DNA synthesis technologies to close the gene writing gap

DNA storage: The future direction for medical cold data storage

DNA storage, characterized by its durability, data density, and cost-effectiveness, is a promising solution for managing the increasing data volumes in healthcare. This review explores state-of-the-art DNA storage technologies, and provides insights into designing a DNA storage system tailored for medical cold data. We anticipate that a practical approach for medical cold data storage will involve establishing regional, in vitro DNA storage centers that can serve multiple hospitals. The immediacy of DNA storage for medical data hinges on the development of novel, high-density, specialized coding methods. Established commercial techniques, such as DNA chemical synthesis and next-generation sequencing (NGS), along with mixed drying with alkaline salts and refined Polymerase Chain Reaction (PCR), potentially represent the optimal options for data writing, reading, storage, and accessing, respectively. Data security could be promised by the integration of traditional digital encryption and DNA steganography. Although breakthrough developments like artificial nucleotides and DNA nanostructures show potential, they remain in the laboratory research phase. In conclusion, DNA storage is a viable preservation strategy for medical cold data in the near future.

Design and structure of overlapping regions in PCA via deep learning

Polymerase cycling assembly (PCA) stands out as the predominant method in the synthesis of kilobase-length DNA fragments. The design of overlapping regions is the core factor affecting the success rate of synthesis. However, there still exists DNA sequences that are challenging to design and construct in the genome synthesis. Here we proposed a deep learning model based on extensive synthesis data to discern latent sequence representations in overlapping regions with an AUPR of 0.805. Utilizing the model, we developed the SmartCut algorithm aimed at designing oligonucleotides and enhancing the success rate of PCA experiments. This algorithm was successfully applied to sequences with diverse synthesis constraints, 80.4 % of which were synthesized in a single round. We further discovered structure differences represented by major groove width, stagger, slide, and centroid distance between overlapping and non-overlapping regions, which elucidated the model's reasonableness through the lens of physical chemistry. This comprehensive approach facilitates streamlined and efficient investigations into the genome synthesis.

Enzymatic de novo oligonucleotide synthesis: Emerging techniques and advancements

Oligonucleotide synthesis serves as a cornerstone of modern life sciences, enabling groundbreaking advancements across molecular diagnostics, therapeutic development, and transformative technologies including DNA data storage and programmable biological systems. While phosphoramidite-based chemical synthesis remains the industrial standard, its limitations in producing long-sequence constructs, cumulative error rates, and reliance on toxic solvents pose significant challenges for next-generation applications. Emerging enzymatic synthesis approaches offer a paradigm shift by harnessing the inherent precision and environmental sustainability of biological systems. This comprehensive review systematically examines the evolving landscape of oligonucleotide synthesis technologies. We first analyze the mechanistic foundations and persistent limitations of conventional chemical methods, followed by a critical evaluation of enzymatic strategies with particular emphasis on terminal deoxynucleotidyl transferase (TdT)-mediated template-independent polymerization. The work provides detailed insights into enzymatic reaction engineering, including substrate specificity profiling of nucleotide analogs and innovative solid-phase synthesis platforms enabling iterative nucleotide addition. Furthermore, we discuss emerging high-throughput synthesis architectures and commercial translation efforts. In summary, this review comprehensively encapsulates the advancements and commercialization status of enzymatic synthesis technologies, offering valuable guidance that can expedite the innovative development of enzymatic oligonucleotide manufacturing platforms.

Recent Advances in Biocatalytic and Chemoenzymatic Synthesis of Oligonucleotides

Access to synthetic oligonucleotides is crucial for applications in diagnostics, therapeutics, synthetic biology, and nanotechnology. Traditional solid phase synthesis is limited by sequence length and complexities, low yields, high costs and poor sustainability. Similarly, polymerase-based approaches such as in vitro transcription and primer extension reactions do not permit any control on the positioning of modifications and display poor substrate tolerance. In response, biocatalytic and chemoenzymatic strategies have emerged as promising alternatives, offering selective and efficient pathways for oligonucleotide synthesis. These methods leverage the precision and efficiency of enzymes to construct oligonucleotides with high fidelity. Recent advancements have focused on optimized systems and/or engineered enzymes enabling the incorporation of chemically modified nucleotides. Biocatalytic approaches, particularly those using DNA/RNA polymerases provide advantages in milder reaction conditions and enhanced sustainability. Chemoenzymatic methods, combining chemical synthesis and enzymes, have proven to be effective in overcoming limitations of traditional solid phase synthesis. This review summarizes recent developments in biocatalytic and chemoenzymatic strategies to construct oligonucleotides, highlighting innovations in enzyme engineering, substrate and reaction condition optimization for various applications. We address crucial details of the methods, their advantages, and limitations as well as important insights for future research directions in oligonucleotide production.

DNA as a promising biomaterial for bone regeneration and potential mechanisms of action

DNA nanotechnology has created new possibilities for the use of DNA in tissue regeneration - an important advance for DNA use beyond its paradigmatic role as the hereditary biomacromolecule. Biomaterials containing synthetic or natural DNA have been proposed for several applications including drug and gene delivery, and more recently, as osteoconductive biomaterials. This review provides an in-depth discussion of studies that have used DNA-based materials for biomineralization and/or bone repair, with expansion on the topic of DNA hydrogels specifically, and the advantages they offer for advancing the field of bone regeneration. Four mechanisms of action for the osteoconductive capabilities of DNA-based materials are discussed, and a proposed model for degradation of these materials and its link to their osteoconductive properties is later presented. Finally, the review considers current limitations of DNA-based materials and summarizes important aspects that need to be addressed for future application of DNA nanotechnology in tissue repair. STATEMENT OF SIGNIFICANCE: Herein we summarize the developing field of DNA-based materials for biomineralization and bone repair, with a focus on DNA hydrogels. We first provide a comprehensive review of different forms of DNA-based materials described thus far which have been shown to enhance bone repair and mineralization (namely DNA coatings, DNA-containing pastes, DNA nanostructures and DNA hydrogels). Next, we describe four different mechanisms by which DNA-based materials could be exerting their osteogenic effect. Then, we propose a novel model that links DNA degradation and osteoconductivity. Lastly, we suggest possible research directions to enhance DNA-based materials for future clinical application. The suggested mechanisms and the proposed model can guide future research to better understand how DNA functions as a mineral- and bone-promoting molecule.

Kinetics and dynamics of oligonucleotide hybridization

The hybridization of short nucleic acid strands is a remarkable spontaneous process that is foundational to biotechnology and nanotechnology and plays a crucial role in gene expression, editing and DNA repair. Decades of research into the mechanism of hybridization have resulted in a deep understanding of its thermodynamics, but many questions remain regarding its kinetics and dynamics. Recent advances in experiments and molecular dynamics simulations of nucleic acids are enabling more direct insight into the structural dynamics of hybridization, which can test long-standing assumptions regarding its mechanism. In this Review, we summarize the current state of knowledge of hybridization kinetics, discuss the barriers to a molecular description of hybridization dynamics, and highlight the new approaches that have begun uncovering the dynamics of hybridization and the duplex ensemble. The kinetics and dynamics of hybridization are highly sensitive to the composition of nucleic acids, and we emphasize recent discoveries and open questions on the role of nucleobase sequence and chemical modifications.

