potentially improving treatment outcomes based on precise molecular characterizations. Overall, leveraging DNA methylation alterations as functional biomarkers holds promise for advancing our understanding of disease progression and refining PDAC management strategies, which could lead to improved patient outcomes and a deeper comprehension of the disease’s underlying biological mechanisms.

Charge Transfer Interaction Dynamics between 2-Methyl-8-hydroxyquinoline and 2,4-Dinitrophenol: Synthesis, Spectroscopic Characterization, DNA Binding and DFT Studies

A novel charge transfer (CT) complex was formed by combining the electron-acceptor 2,4-dinitrophenol (DNP) with the electron-donor 2-methyl-8-hydroxyquinoline (MHQ). The complex obtained was further characterized using both experimental and theoretical methods. The Benesi-Hildebrand equation can be utilized to determine various spectroscopic physical measurements such as the molar absorptivity (εCT) and formation constant (KCT). The CT complex has a stoichiometry of 1:1. Multiple spectroscopic methods were employed to investigate the resultant solid compound. The existence of charge and proton transfer in the resultant complex was confirmed by FT-IR, 1H NMR, SEM-EDX and powder-XRD studies. An electron absorption spectroscopy examination was done to analyze the complex DNA binding capability. The resulting complex was determined to have an intercalative binding mechanism, with an intrinsic binding constant (Kb) value of 4.2 × 106 M-1. The experimental results were corroborated by performing theoretical calculations using DFT using a CAM-B3LYP/6-31G(d,p) basis set. The geometrical parameters, electrostatic potential maps (MEPs) and Mullikan charges were computed and examined in agreement with the experimental observations. In addition to electron transmission, the stability of the complex is influenced by the presence of a hydrogen bond.

Ultra-sensitive immobilization-free homogeneous electrochemiluminescence biosensor for thrombin detection via electrostatic interaction and Exo I-powered signal amplification

Herein, we present the development of an ultra-sensitive immobilization-free homogeneous electrochemiluminescence (ECL) biosensor, leveraging the electrostatic repulsion between a negatively charged indium tin oxide (ITO) electrode and DNA and exonuclease I (Exo I)-powered signal amplification, to achieve highly efficient detection of thrombin. Specifically, the aptamer and the complementary DNA engage in the formation of a double-stranded DNA (dsDNA) complex. This negatively charged dsDNA structure subsequently associates with a positively charged ECL indicator, namely ruthenium phenanthroline (Ru(phen)32+), resulting in the generation of the dsDNA-Ru(phen)32+ ECL probe. The negatively charged dsDNA-Ru(phen)32+ experiences electrostatic repulsion from the negatively charged ITO electrode, resulting in a low ECL signal. Nonetheless, upon the addition of thrombin, the aptamer preferentially binds to thrombin, triggering the releases of the embedded Ru(phen)32+ facilitated by Exo I and hence resulting in a robust and enhanced ECL signal. The amplified ECL signal is linearly correlated with the logarithm of thrombin concentration within a detection range spanning from 10 fmol/mL to 50 pmol/mL, with a remarkable detection limit of 3.21 fmol/mL. This strategy eliminates the need for cumbersome labeling steps, avoids the electrode modification process, overcoming the low immobilization efficiency of aptamers and poor signal transduction of indicators labeled at the end of DNA.

Design of Experiments to Tailor the Potential of BSA-Coated Peptide Nanocomplexes for Temozolomide/p53 Gene Co-Delivery

