DNA Synthesizer Research Articles

Synthesis of 1,4-azaphosphinine nucleosides and evaluation as inhibitors of human cytidine deaminase and APOBEC3A.

Nucleoside and polynucleotide cytidine deaminases (CDAs), such as CDA and APOBEC3, share a similar mechanism of cytosine to uracil conversion. In 1984, phosphapyrimidine riboside was characterised as the most potent inhibitor of human CDA, but the quick degradation in water limited the applicability as a potential therapeutic. To improve stability in water, we synthesised derivatives of phosphapyrimidine nucleoside having a CH2 group instead of the N3 atom in the nucleobase. A charge-neutral phosphinamide and a negatively charged phosphinic acid derivative had excellent stability in water at pH 7.4, but only the charge-neutral compound inhibited human CDA, similar to previously described 2'-deoxyzebularine (Ki = 8.0 ± 1.9 and 10.7 ± 0.5 µM, respectively). However, under basic conditions, the charge-neutral phosphinamide was unstable, which prevented the incorporation into DNA using conventional DNA chemistry. In contrast, the negatively charged phosphinic acid derivative was incorporated into DNA instead of the target 2'-deoxycytidine using an automated DNA synthesiser, but no inhibition of APOBEC3A was observed for modified DNAs. Although this shows that the negative charge is poorly accommodated in the active site of CDA and APOBEC3, the synthetic route reported here provides opportunities for the synthesis of other derivatives of phosphapyrimidine riboside for potential development of more potent CDA and APOBEC3 inhibitors.

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

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. 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. 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. 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.

An open-source, 3D printed inkjet DNA synthesizer

Synthetic oligonucleotides have become a fundamental tool in a wide range of biological fields, including synthetic biology, biosensing, and DNA storage. Reliable access to equipment for synthesizing high-density oligonucleotides in the laboratory ensures research security and the freedom of research expansion. In this study, we introduced the Open-Source Inkjet DNA Synthesizer (OpenIDS), an open-source inkjet-based microarray synthesizer that offers ease of construction, rapid deployment, and flexible scalability. Utilizing 3D printing, Arduino, and Raspberry Pi, this newly designed synthesizer achieved robust stability with an industrial inkjet printhead. OpenIDS maintains low production costs and is therefore suitable for self-fabrication and optimization in academic laboratories. Moreover, even non-experts can create and control the synthesizer with a high degree of freedom for structural modifications. Users can easily add printheads or alter the design of the microarray substrate according to their research needs. To validate its performance, we synthesized oligonucleotides on 144 spots on a 15 × 25-mm silicon wafer filled with controlled pore glass. The synthesized oligonucleotides were analyzed using urea polyacrylamide gel electrophoresis.

Enzymatic Preparation of DNA with an Expanded Genetic Alphabet Using Terminal Deoxynucleotidyl Transferase and Its Applications.

Efficient preparation of DNA oligonucleotides containing unnatural nucleobases (UBs) that can pair with their cognates to form unnatural base pairs (UBPs) is an essential prerequisite for the application of UBPs in vitro and in vivo. Traditional preparation of oligonucleotides containing unnatural nucleobases largely relies on solid-phase synthesis, which needs to use unstable nucleoside phosphoramidites and a DNA synthesizer, and is environmentally unfriendly and limited in product length. To overcome these limitations of solid-phase synthesis, we developed enzymatic methods for daily laboratory preparation of DNA oligonucleotides containing unnatural nucleobase dNaM, dTPT3, or one of the functionalized dTPT3 derivatives, which can be used for orthogonal DNA labeling or the preparation of DNAs containing UBP dNaM-dTPT3, one of the most successful UBPs to date, based on the template-independent polymerase terminal deoxynucleotidyl transferase (TdT). Here, we first provide a detailed procedure for the TdT-based preparation of DNA oligonucleotides containing 3'-nucleotides of dNaM, dTPT3, or one of dTPT3 derivatives. We then present the procedures for enzyme-linked oligonucleotide assay (ELONA) and imaging of bacterial cells using DNA oligonucleotides containing 3'-nucleotides of dTPT3 derivatives with different functional groups. The procedure for enzymatic synthesis of DNAs containing an internal UBP dNaM-dTPT3 is also described. Hopefully, these methods will greatly facilitate the application of UBPs and the construction of semi-synthetic organisms with an expanded genetic alphabet.

Enzymatic synthesis of ligand-bearing oligonucleotides for the development of metal-responsive DNA materials.