The design and engineering of synthetic genomes

Synthetic genomics seeks to design and construct entire genomes to mechanistically dissect fundamental questions of genome function and to engineer organisms for diverse applications, including bioproduction of high-value chemicals and biologics, advanced cell therapies, and stress-tolerant crops. Recent progress has been fuelled by advancements in DNA synthesis, assembly, delivery and editing. Computational innovations, such as the use of artificial intelligence to provide prediction of function, also provide increasing capabilities to guide synthetic genome design and construction. However, translating synthetic genome-scale projects from idea to implementation remains highly complex. Here, we aim to streamline this implementation process by comprehensively reviewing the strategies for design, construction, delivery, debugging and tailoring of synthetic genomes as well as their potential applications.

High-performance protocol for ultra-short DNA sequencing using Oxford Nanopore Technology (ONT)

In recent years, Oxford Nanopore Technologies (ONT) has gained substantial attention across various domains of nucleic acid research, owing to its unique advantages over other sequencing platforms. Originally developed for long-read sequencing, ONT technology has evolved, with recent advancements enhancing its applicability beyond long reads to include short, synthetic DNA-based applications. However, sequencing short DNA fragments with nanopore technology often results in lower data quality, likely due to the absence of protocols optimised for these fragment sizes. To address this challenge, we refined the standard ONT library preparation protocol to improve its performance for ultra-short DNA targets. By utilising the same core reagents required for conventional ONT workflows, we introduced targeted alterations to enhance compatibility with shorter fragment lengths. We then benchmarked these adjustments against libraries prepared using the standard ONT protocol. Here, we present a comprehensive, step-by-step protocol that is accessible to researchers of various technical expertise, facilitating high-quality sequencing of ultra-short DNA fragments. This protocol represents a significant improvement in sequencing quality for short DNA sequences using ONT technology, broadening the range of possible applications.

ReLume: Enhancing DNA storage data reconstruction with flow network and graph partitioning

DNA storage is an ideal alternative to silicon-based storage, but focusing on data writing alone cannot address the inevitable errors and durability issues. Therefore, we propose ReLume, a DNA storage data reconstruction method based on flow networks and graph partitioning technology, which can accomplish the data reconstruction task of millions of reads on a laptop with 24 GB RAM. The results show that ReLume copes well with many types of errors, more than doubles sequence recovery rates, and reduces memory usage by about 60 %. ReLume is 10 times more durable than other representative methods, meaning that data can be read without loss after 100 years. Results from the wet lab DNA storage dataset show that ReLume's sequence recovery rates of 73 % and 93.2 %, respectively, significantly outperform existing methods. In summary, ReLume effectively overcomes the accuracy and hardware limitations and provides a feasible idea for the portability of DNA storage.

Engineered Living Memory Microspheroid-Based Archival File System for Random Accessible In Vivo DNA Storage

Given its exceptional durability and high information density, deoxyribonucleic acid (DNA) has the potential to meet the escalating global demand for data storage if it can be stored efficiently and accessed randomly in exabyte-to-yottabyte-scale databases. Here, this work introduces the Engineered Living Memory Microspheroid (ELMM) as a novel material for DNA data storage, retrieval, and management. This work engineers a plasmid library and devises a random access strategy pairing plasmid function with DNA data in a key-value format. Each DNA segment is integrated with its corresponding plasmid, introduced into bacteria, and encapsulated within matrix material via droplet microfluidics within 5 min. ELMMs can be stored at room temperature following lyophilization and, upon rehydration, each type of ELMM exhibits specific functions expressed by the plasmids, allowing for physical differentiation based on these characteristics. This work demonstrates fluorescent expression as the plasmid function and employs fluorescence-based sorting access image files in a prototype database. By utilizing N optical channels, to retrieve 2N file types, each with a minimum of 10 copies. ELMM offers a digital-to-biological information solution, ensuring the preservation, access, replication, and management of files within large-scale DNA databases.

dsDAP: An efficient method for high-abundance DNA-encoded library construction in mammalian cells

DNA-encoded libraries are invaluable tools for high-throughput screening and functional genomics studies. However, constructing high-abundance libraries in mammalian cells remains challenging. Here, we present dsDNA-assembly-PCR (dsDAP), a novel Gibson-assembly-PCR strategy for creating DNA-encoded libraries, offering improved flexibility and efficiency over previous methods. We demonstrated this approach by investigating the impact of translation initiation sequences (TIS) on protein expression in HEK293T cells. Both CRISPR-Cas9 and piggyBac systems were employed for genomic integration, allowing comparison of different integration methods. Our results confirmed the importance of specific nucleotides in the TIS region, particularly the preference for adenine at the -3 position in high-expression sequences. We also explored the effects of library dilution on genotype-phenotype correlations. This Gibson-assembly-PCR strategy overcomes limitations of existing methods, such as restriction enzyme dependencies, and provides a versatile tool for constructing high-abundance libraries in mammalian cells. Our approach has broad applications in functional genomics, drug discovery, and the study of gene regulation.

Towards next-generation DNA encryption via an expanded genetic system

Information encryption based on DNA data archiving, referred to as DNA encryption, has been advocated for decades and has become highly appealing owing to its remarkable advantages, e.g. high storage capacity, complexity and programmability. Early DNA encryption schemes primarily leveraged the natural four-letter genetic alphabet for data storage, with message-storing DNA sequences easily decrypted by routine DNA sequencing, which is consequently vulnerable to attack and faces severe security challenges. Here, an unnatural base pair (UBP), dNaM-dTPT3, was introduced into the message and/or index DNA sequences, which can be stored either in vitro or in vivo; this approach achieved the bioorthogonal encryption of 'secret' messages, where message DNAs could be selectively, faithfully and readily retrieved or read exclusively in the presence of unnatural bases. Furthermore, a separative computational algorithm, named IM-Codec, was developed to encrypt the data into a 'key sequence' and an 'information sequence' through UBP insertion. Finally, a UBP-based multilevel DNA encryption approach was developed and validated for data encryption and decryption. The employment of the UBP expanded genetic system for data encryption should provide valuable solutions for archiving highly confidential data and thus usher in a new era of DNA encryption.

Natural, modified and conjugated carbohydrates in nucleic acids

Storage of genetic information in DNA occurs through a unique ordering of canonical base pairs. However, this would not be possible in the absence of the sugar-phosphate backbone which is essential for duplex formation. While over a hundred nucleobase modifications have been identified (mainly in RNA), Nature is rather conservative when it comes to alterations at the level of the (deoxy)ribose sugar moiety. This trend is not reflected in synthetic analogues of nucleic acids where modifications of the sugar entity is commonplace to improve the properties of DNA and RNA. In this review article, we describe the main incentives behind sugar modifications in nucleic acids and we highlight recent progress in this field with a particular emphasis on therapeutic applications, the development of xeno-nucleic acids (XNAs), and on interrogating nucleic acid etiology. We also describe recent strategies to conjugate carbohydrates and oligosaccharides to oligonucleotides since this represents a particularly powerful strategy to improve the therapeutic index of oligonucleotide drugs. The advent of glycoRNAs combined with progress in nucleic acid and carbohydrate chemistry, protein engineering, and delivery methods will undoubtedly yield more potent sugar-modified nucleic acids for therapeutic, biotechnological, and synthetic biology applications.