Background: Gene therapy can be viewed as a promising/valuable therapeutic approach directed to cancer treatment, including glioblastoma. Concretely, the combination of gene therapy with chemotherapy could increase its therapeutic index due to a synergistic effect. In this context, bovine serum albumin (BSA)-coated temozolomide (TMZ)-peptide (WRAP5)/p53 gene-based plasmid DNA complexes were developed to promote payload co-delivery. Methods: Design of experiments (DoE) was employed to unravel the BSA-coated TMZ-WRAP5/p53 nanocomplexes with the highest potential by considering the nitrogen to phosphate groups ratio (N/P), and the BSA concentration as inputs and the size, polydispersity index, surface charge and p53-based plasmid complexation capacity (CC) as DoE outputs. Results: The obtained quadratic models were statistically significant (p-value < 0.05) with an adequate coefficient of determination, and the correspondent optimal points were successfully validated. The optimal complex formulation had N/P of 1.03, a BSA concentration of 0.08%, a size of approximately 182 nm, a zeta potential of +9.8 mV, and a pDNA CC of 96.5%. The optimal nanocomplexes are approximately spherical. A cytotoxicity assay showed that these BSA-coated TMZ-WRAP5/p53 complexes did not elicit toxicity in normal brain cells, and a hemolysis study demonstrated the hemocompatibility of the complexes. The complexes were stable in cell culture medium and fetal bovine serum and assured pDNA protection and release. Moreover, the optimal BSA-coated complexes were able of gene transcription and promoted a significant inhibition of glioblastoma cell viability. Conclusions: The reported findings instigate the development of future research to evaluate their potential utility to TMZ/p53 co-delivery. The DoE tool proved to be a powerful approach to explore and tailor the composition of BSA-coated TMZ-WRAP5/p53 complexes, which are expected to contribute to the progress toward a more efficient therapy against cancer and, more specifically, against glioblastoma.

Development of a novel computational technique to create DNA and cell geometrical models for Geant4-DNA

BackgroundThis study aimed to develop a novel human cell geometry for the Geant4-DNA simulation toolkit that explicitly incorporates all 23 chromosome pairs of the human cell. This approach contrasts with the existing, default human cell, geometrical model, which utilizes a continuous Hilbert curve. MethodsA Python-based tool named “complexDNA” was developed to facilitate the design of both simple and complex DNA geometries. This tool was employed to construct a human cell geometry with individual pairs of chromosomes. Subsequently, the performance of this chromosomal model was compared to the standard human cell model provided in the “molecularDNA” Geant4-DNA example. ResultsSimulations using the new chromosomal model revealed minimal discrepancies in DNA damage yield and fragment size distribution compared to the default human cell model. Notably, the chromosomal model demonstrated significant computational efficiency, requiring approximately three times less simulation time to achieve equivalent results. ConclusionsThis work highlights the importance of incorporating chromosomal structure into human cell models for radiation biology research. The “complexDNA” tool offers a valuable resource for creating intricate DNA structures for future studies. Further refinements, such as implementing smaller voxels for euchromatin regions, are proposed to enhance the model’s accuracy.

SETD3-mediated histidine methylation of MCM7 regulates DNA replication by facilitating chromatin loading of MCM.

The minichromosome maintenance complex (MCM) DNA helicase is an important replicative factor during DNA replication. The proper chromatin loading of MCM is a key step to ensure replication initiation during S phase. Because replication initiation is regulated by multiple biological cues, additional changes to MCM may provide better understanding towards this event. Here, we report that histidine methyltransferase SETD3 promotes DNA replication in a manner dependent on enzymatic activity. Nascent-strand sequencing (NS-seq) shows that SETD3 regulates replication initiation, as depletion of SETD3 attenuates early replication origins firing. Biochemical studies reveal that SETD3 binds MCM mainly during S phase, which is required for the CDT1-mediated chromatin loading of MCM. This MCM loading relies on histidine-459 methylation (H459me) on MCM7 which is catalyzed by SETD3. Impairment of H459 methylation attenuates DNA synthesis and chromatin loading of MCM. Furthermore, we show that CDK2 phosphorylates SETD3 at Serine-21 during the G1/S phase, which is required for DNA replication and cell cycle progression. These findings demonstrate a novel mechanism by which SETD3 methylates MCM to regulate replication initiation.

Convolutional network learning of self-consistent electron density via grid-projected atomic fingerprints

The self-consistent field (SCF) generation of the three-dimensional (3D) electron density distribution (ρ) represents a fundamental aspect of density functional theory (DFT) and related first-principles calculations, and how one can shorten or bypass the SCF loop represents a critical question in electronic structure theory from both practical and fundamental standpoints. Herein, a machine learning strategy, DeepSCF, is presented in which the map between the SCF ρ and the initial guess density (ρ0) constructed by the summation of neutral atomic densities is learned using 3D convolutional neural networks (CNNs). High accuracy and transferability of DeepSCF are achieved by first encoding ρ0 on a 3D grid and then expanding the input features to include atomic fingerprints beyond ρ0. The prediction of the residual density (δρ) rather than ρ itself is targeted, and given that δρ is indicative of chemical bonding information, a dataset of small-sized organic molecules featuring diverse bonding characters is adopted. The fidelity of DeepSCF is finally enhanced by subjecting the atomic geometries of the dataset to random rotations and strains. The effectiveness of DeepSCF is demonstrated using a complex carbon nanotube-based DNA sequencer model. This work evidences that the nearsightedness in electronic structure can be optimally represented via the spatial locality in CNNs, offering insight into the success of various machine learning-based atomistic materials simulations.