Principles and Design of Molecular Tools for Sensing and Perturbing Cell Surface Receptor Activity

Cell-surface receptors are vital for controlling numerous cellular processes with their dysregulation being linked to disease states. Therefore, it is necessary to develop tools to study receptors and the signaling pathways they control. This Review broadly describes molecular approaches that enable 1) the visualization of receptors to determine their localization and distribution; 2) sensing receptor activation with permanent readouts as well as readouts in real time; and 3) perturbing receptor activity and mimicking receptor-controlled processes to learn more about these processes. Together, these tools have provided valuable insight into fundamental receptor biology and helped to characterize therapeutics that target receptors.

Customized Controllable Pyrophosphate Nanosensor Based on Lanthanide Metal-Organic Frameworks for Accurate and Sensitive Detection of Nucleic Acids

Pyrophosphate (PPi) and nucleic acid amplification play a critical role in medical diagnostics, making the development of precise nanosensors essential. Lanthanide metal-organic frameworks (Ln-MOFs) are increasingly recognized for their potential in advanced luminescent biosensing applications. However, research on customized controllable responses in Ln-MOF nanosensors is still lacking, which is critical for the molecular-level modular design. In this work, we introduce a ligand engineering strategy to regulate coordination-induced antenna effect emission in Ln-MOFs, optimizing their pyrophosphate (PPi) sensing from fluorescence turn-off to turn-on modes. By tuning the coordination environment through ligand programming, we discovered a "near coordination compensation" effect, allowing for controllable transitions between aggregation-induced emission and quenching (AIE/AIQ). This reversible response was supported by density functional theory calculations. Using a Eu3+/Tb3+ dual-emission Ln-MOF designed with 2,6-pyridinedicarboxylic acid as the optimized ligand, we developed a self-correcting PPi nanosensor with a detection limit of 0.2 μM. Moreover, this system enabled ultrasensitive nucleic acid detection, achieving a limit of detection (LOD) as low as 1 fM, with applications in DNA pyrosequencing, qPCR, and DNA epigenetic modification (5-formylcytosine) analysis. These findings shed light on the structural and photophysical factors controlling Ln-MOF luminescence, offering a promising platform for highly accurate and sensitive nucleic acid detection in biomedical diagnostics.

Super-resolving chromatin in its own terms: Recent approaches to portray genomic organization

Chromatin organizes in a highly hierarchical manner that affects gene regulation. While many discoveries in the field have been driven by genomic techniques, super-resolution microscopy has proved to be an essential method to fully understand folding in single cells. In this article we summarize the main strategies to probe chromatin architecture using single-molecule localization microscopy and some of the key findings this has enabled. We specifically focus on the recent developments in techniques using oligonucleotide libraries and how their versatility drives multiplexing. These multiplexed libraries allow to super-resolve architectural proteins, DNA folding and transcription. We compare the latest results in this field and reflect about the future of these methods.

A Robust and Efficient Representation-based DNA Storage Architecture by Deep Learning

As one main form of multimedia data, images play a critical role in various applications. In this paper, a representation-based architecture is proposed which takes advantage of the outstanding representation and image-generation abilities of deep learning (DL). This architecture includes two DL models: an autoencoder and a U-Net network which achieve the representation, construction, and refinement of images from the noisy reads in DNA storage. Simulation experiments demonstrate that it can reconstruct images of moderate quality in scenarios where insertion-deletion-substitution (IDS) errors are less than 6%. Combined with the feature quantization, it also offers a flexible way to achieve a balanced trade-off between compression ratio and image quality by selecting an approximate representation channel number. Additionally, the quality of images can be boosted by using multiple reads which are a common situation in DNA storage. A wet lab practice that successfully reconstructs an image stored in 14 plasmids further proves the feasibility of the proposed architecture. Instead of storing the original image information, the representation-based architecture provides a competitive solution which achieves robust and efficient DNA storage for large-scale image applications.

Antitumor Efficacy of Interleukin 12-Transfected Mesenchymal Stem Cells in B16-F10 Mouse Melanoma Tumor Model

Background/Objectives: Mesenchymal stromal cells (MSCs) hold the potential for tumor-targeted gene delivery due to their ex vivo manipulability, low immunogenicity, scalability, and inherent tumor-homing properties. Despite the widespread use of viral vectors for MSC genetic modification, safety concerns have prompted interest in non-viral alternatives, such as gene electrotransfer (GET). This study aimed to optimize GET parameters for MSCs transfection, assess MSCs biodistribution after in vivo administration, and evaluate the therapeutic potential of interleukin-12 (IL-12)-modified MSCs in a mouse melanoma model. Methods: Human MSCs were isolated from umbilical cords under ethically approved protocols. GET protocols were optimized using a fluorescent reporter gene to evaluate transfection efficiency and cell viability. MSC biodistribution was examined following intravenous and intratumoral injections in murine tumor models using luminescent reporter gene. The therapeutic efficacy of IL-12-modified MSCs was assessed in a syngeneic mouse melanoma model. Results: Optimized GET protocols achieved a transfection efficiency of 80% and a cell viability of 90%. Biodistribution studies demonstrated effective tumor retention of MSCs following intratumoral injections, whereas intravenous administration resulted in predominant cell localization in the lungs. IL-12-modified MSCs injected intratumorally significantly inhibited tumor growth, delaying tumor progression by five days compared to controls. Conclusions: Optimized GET conditions enabled high-efficiency, high-viability MSCs transfection, facilitating their use as effective vehicles for localized cytokine delivery. While the innate tumor tropism of MSCs was not conclusively demonstrated, the study highlights the potential of GET as a reliable non-viral gene delivery platform and underscores the therapeutic promise of IL-12-modified MSCs in tumor-targeted gene therapy.

Oligonucleotide subsets selection by single nucleotide resolution barcode identification

Effective subset selection from complex oligonucleotide libraries is crucial for genomics, synthetic biology, and DNA data storage. The polymerase chain reaction, foundational for amplifying target subsets is limited by primer design and length for specificity, which constrains the scalability of oligo libraries and increases the synthesis burden for primers. We introduce an oligo subset selection methodology that utilizes sequence-specific cyclic nucleotide synthesis and blocking of the template oligos. This approach eliminates the need for primers for selective hybridization and enables the encoding and selection of hundreds of subsets with barcode lengths of fewer than five nucleotides. Moreover, cyclic selection enables a hierarchical data structure in the oligo library, enhancing the programmability. This advancement offers a scalable and cost-effective solution for handling complex oligo libraries.

High-throughput discovery of inhibitory protein fragments with AlphaFold

Peptides can bind to specific sites on larger proteins and thereby function as inhibitors and regulatory elements. Peptide fragments of larger proteins are particularly attractive for achieving these functions due to their inherent potential to form native-like binding interactions. Recently developed experimental approaches allow for high-throughput measurement of protein fragment inhibitory activity in living cells. However, it has thus far not been possible to predict de novo which of the many possible protein fragments bind to protein targets, let alone act as inhibitors. We have developed a computational method, FragFold, that employs AlphaFold to predict protein fragment binding to full-length proteins in a high-throughput manner. Applying FragFold to thousands of fragments tiling across diverse proteins revealed peaks of predicted binding along each protein sequence. Comparisons with experimental measurements establish that our approach is a sensitive predictor of fragment function: Evaluating inhibitory fragments from known protein-protein interaction interfaces, we find 87% are predicted by FragFold to bind in a native-like mode. Across full protein sequences, 68% of FragFold-predicted binding peaks match experimentally measured inhibitory peaks. Deep mutational scanning experiments support the predicted binding modes and uncover superior inhibitory peptides in high throughput. Further, FragFold is able to predict previously unknown protein binding modes, explaining prior genetic and biochemical data. The success rate of FragFold demonstrates that this computational approach should be broadly applicable for discovering inhibitory protein fragments across proteomes.

Data Readout Techniques for DNA-Based Information Storage

DNA is a natural chemical substrate that carries genetic information, which also serves as a powerful toolkit for storing digital data. Compared to traditional storage media, DNA molecules offer higher storage density, longer lifespan, and lower maintenance energy consumption. In DNA storage process, data readout is a critical step that bridges the gap between DNA molecular/structures with stored digital information. With the continued development of strategies in DNA data storage technology, the readout techniques have evolved. However, there is a lack of systematic introduction and discussion on the readout techniques for reported DNA data storage systems, especially the correlation between the design of the data storage system and the corresponding selection of readout techniques. This review first introduces two main categories of DNA data storage units (i.e., sequence and structure) and their corresponding readout techniques (i.e., sequencing and nonsequencing methods), and then reviewed representative examples of notable advancements in DNA data storage technology, focusing on data storage unit design, and readout technique selection. It also introduces emerging approaches to assist data readout techniques, such as implementation of microfluidic and fluorescent probes. Finally, the paper discusses the limitations, challenges, and potential of DNA data readout approaches.

RH2Fusion: A universal tool for precise DNA fragment assembly

Despite its limitations, restriction enzyme (RE)-mediated cleavage remains the prevalent method for generating sticky ends in DNA assembly. Here, we present RNase HII Fusion (RH2Fusion), a robust system for user-defined sticky ends, enabling scarless assembly of multiple DNA fragments alongside simultaneous site-directed mutagenesis (SDM) at multiple sites. In bacterial cells, DNA fragments with ribonucleotide modifications are expected to form complementary 3' overhangs after RNase HII treatment, followed by annealing and recombination via the bacterial self-repair system. In vitro, RNase HII-mediated cleavage produces similar overhangs, which are subsequently processed and ligated by YgdG and T4 DNA ligase, enabling efficient DNA assembly. We report for the first time that Escherichia coli Exonuclease IX (YgdG) possesses ribonuclease-specific cleavage activity, selectively cleaving ribonucleotides without cleaving deoxyribonucleotides. Through the fusion of RNase HII and YgdG, novel constructs RNase RY (RNase HII-YgdG) and RNase YR (YgdG-RNase HII) are generated, each showcasing dual enzyme functionality. In conclusion, RH2Fusion offers a rapid, effective, and versatile alternative for DNA assembly, empowering researchers across diverse fields like synthetic biology and genetic engineering. This transformative tool is poised to significantly enhance the capabilities of DNA manipulation and advance molecular biology research.

Long oligos: direct chemical synthesis of genes with up to 1728 nucleotides

The longest oligos that can be chemically synthesized are considered to be 200-mers. Here, we report direct synthesis of an 800-mer green fluorescent protein gene and a 1728-mer Φ29 DNA polymerase gene on an automated synthesizer. Key innovations that enabled this breakthrough include conducting the synthesis on a smooth surface rather than within the pores of traditional supports, and the use of the powerful catching-by-polymerization (CBP) method for isolating the full-length oligos from a complex mixture. Conducting synthesis on a smooth surface not only eliminated the steric hindrance that would otherwise prevent long oligo assembly, but also, surprisingly, drastically reduced synthesis errors. Compared with the benchmark PCR assembly gene synthesis method, the direct long oligo synthesis method has the advantages of higher probability to succeed, fewer sequence restrictions, and being able to synthesize long oligos containing difficult elements such as unusually stable higher-order structures, long repeats, and site-specific modifications. The method is expected to open doors for various projects in areas such as synthetic biology, gene editing, and protein engineering.

Nucleic acid joining enzymes: biological functions and synthetic applications beyond DNA

DNA-joining by ligase and polymerase enzymes has provided the foundational tools for generating recombinant DNA and enabled the assembly of gene and genome-sized synthetic products. Xenobiotic nucleic acid (XNA) analogues of DNA and RNA with alternatives to the canonical bases, so-called 'unnatural' nucleobase pairs (UBP-XNAs), represent the next frontier of nucleic acid technologies, with applications as novel therapeutics and in engineering semi-synthetic biological organisms. To realise the full potential of UBP-XNAs, researchers require a suite of compatible enzymes for processing nucleic acids on a par with those already available for manipulating canonical DNA. In particular, enzymes able to join UBP-XNA will be essential for generating large assemblies and also hold promise in the synthesis of single-stranded oligonucleotides. Here, we review recent and emerging advances in the DNA-joining enzymes, DNA polymerases and DNA ligases, and describe their applications to UBP-XNA manipulation. We also discuss the future directions of this field which we consider will involve two-pronged approaches of enzyme biodiscovery for natural UBP-XNA compatible enzymes, coupled with improvement by structure-guided engineering.

Sequence-Defined DNA Polymers: New Tools for DNA Nanotechnology and Nucleic Acid Therapy