DNA Catalysis: Design, Function, and Optimization.

Catalytic DNA has gained significant attention in recent decades as a highly efficient and tunable catalyst, thanks to its flexible structures, exceptional specificity, and ease of optimization. Despite being composed of just four monomers, DNA's complex conformational intricacies enable a wide range of nuanced functions, including scaffolding, electrocatalysis, enantioselectivity, and mechano-electro spin coupling. DNA catalysts, ranging from traditional DNAzymes to innovative DNAzyme hybrids, highlight the remarkable potential of DNA in catalysis. Recent advancements in spectroscopic techniques have deepened our mechanistic understanding of catalytic DNA, paving the way for rational structural optimization. This review will summarize the latest studies on the performance and optimization of traditional DNAzymes and provide an in-depth analysis of DNAzyme hybrid catalysts and their unique and promising properties.

ROS‐Activatable Prodrug of Doxazolidine as Novel Cancer Therapy Paradigm

AbstractOvercoming severe side effects from anticancer agents without decreasing their effects on tumor growth is a major challenge. A prodrug technology is reported using agents that are spatiotemporally activated primarily in tumors while the extratumoral toxicity to healthy cells is minimized. A ROS‐activatable prodrug of a strong anticancer agent, doxazolidine (doxaz), is developed. Doxaz is a DNA alkylating agent with a half‐life of 3 min and significantly higher cytotoxicity than the clinically used parental compound doxorubicin (dox). Importantly, doxaz is not affected by p‐glycoprotein expression since it irreversibly alkylates DNA while dox inhibits the topoisomerase II DNA complex. As drug activators, reactive oxygen species (ROS) are already produced inside cancer cells in higher abundance than in normal cells but additionally generated by external stimuli such as radionuclides (via radiolysis of water) and/or ROS‐inducing drugs. We synthesized the prodrug, Doxaz‐BA, and evaluated its efficacy in vitro in cell cultures and then in vivo in xenograft mouse models. Doxaz‐BA is effective in a broad range of cancer cells since most cancer cells produce higher levels of ROS. Combining with clinically relevant radiotracers such as 18F‐FDG or other tumor‐tropic agents / ROS inducing drugs results in a tumor‐specific and enhanced localized therapy paradigm.

The N-terminal activation function AF-1 domain of ERα interacts directly with the C-terminal AF-2-holding ligand-binding domain to recruit the coactivator proteins.

Cryoelectron microscopy (cryo-EM) clarified the quaternary structure of the DNA complex of coactivator-bound estrogen receptor alpha (ERα), revealing the adjacency of the N-terminal domain (NTD) and C-terminal ligand-binding domain (LBD). ERα-NTD and LBD constitute activation function 1 (AF-1) and activation function 2 (AF-2), respectively. These domains are essential for transcription activation. Their spatial proximity was judged to be essential for ERα to recruit the SRC coactivator proteins. In the present study, we first evaluated untethered free ERα-NTD(AF-1) [residues 1-180] and its-truncated desNTD(AF-1)-ERα [residues 181-595] in a luciferase reporter gene assay. ERα-NTD(AF-1) was completely inactive, whereas desNTD(AF-1)-ERα exhibited 66% activity of wild-type ERα. Surprisingly, ERα-NTD(AF-1) was found to inhibit desNTD(AF-1)-ERα markedly. Therefore, assuming that ERα-NTD(AF-1) must also inhibit wild-type full-length ERα, we co-expressed ERα-NTD(AF-1) and full-length ERα. As expected, ERα-NTD(AF-1) inhibited ERα in a dose-dependent manner, but non-competitively for 17β-estradiol. When their intracellular transport was examined immunocytochemically, ERα-NTD(AF-1) showed a distinct translocation from the cytoplasm to the nucleus, despite being expressed solely in the cytoplasm without full-length ERα. This nuclear translocation was attributable to a direct interaction between ERα-NTD(AF-1) and full-length ERα consisting of the nuclear localization signal. The present results demonstrated that, in full-length ERα, the N-terminally tethered NTD(AF-1) domain collaborates with the C-terminal LBD(AF-2) for coactivator recruitment.