Structural DNA nanotechnology offers a unique self-assembly toolbox to construct soft materials of arbitrary complexity, through bottom-up approaches including DNA origami, brick, wireframe, and tile-based assemblies. This toolbox can be expanded by incorporating interactions orthogonal to DNA base-pairing such as metal coordination, small molecule hydrogen bonding, π-stacking, fluorophilic interactions, or the hydrophobic effect. These interactions allow for hierarchical and long-range organization in DNA supramolecular assemblies through a DNA-minimal approach: the use of fewer unique DNA sequences to make complex structures. Here we describe our research group's work to integrate these orthogonal interactions into DNA and its supramolecular assemblies. Using automated solid phase techniques, we synthesized sequence-defined DNA polymers (SDPs) featuring a wide range of functional groups, achieving high yields in the process. These SDPs can assemble into not only isotropic spherical morphologies─such as spherical nucleic acids (SNAs)─but also into anisotropic nanostructures such as 1D nanofibers and 2D nanosheets. Our structural and molecular modeling studies revealed new insights into intermolecular chain packing and intramolecular chain folding, influenced by phosphodiester positioning and SDP sequence. Using these new self-assembly paradigms, we created hierarchical, anisotropic assemblies and developed systems exhibiting polymorphism and chiroptical behavior dependent on the SDP sequence. We could also precisely control the size of our nanofiber assemblies via nucleation-growth supramolecular polymerization and create compartmentalized nanostructures capable of precise surface functionalization.The exquisite control over sequence, composition, and length allowed us to combine our SDPs with nanostructures including DNA wireframe assemblies such as prisms, nanotubes, and cubes to create hybrid, stimuli-responsive assemblies exhibiting emergent structural and functional modes. The spatial control of our assemblies enabled their use as nanoreactors for chemical transformations in several ways: via hybridization chain reaction within SNA coronas, through chemical conjugation within SNA cores, and through a molecular "printing" approach within wireframe assemblies for nanoscale information transfer and the creation of anisotropic "DNA-printed" polymer particles.We have also employed our SDP nanostructures toward biological and therapeutic applications. We demonstrated that our SNAs could serve as both extrinsic and intrinsic therapeutic platforms, with improved cellular internalization and biodistribution profiles, and excellent gene silencing activities. Using SDPs incorporating hydrophobic dendrons, high-affinity and highly specific oligonucleotide binding to human serum albumin was demonstrated. These structures showed an increased stability to nuclease degradation, reduced nonspecific cellular uptake, no toxicity even at high concentrations, and excellent biodistribution beyond the liver, resulting in unprecedented gene silencing activity in various tissues.Control over the sequence has thus presented us with a unique polymeric building block in the form of the SDP, which combines the chemical and structural diversity of polymers with the programmability of DNA. By linking these orthogonal assembly languages, we have discovered new self-assembly rules, created DNA-minimal nanostructures, and demonstrated their utility through a range of applications. Developing this work further will open new avenues in the fields of DNA nanomaterials, nucleic acid therapeutics, as well as block copolymer self-assembly.

Data storage based on the absence of nucleotides using a bacteriophage abortive infection system reverse transcriptase

DNA molecules are a promising data storage medium for the future; however, effective de novo synthesis of DNA using an enzyme that catalyzes the polymerization of natural nucleoside triphosphates in a user-defined manner, without the need for multiple injections of polymerase, remains a challenge. In the present study, we demonstrated that the bacteriophage abortive infection system reverse transcriptase AbiK from Lactococcus lactis facilitates such an approach. We employed surface plasmon resonance to monitor the polymerization of the DNA strand with a user-defined sequence of multiple segments through a sequential buffer exchange process. Using this method, we synthesized synthetic DNA with segments of random length and a sequence consisting of only three of the four natural nucleotides. The information is encoded using the absence of one nucleotide in each segment. We demonstrated that synthetic DNA can be stored on the chip, and when the DNA is released from the chip, the second strand can be synthesized and read by sequencing. Our setup facilitates a writing speed of one nucleotide in less than 1 s and holds enormous potential for synthesizing DNA for data storage.

Massively parallel homogeneous amplification of chip-scale DNA for DNA information storage (MPHAC-DIS)

Chip scale DNA synthesis offers a high-throughput and cost-effective method for large-scale DNA-based information storage. Nevertheless, unbiased information retrieval from low-copy-number sequences remains a barricade that largely arises from the indispensable DNA amplification. Here, we devise a simulation-guided quantitative primer-template hybridization strategy to realize massively parallel homogeneous amplification of chip-scale DNA for DNA information storage (MPHAC-DIS). Using a fixed-energy primer design, we demonstrate the unbiasedness of MPHAC for amplifying 100,000-plex sequences. Simulations reveal that MPHAC achieves a fold-80 value of 1.0 compared to 3.2 with conventional fixed-length primers, lowering costs by up to four orders of magnitude through reduced over-sequencing. The MPHAC-DIS system using 35,406 encoded oligonucleotide allows simultaneous access of multimedia files including text, images, and videos with high decoding accuracy at very low sequencing depths. Specifically, even a ~ 1 ×  sequencing depth, with the combination of machine learning, results in an acceptable decoding accuracy of ~80%. The programmable and predictable MPHAC-DIS method thus opens new door for DNA-based large-scale data storage with potential industrial applications.

On-Chip DNA Assembly via Dielectrophoresis

On-chip gene synthesis has the potential to improve the synthesis throughput and reduce the cost exponentially. While there exist several microarray-based oligo synthesis technologies, on-chip gene assembly has yet to be demonstrated. This work introduces a novel on-chip DNA assembly method via dielectrophoresis (DEP) that can potentially be integrated with microarray-based oligo synthesis on the same chip. Our DEP chip can selectively manipulate oligos and guide their movement without perturbing the surrounding fluid medium, thus aiding in DNA assembly. Helical forked electrode design has been optimized for compatibility with DEP, ensuring efficient control over target oligos. By applying an alternating current signal set at 2 MHz, we successfully achieve the desired directed movement of oligonucleotides. Additionally, chemical treatments combined with photoirradiation enabled the connection of complementary gene sequences and the subsequent release of single-stranded DNA products. Sequencing results validate the effective assembly of DNA fragments, approximately 500 base pairs in length, using our DEP device.

Exploring DNA Computers: Advances in Storage, Cryptography and Logic Circuits

Over the last four decades, research on DNA as a functional material has primarily focused on its predictable conformation and programmable interaction. However, its low energy consumption, high responsiveness and sensitivity also make it ideal for designing specific signaling pathways, and enabling the development of molecular computers. This review mainly discusses recent advancements in the utilization of DNA nanotechnology for molecular computer, encompassing applications in storage, cryptography and logic circuits. It elucidates the challenges encountered in the application process and presents solutions exemplified by representative works. Lastly, it delineates the challenges and opportunities within this filed.

Site-saturation mutagenesis of 500 human protein domains

Missense variants that change the amino acid sequences of proteins cause one-third of human genetic diseases1. Tens of millions of missense variants exist in the current human population, and the vast majority of these have unknown functional consequences. Here we present a large-scale experimental analysis of human missense variants across many different proteins. Using DNA synthesis and cellular selection experiments we quantify the effect of more than 500,000 variants on the abundance of more than 500 human protein domains. This dataset reveals that 60% of pathogenic missense variants reduce protein stability. The contribution of stability to protein fitness varies across proteins and diseases and is particularly important in recessive disorders. We combine stability measurements with protein language models to annotate functional sites across proteins. Mutational effects on stability are largely conserved in homologous domains, enabling accurate stability prediction across entire protein families using energy models. Our data demonstrate the feasibility of assaying human protein variants at scale and provides a large consistent reference dataset for clinical variant interpretation and training and benchmarking of computational methods.

Vector-Free Deep Tissue Targeting of DNA/RNA Therapeutics via Single Capacitive Discharge Conductivity-Clamped Gene Electrotransfer

Viral vector and lipid nanoparticle based gene delivery have limitations around spatiotemporal control, transgene packaging size, and vector immune reactivity, compromising translation of nucleic acid (NA) therapeutics. In the emerging field of DNA and particularly RNA-based gene therapies, vector-free delivery platforms are identified as a key unmet need. Here, this work addresses these challenges through gene electrotransfer (GET) of "naked" polyanionic DNA/mRNA using a single needle form-factor which supports "electro-lens" based compression of the local electric field, and local control of tissue conductivity, enabling single capacitive discharge minimal charge gene delivery. Proof-of-concept studies for "single capacitive discharge conductivity-clamped gene electrotransfer" (SCD-CC-GET) deep tissue delivery of naked DNA and mRNA in the mouse hindlimb skeletal muscle achieve stable (>18 month) expression of luciferase reporter synthetic DNA, and mRNA encoding the reporter yield rapid onset (<3 h) high transient expression for several weeks. Delivery of DNAs encoding secreted alkaline phosphatase and Cal/09 influenza virus hemagglutinin antigen generate high systemic circulating recombinant protein levels and antibody titres. The findings support adoption of SCD-CC-GET for vaccines and immunotherapies, and extend the utility of this technology to meet the demand for efficient vector-free, precision, deep tissue delivery of NA therapeutics.

The need for adaptability in detection, characterization, and attribution of biosecurity threats

Modern biotechnology necessitates robust biosecurity protocols to address the risk of engineered biological threats. Current efforts focus on screening DNA and rejecting the synthesis of dangerous elements but face technical and logistical barriers. Screening should integrate into a broader strategy that addresses threats at multiple stages of development and deployment. The success of this approach hinges upon reliable detection, characterization, and attribution of engineered DNA. Recent advances notably aid the potential to both develop threats and analyze them. However, further work is needed to translate developments into biosecurity applications. This work reviews cutting-edge methods for DNA analysis and recommends avenues to improve biosecurity in an adaptable manner.

Empowering DNA-Based Information Processing: Computation and Data Storage

Information processing is a critical topic in the digital age, as silicon-based circuits face unprecedented challenges such as data explosion, immense energy consumption, and approaching physical limits. Deoxyribonucleic acid (DNA), naturally selected as a carrier for storing and using genetic information, possesses unique advantages for information processing, which has given rise to the emerging fields of DNA computing and DNA data storage. To meet the growing practical demands, a wide variety of materials and interfaces have been introduced into DNA information processing technologies, leading to significant advancements. This review summarizes the advances in materials and interfaces that facilitate DNA computation and DNA data storage. We begin with a brief overview of the fundamental functions and principles of DNA computation and DNA data storage. Subsequently, we delve into DNA computing systems based on various materials and interfaces, including microbeads, nanomaterials, DNA nanostructures, hydrophilic-hydrophobic compartmentalization, hydrogels, metal-organic frameworks, and microfluidics. We also explore DNA data storage systems, encompassing encapsulation materials, microfluidics techniques, DNA nanostructures, and living cells. Finally, we discuss the current bottlenecks and obstacles in the fields and provide insights into potential future developments.

Inert splint-driven oligonucleotide assembly

In this study, we introduce a new in vitro method for oligonucleotide fragment assembly. Unlike polymerase chain assembly and ligase chain assembly that rely on short, highly purified oligonucleotides, our method, named Splynthesis, uses a one-tube, splint-driven assembly reaction. Splynthesis connects standard-desalted "contig" oligos (∼150 nt in length) via shorter "splint" oligos harboring 5' and 3' blocking modifications to prevent off-target ligation and amplification events. We demonstrate the Splynthesis method to assemble a 741-bp gene fragment. We verify the assembled polymerase chain reaction product using standard molecular biology techniques, as well as long-read Oxford Nanopore sequencing, and confirm that the product is cloneable via molecular means, as well as Sanger sequencing. This approach is applicable for synthetic biology, directed evolution, functional protein assays, and potentially even splint-based ligase chain reaction assays.

Advancing microbiota therapeutics: the role of synthetic biology in engineering microbial communities for precision medicine

Over recent years, studies on microbiota research and synthetic biology have explored novel approaches microbial manipulation for therapeutic purposes. However, fragmented information is available on this aspect with key insights scattered across various disciplines such as molecular biology, genetics, bioengineering, and medicine. This review aims to the transformative potential of synthetic biology in advancing microbiome research and therapies, with significant implications for healthcare, agriculture, and environmental sustainability. By merging computer science, engineering, and biology, synthetic biology allows for precise design and modification of biological systems via cutting edge technologies like CRISPR/Cas9 gene editing, metabolic engineering, and synthetic oligonucleotide synthesis, thus paving the way for targeted treatments such as personalized probiotics and engineered microorganisms. The review will also highlight the vital role of gut microbiota in disorders caused by its dysbiosis and suggesting microbiota-based therapies and innovations such as biosensors for real-time gut health monitoring, non-invasive diagnostic tools, and automated bio foundries for better outcomes. Moreover, challenges including genetic stability, environmental safety, and robust regulatory frameworks will be discussed to understand the importance of ongoing research to ensure safe and effective microbiome interventions.

Elucidating sequence-function relationships in a template-independent polymerase to enable novel DNA recording applications

Harnessing DNA as a high-density storage medium for information storage and molecular recording of signals has been of increasing interest in the biotechnology field. Recently, progress in enzymatic DNA synthesis, DNA digital data storage, and DNA-based molecular recording has been made by leveraging the activity of the template-independent DNA polymerase, terminal deoxynucleotidyl transferase (TdT). TdT adds deoxyribonucleotides to the 3' end of single-stranded DNA, generating random sequences of single-stranded DNA. TdT can use several divalent cations for its enzymatic activity and exhibits shifts in deoxyribonucleotide incorporation frequencies in response to changes in its reaction environment. However, there is limited understanding of sequence-structure-function relationships regarding these properties, which in turn limits our ability to modulate TdT to further advance TdT-based tools. Most TdT literature to-date explores the activity of murine, bovine or human TdTs; studies probing TdT sequence and structure largely focus on strictly conserved residues that are functionally critical to TdT activity. Here, we explore non-conserved TdT sequence space by surveying the natural diversity of TdT. We characterize a diverse set of TdT homologs from different organisms and identify several TdT residues/regions that confer differences in TdT behavior between homologs. The observations in this study can design rules for targeted TdT libraries, in tandem with a screening assay, to modulate TdT properties. Moreover, the data can be useful in guiding further studies of potential residues of interest. Overall, we characterize TdTs that have not been previously studied in the literature, and we provide new insights into TdT sequence-function relationships.

Optimizing fountain codes for DNA data storage

Fountain codes, originally developed for reliable multicasting in communication networks, are effectively applied in various data transmission and storage systems. Their recent use in DNA data storage systems has unique challenges, since the DNA storage channel deviates from the traditional Gaussian white noise erasure model considered in communication networks and has several restrictions as well as special properties. Thus, optimizing fountain codes to address these challenges promises to improve their overall usability in DNA data storage systems. In this article, we present several methods for optimizing fountain codes for DNA data storage. Apart from generally applicable optimizations for fountain codes, we propose optimization algorithms to create tailored distribution functions of fountain codes, which is novel in the context of DNA data storage. We evaluate the proposed methods in terms of various metrics related to the DNA storage channel. Our evaluation shows that optimizing fountain codes for DNA data storage can significantly enhance the reliability and capacity of DNA data storage systems. The developed methods represent a step forward in harnessing the full potential of fountain codes for DNA-based data storage applications. The new coding schemes and all developed methods are available under a free and open-source software license.