Integrating Single-Walled Carbon Nanotubes into Supramolecular Assemblies: From Basic Interactions to Emerging Applications.

Integrating single-walled carbon nanotubes (SWCNTs) into supramolecular self-assemblies harnesses the distinctive mechanical, optical, and electronic properties of the nanoparticles alongside the structural and chemical properties of the assemblies. Organic molecules capable of forming supramolecular assemblies through hydrophobic, van der Waals, and π-π interactions have been demonstrated to be particularly effective in dispersing and functionalizing SWCNTs, as these same interactions facilitate the binding to the hydrophobic graphene-like surface of the SWCNTs. This review discusses a variety of self-assembling structures that were shown to integrate SWCNTs, ranging from simple micelles and ring structures to complex DNA origami and three-dimensional hydrogels formed by low-molecular-weight gelators. We explore the integration of SWCNTs into various supramolecular assemblies and highlight emerging applications of these composite materials, such as the mechanical enforcement of self-assembling hydrogels and leveraging the near-infrared (NIR) fluorescence properties of SWCNTs for monitoring the molecular self-assembly process. Notably, the distinctive NIR fluorescence of SWCNTs, which overlaps with the biological transparency window, offers significant opportunities for noninvasive sensing applications within the supramolecular platforms. Future research into a deeper understanding of the interactions between SWCNTs and different supramolecular frameworks will expand the potential applications of SWCNT-integrated supramolecular assemblies in fields like biomedical engineering, electronic devices, and environmental sensing.

Ultrasensitive Amplification-Free Quantification of a Methyl CpG-Rich Cancer Biomarker by Single-Molecule Kinetic Fingerprinting.

The most well-studied epigenetic marker in humans is the 5-methyl modification of cytosine in DNA, which has great potential as a disease biomarker. Currently, quantification of DNA methylation relies heavily on bisulfite conversion followed by PCR amplification and NGS or microarray analysis. PCR is subject to potential bias in differential amplification of bisulfite-converted methylated versus unmethylated sequences. Here, we combine bisulfite conversion with single-molecule kinetic fingerprinting to develop an amplification-free assay for DNA methylation at the branched-chain amino acid transaminase 1 (BCAT1) promoter. Our assay selectively responds to methylated sequences with a limit of detection below 1 fM and a specificity of 99.9999%. Evaluating complex genomic DNA matrices, we reliably distinguish <5% DNA methylation at the BCAT1 promoter in whole blood DNA from completely unmethylated whole-genome amplified DNA. Taken together, these results demonstrate the feasibility and sensitivity of our amplification-free, single-molecule quantification approach to improve the early detection of methylated cancer DNA biomarkers.

Charging of DNA Complexes in Positive-Mode Native Electrospray Ionization Mass Spectrometry.

Native mass spectrometry (nMS) provides insights into the structures and dynamics of biomacromolecules in their native-like states by preserving noncovalent interactions through "soft" electrospray ionization (ESI). For native proteins, the number of charges that are acquired scales with the surface area and mass. Here, we explore the effect of highly negatively charged DNA on the ESI charge of protein complexes and find a reduction of the mass-to-charge ratio as well as a greater variation. The charge state distributions of pure DNA assemblies show a lower mass-to-charge ratio than proteins due to their greater density in the gas phase, whereas the charge of protein-DNA complexes can additionally be influenced by the distribution of the ESI charges, ion pairing events, and collapse of the DNA components. Our findings suggest that structural features of protein-DNA complexes can result in lower charge states than expected for proteins.

Development of a forensic DNA research grade test material.

Advancements in forensic DNA typing technology and methods have increased sensitivity and, while beneficial, carry the weight of more challenging profile interpretation. In response, the forensic DNA community has often requested more complex reference materials to address commonly encountered measurement and interpretation issues such as complex DNA mixtures, DNA degradation, and PCR inhibition. The National Institute of Standards and Technology (NIST) released Research Grade Test Material 10235: Forensic DNA Typing Resource Samples to support the forensic DNA community. Components include three single source samples, two degraded samples, and three mixture samples. As part of the Research Grade Test Material (RGTM) process, automated methods for bottling, alternative sample tube types, and the addition of carrier RNA for stabilizing low-quantity samples were investigated. Both internal and external testing demonstrate the stability of the material over time at 4°C through qPCR testing. In the development of a data portal, users have been allowed to anonymously upload results and compare their data with NIST and others. This report describes the preparation and stability of this material.