A Nonlinear Peptide Topology for Synthetic Virions

a nonlinear de novo peptide topology for the assembly of synthetic virions is reported. The topology is a backbone cyclized amino-acid sequence in which polar l- and hydrophobic d-amino acid residues of the same-type alternate. This arrangement introduces pseudo C4 symmetries of side chains within the same cyclopeptide ring, allowing for the lateral propagation of cyclopeptides into networks with a [3/6, 4]-fold rotational symmetry closing into virus-like shells. A combination of computational and experimental approaches was used to establish that the topology forms morphologically uniform, nonaggregating and nontoxic nanoscale shells. These effectively encapsulate genetic cargo and promote its intracellular delivery and a target genetic response. The design introduces a nanotechnology inspired solution for engineering virus-like systems thereby expanding traditional molecular biology approaches used to create artificial biology to chemical space.

A Massively Parallel In Vivo Assay of TdT Mutants Yields Variants with Altered Nucleotide Insertion Biases

Terminal deoxynucleotidyl transferase (TdT) is a unique DNA polymerase capable of template-independent extension of DNA. TdT's de novo DNA synthesis ability has found utility in DNA recording, DNA data storage, oligonucleotide synthesis, and nucleic acid labeling, but TdT's intrinsic nucleotide biases limit its versatility in such applications. Here, we describe a multiplexed assay for profiling and engineering the bias and overall activity of TdT variants with high throughput. In our assay, a library of TdTs is encoded next to a CRISPR-Cas9 target site in HEK293T cells. Upon transfection of Cas9 and sgRNA, the target site is cut, allowing TdT to intercept the double-strand break and add nucleotides. Each resulting insertion is sequenced alongside the identity of the TdT variant that generated it. Using this assay, 25,623 unique TdT variants, constructed by site-saturation mutagenesis at strategic positions, were profiled. This resulted in the isolation of several altered-bias TdTs that expanded the capabilities of our TdT-based DNA recording system, Cell HistorY Recording by Ordered InsertioN (CHYRON), by increasing the information density of recording through an unbiased TdT and achieving dual-channel recording of two distinct inducers (hypoxia and Wnt) through two differently biased TdTs. Select TdT variants were also tested in vitro, revealing concordance between each variant's in vitro bias and the in vivo bias determined from the multiplexed high throughput assay. Overall, our work and the multiplex assay it features should support the continued development of TdT-based DNA recorders, in vitro applications of TdT, and further study of the biology of TdT.

DNA-Based Complexes and Composites: A Review of Fabrication Methods, Properties, and Applications

Deoxyribonucleic acid (DNA), a macromolecule that stores genetic information in organisms, has recently been gradually developed into a building block for new materials due to its stable chemical structure and excellent biocompatibility. The efficient preparation and functional integration of various molecular complexes and composite materials based on nucleic acid skeletons have been successfully achieved. These versatile materials possess excellent physical and chemical properties inherent to certain inorganic or organic molecules but are endowed with specific physiological functions by nucleic acids, demonstrating unique advantages and potential applications in materials science, nanotechnology, and biomedical engineering in recent years. However, issues such as the production cost, biological stability, and potential immunogenicity of DNA have presented some unprecedented challenges to the application of these materials in the field. This review summarizes the cutting-edge manufacturing techniques and unique properties of DNA-based complexes and composites and discusses the trends, challenges, and opportunities for the future development of nucleic acid-based materials.

An Effective DNA-Based File Storage System for Practical Archiving and Retrieval of Medical MRI Data

DNA-based data storage is a new technology in computational and synthetic biology, that offers a solution for long-term, high-density data archiving. Given the critical importance of medical data in advancing human health, there is a growing interest in developing an effective medical data storage system based on DNA. Data integrity, accuracy, reliability, and efficient retrieval are all significant concerns. Therefore, this study proposes an Effective DNA Storage (EDS) approach for archiving medical MRI data. The EDS approach incorporates three key components (i) a novel fraction strategy to address the critical issue of rotating encoding, which often leads to data loss due to single base error propagation; (ii) a novel rule-based quaternary transcoding method that satisfies bio-constraints and ensure reliable mapping; and (iii) an indexing technique designed to simplify random search and access. The effectiveness of this approach is validated through computer simulations and biological experiments, confirming its practicality. The EDS approach outperforms existing methods, providing superior control over bio-constraints and reducing computational time. The results and code provided in this study open new avenues for practical DNA storage of medical MRI data, offering promising prospects for the future of medical data archiving and retrieval.

Parallel molecular data storage by printing epigenetic bits on DNA

DNA storage has shown potential to transcend current silicon-based data storage technologies in storage density, longevity and energy consumption1-3. However, writing large-scale data directly into DNA sequences by de novo synthesis remains uneconomical in time and cost4. We present an alternative, parallel strategy that enables the writing of arbitrary data on DNA using premade nucleic acids. Through self-assembly guided enzymatic methylation, epigenetic modifications, as information bits, can be introduced precisely onto universal DNA templates to enact molecular movable-type printing. By programming with a finite set of 700 DNA movable types and five templates, we achieved the synthesis-free writing of approximately 275,000 bits on an automated platform with 350 bits written per reaction. The data encoded in complex epigenetic patterns were retrieved high-throughput by nanopore sequencing, and algorithms were developed to finely resolve 240 modification patterns per sequencing reaction. With the epigenetic information bits framework, distributed and bespoke DNA storage was implemented by 60 volunteers lacking professional biolab experience. Our framework presents a new modality of DNA data storage that is parallel, programmable, stable and scalable. Such an unconventional modality opens up avenues towards practical data storage and dual-mode data functions in biomolecular systems.

High-throughput discovery of inhibitory protein fragments with AlphaFold

Peptides can bind to specific sites on larger proteins and thereby function as inhibitors and regulatory elements. Peptide fragments of larger proteins are particularly attractive for achieving these functions due to their inherent potential to form native-like binding interactions. Recently developed experimental approaches allow for high-throughput measurement of protein fragment inhibitory activity in living cells. However, it has thus far not been possible to predict de novo which of the many possible protein fragments bind to protein targets, let alone act as inhibitors. We have developed a computational method, FragFold, that employs AlphaFold to predict protein fragment binding to full-length proteins in a high-throughput manner. Applying FragFold to thousands of fragments tiling across diverse proteins revealed peaks of predicted binding along each protein sequence. Comparisons with experimental measurements establish that our approach is a sensitive predictor of fragment function: Evaluating inhibitory fragments from known protein-protein interaction interfaces, we find 87% are predicted by FragFold to bind in a native-like mode. Across full protein sequences, 68% of FragFold-predicted binding peaks match experimentally measured inhibitory peaks. Deep mutational scanning experiments support the predicted binding modes and uncover superior inhibitory peptides in high throughput. Further, FragFold is able to predict previously unknown protein binding modes, explaining prior genetic and biochemical data. The success rate of FragFold demonstrates that this computational approach should be broadly applicable for discovering inhibitory protein fragments across proteomes.