Repeat-mediated recombination results in Complex DNA structure of the mitochondrial genome of Trachelospermum jasminoides

BackgroundTrachelospermum jasminoides has medicinal and ornamental value and is widely distributed in China. Although the chloroplast genome has been documented, the mitochondrial genome has not yet been studied.ResultsThe mitochondrial genome of T. jasminoides was assembled and functionally annotated using Illumina and nanopore reads. The mitochondrial genome comprises a master circular molecular structure of 605,764 bp and encodes 65 genes: 39 protein-coding genes, 23 transfer RNA (tRNA) genes and 3 ribosomal RNA genes. In addition to the single circular conformation, we found many alternative conformations of the T. jasminoides mitochondrial genome mediated by 42 repetitive sequences. Six repetitive sequences (DRS01–DRS06) were supported by nanopore long reads, polymerase chain reaction (PCR) amplifications, and Sanger sequencing of the PCR products. Eleven homologous fragments were identified by comparing the mitochondrial and chloroplast genome sequences, including three complete tRNA genes. Moreover, 531 edited RNA sites were identified in the protein-coding sequences based on RNA sequencing data, with nad4 having the highest number of sites (54).ConclusionTo our knowledge, this is the first description of the mitochondrial genome of T. jasminoides. Our results demonstrate the existence of multiple conformations. These findings lay a foundation for understanding the genetics and evolutionary dynamics of Apocynaceae.

Chemically engineered polyethylenimine conjugates for mannose receptor-mediated gene delivery with potential antimicrobial and anticancer activity

Polyethylenimines exhibit unique intrinsic properties, which make them potential gene delivery agents. However, nonspecific interactions and cytotoxicity in the cells/tissues have significantly hampered their use in clinical applications. To subside these concerns, plant-based cyclitols, shikimic and quinic acids, have been tethered to polyethylenimine (PEI) to fabricate shikimoyl-PEI (SP) and quinoyl-PEI (QP) conjugates under mild coupling conditions. On interactions with plasmid DNA, the size and zeta potential of SP and QP complexes were found in the range of ∼245–158 nm and ∼ +22–10 mV, respectively. Subsequent assessment of these complexes revealed that cytocompatibility (∼90%–94%) and transfection efficiency (∼90% cells transfected) were significantly higher as compared to the native PEI/pDNA and Lipofectamine/pDNA complexes. Further, a higher degree of pDNA release was also obtained from SP/DNA and QP/DNA complexes. A decrease in GFP expression was observed in a competitive assay on RAW 264.7 cells, which reflected receptor-mediated internalization of SP and QP/DNA complexes. Besides, both SP and QP conjugates also displayed efficient antimicrobial activity against differential pathogenic strains of bacteria. Of these conjugates, QP conjugates exhibited promising anticancer activity against variable cell lines such as RAW 264.7, MCF-7, HepG2 cells. Altogether, these results advocate the promising potential of SP and QP conjugates as efficient gene delivery agents having effective antimicrobial and anticancer competence.

Subtraction-based DNA Origami Cryptography by using Structural Defects for Information Encryption.

Conventional cryptographic methods rely on increased computational complexity to counteract the threat posed by growing computing power for sustainable protection. DNA cryptography circumvents this threat by leveraging complex DNA recognition to maintain information security. Specifically, DNA origami has been repurposed for cryptography, using programmable folding of the long scaffold strand carrying additional tagged strands for information encryption. Herein, a subtraction-based cryptographic strategy is presented that uses structural defects on DNA origami to contain encrypted information. Designated staple strands are removed from the staple pool with "hook" strands to create active defect sites on DNA origami for information encryption. These defects can be filled by incubating the structures with the intact pool of biotinylated staple strands, resulting in biotin patterns that can be used for protein-binding steganography. The yields of individual protein pixels reached over 91%, and self-correction codes are implemented to aid the information recovery. Furthermore, the encrypted organization of defective DNA origami structures is investigated to explore the potential of this method for scalable information storage. This method uses DNA origami to encrypt information in hidden structural features, utilizing subtraction for robust cryptography while ensuring the safety and recovery of data.