Template-dependent DNA ligation for the synthesis of modified oligonucleotides

Chemical modification of DNA is a common strategy to improve the properties of oligonucleotides, particularly for therapeutics and nanotechnology. Existing synthetic methods essentially rely on phosphoramidite chemistry or the polymerization of nucleoside triphosphates but are limited in terms of size, scalability, and sustainability. Herein, we report a robust alternative method for the de novo synthesis of modified oligonucleotides using template-dependent DNA ligation of shortmer fragments. Our approach is based on the fast and scaled accessibility of chemically modified shortmer monophosphates as substrates for the T3 DNA ligase. This method has shown high tolerance to chemical modifications, flexibility, and overall efficiency, thereby granting access to a broad range of modified oligonucleotides of different lengths (20 → 120 nucleotides). We have applied this method to the synthesis of clinically relevant antisense drugs and ultramers containing diverse modifications. Furthermore, the designed chemoenzymatic approach has great potential for diverse applications in therapeutics and biotechnology.

Engineered Transcription Factor Binding Arrays for DNA-based Gene Expression Control in Mammalian Cells

Manipulating gene expression in mammalian cells is critical for cell engineering applications. Here we explore the potential of transcription factor (TF) recognition element arrays as DNA tools for modifying free TF levels in cells and thereby controlling gene expression. We first demonstrate proof-of-concept, showing that Tet TF-binding recognition element (RE) arrays of different lengths can tune gene expression and alter gene circuit performance in a predictable manner. We then open-up the approach to interface with any TF with a known binding site by developing a new method called Cloning Troublesome Repeats in Loops (CTRL) that can assemble plasmids with up to 256 repeats of any RE sequence. Transfection of RE array plasmids assembled by CTRL into mammalian cells show potential to modify host cell gene regulation at longer array sizes by sequestration of the TF of interest. RE array plasmids built using CTRL were demonstrated to target both synthetic and native mammalian TFs, illustrating the ability to use these tools to modulate genetic circuits and instruct cell fate. Together this work advances our ability to assemble repetitive DNA arrays and showcases the use of TF-binding RE arrays as a method for manipulating mammalian gene expression, thus expanding the possibilities for mammalian cell engineering.

Recent progress in DNA data storage based on high-throughput DNA synthesis

DNA data storage has emerged as a solution for storing massive volumes of data by utilizing nucleic acids as a digital information medium. DNA offers exceptionally high storage density, long durability, and low maintenance costs compared to conventional storage media such as flash memory and hard disk drives. DNA data storage consists of the following steps: encoding, DNA synthesis (i.e., writing), preservation, retrieval, DNA sequencing (i.e., reading), and decoding. Out of these steps, DNA synthesis presents a bottleneck due to imperfect coupling efficiency, low throughput, and excessive use of organic solvents. Overcoming these challenges is essential to establish DNA as a viable data storage medium. In this review, we provide the overall process of DNA data storage, presenting the recent progress of each step. Next, we examine a detailed overview of DNA synthesis methods with an emphasis on their limitations. Lastly, we discuss the efforts to overcome the constraints of each method and their prospects.

Mutagenesis techniques for evolutionary engineering of microbes - exploiting CRISPR-Cas, oligonucleotides, recombinases, and polymerases

The natural process of evolutionary adaptation is often exploited as a powerful tool to obtain microbes with desirable traits. For industrial microbes, evolutionary engineering is often used to generate variants that show increased yields or resistance to stressful industrial environments, thus obtaining superior microbial cell factories. However, even in large populations, the natural supply of beneficial mutations is typically low, which implies that obtaining improved microbes is often time-consuming and inefficient. To overcome this limitation, different techniques have been developed that boost mutation rates. While some of these methods simply increase the overall mutation rate across a genome, others use recent developments in DNA synthesis, synthetic biology, and CRISPR-Cas techniques to control the type and location of mutations. This review summarizes the most important recent developments and methods in the field of evolutionary engineering in model microorganisms. It discusses how both in vitro and in vivo approaches can increase the genetic diversity of the host, with a special emphasis on in vivo techniques for the optimization of metabolic pathways for precision fermentation.

Substitution Attacks: A Catalyst to Reframe the DNA Manufacturing Cyberbiosecurity Landscape in the Age of Benchtop Synthesizers

Background

The advent of easy-to-use benchtop DNA synthesizers has ushered in a transformative era in biotechnology, extending the capabilities of DNA synthesis to nonspecialists. However, this revolution in access to this technology exposes several vulnerabilities, notably in the form of substitution attacks. These attacks exploit the intricate interplay between the digital domain of DNA sequences and the physical reality of synthesis instruments, posing substantial threats to biosecurity.

Content

This article delves deeply into the dynamic and multifaceted landscape of cyberbiosecurity, specifically emphasizing a novel attack vector that evades traditional screening algorithms. To achieve this, the article explores algorithmic approaches designed to screen DNA sequences, shedding light on the vulnerabilities exposed by substitution attacks and recontextualizing the cyberbiosecurity actor landscape in the context of the entire DNA manufacturing process.

Summary

The exploration of cyberbiosecurity brings existing vulnerabilities in DNA screening algorithms to light and sets the stage for future research and policy considerations. By emphasizing opportunities for a comprehensive, multipronged approach rooted in end-to-end practical DNA manufacturing, this study provides a foundation for advancing both knowledge and strategies in the realm of cyberbiosecurity.

Recommendations

This article serves as a clarion call for increased vigilance and innovation in navigating the intricate landscape of cyberbiosecurity. Effectively understanding and mitigating substitution attacks is necessary to safeguard the integrity of synthesized genetic material, particularly in the context of the democratization of DNA synthesis technology.

Combinative workflow for mRNA vaccine development

Recently, mRNA has gained a lot of attention in the field of vaccines, gene therapy, and protein replacement therapies. Herein, we are demonstrating a comprehensive approach to designing, cloning, and characterizing an antigenic cassette for the development of mRNA vaccine for COVID-19. The gene encoding the antigenic spike protein of the SARS-CoV-2 Omicron variant (B.1.1.529) was designed using the databases, characterized by in-silico tools, and assembled using overlapping oligonucleotide-based assembly by PCR. Next, the gene was cloned, mRNA was synthesized, and characterized using orthogonal approaches (Capillary electrophoresis, Sanger DNA sequencing, Next-generation sequencing, HPLC, qPCR, etc.). Furthermore, the antigen expression was monitored in-vitro using an animal cell model by western blot, flow cytometer, and surface plasmon resonance. The demonstrated approach has also been followed for developing the mRNA vaccines for various other indications such as Malaria, Herpes, Dengue, HPV, etc.