Metal-mediated artificial base pairs are some of the most promising building blocks for constructing DNA-based supramolecules and functional materials. These base pairs are formed by coordination bonds between ligand-type nucleobases and a bridging metal ion and have been exploited to develop metal-responsive DNA materials and DNA-templated metal arrays. In this review, we provide an overview of methods for the enzymatic synthesis of DNA strands containing ligand-type artificial nucleotides that form metal-mediated base pairs. Conventionally, ligand-bearing DNA oligomers have been synthesized via solid-phase synthesis using a DNA synthesizer. In recent years, there has been growing interest in enzymatic methods as an alternative approach to synthesize ligand-bearing DNA oligomers, because enzymatic reactions proceed under mild conditions and do not require protecting groups. DNA polymerases are used to incorporate ligand-bearing unnatural nucleotides into DNA, and DNA ligases are used to connect artificial DNA oligomers to natural DNA fragments. Template-independent polymerases are also utilized to post-synthetically append ligand-bearing nucleotides to DNA oligomers. In addition, enzymatic replication of DNA duplexes containing metal-mediated base pairs has been intensively studied. Enzymatic methods facilitate the synthesis of DNA strands containing ligand-bearing nucleotides at both internal and terminal positions. Enzymatically synthesized ligand-bearing DNAs have been applied to metal-dependent self-assembly of DNA structures and the allosteric control of DNAzyme activity through metal-mediated base pairing. Therefore, the enzymatic synthesis of ligand-bearing oligonucleotides holds great potential in advancing the development of various metal-responsive DNA materials, such as molecular sensors and machines, providing a versatile tool for DNA supramolecular chemistry and nanotechnology.

One-Pot Enzymatic Preparation of Oligonucleotides with an Expanded Genetic Alphabet via Controlled Pause and Restart of Primer Extension: Making Unnatural Out of Natural.

The genetic alphabet of life has been dramatically expanded via the development of unnatural base pairs (UBPs) that work as efficiently as natural base pairs in the storage and retrieval of genetic information. Among the most predominant UBPs, dNaM-dTPT3 and its analogues have been successfully employed to build semisynthetic cells with a functional six-letter genome. With the rapidly growing applications of UBPs in vitro and in vivo, there is an ever-increasing demand for DNA oligonucleotides containing unnatural bases (UBs) at desired positions. Conventional solid-phase synthesis of oligonucleotides has intrinsic limitations and needs to use unstable unnatural phosphoramidites and a DNA synthesizer, so it does not meet the daily urgent requirement for a few UB-containing DNA oligonucleotides in the laboratory. In this work, we develop a one-pot enzymatic method for preparing dNaM- or dTPT3-containing DNA oligonucleotides via controlled pause and restart of primer extension mediated by Klenow fragment (exo-). By systematic optimization of the reaction conditions, high efficiencies and product purities have been achieved. The universality of this method for preparing DNA oligonucleotides containing dNaM or dTPT3 in different sequence contexts is also demonstrated. This method allows convenient production of an arbitrary UB-containing DNA oligonucleotide in a single test tube with only two natural DNA oligonucleotides, stable nucleoside triphosphates, Klenow fragment (exo-), and other common reagents in the laboratory, providing the lowest cost and the highest simplicity for the enzymatic preparation of UB-containing oligonucleotides. Clearly, this method has great potential to facilitate the in vitro and in vivo applications of the UBPs.

Adjuvant Oligonucleotide Vaccine Increases Survival and Improves Lung Tissue Condition of B6.Cg-Tg (K18-ACE2)2 Transgenic Mice

The main problem in creating anti-coronavirus vaccines that target mainly proteins of the outer membrane of the virus is the rapid variability in the RNA genome of the pathogen that encodes these proteins. In addition, the introduction of technologies that can affordably and quickly produce flexible vaccine formulas that easily adapt to the emergence of new subtypes of SARS-CoV-2 is required. Universal adjuvant oligonucleotide vaccines based on conserved regions of the SARS-CoV-2 genome can take into account the dynamics of rapid changes in the virus genome, as well as be easily synthesized on automatic DNA synthesizers in large quantities in a short time. In this brief report, the effectiveness of four phosphorothioate constructs of the La-S-so-type adjuvant oligonucleotide vaccine is evaluated on B6.Cg-Tg (K18-ACE2)2 transgenic mice for the first time. In our primary trials, the oligonucleotide vaccine increased the survival rate of animals infected with SARS-CoV-2 and also reduced the destructive effects of the virus on the lung tissue of mice, activating both their innate and adaptive immunity. The obtained results show that the development of adjuvant oligonucleotide vaccine constructs of the La-S-so type is an affordable and efficient platform for the prevention of coronavirus infections, including those caused by SARS-CoV-2.

The Application of al-Intiqal (the transition) on Synthetically Modified Organisms (SMOs): An Analysis from Shariah and Science Approaches

Synthetic biology, or SynBio, is a fast-growing technology, that combines biology, chemistry, computer science, and engineering, producing synthetically modified organisms (SMOs), in which organisms for which a large part or the entire genome has been designed using computer-aided design tool and chemically synthesized. Concern arises when (deoxyribonucleic acid) DNA constructs are made up of impure (najs) substances in Shariah as raw material, like transfer of engineered pig cells with modified genomes. One of alternative verification methods of Shariah law, namely al-Intiqal (the transition), can assist Muslim jurists in determining legal rulings on particular Halal contemporary issues, as there is no explicit information about genetic modified technology in the Qur’an or Hadith. This study aims to determine the theory of al-Intiqal (the transition) from Shariah and science approaches and apply the structure and division of al-Intiqal (the transition) on SMOs productions, like synthetic spider silk and humanized pig organ. Qualitative methods were applied including library research, fiqh adaptation (al-takyif al-fiqhi), and semi structured in-depth interview. Study shows that two divisions of al-Intiqal (the transition) can be applied within SMOs productions, which are al-Intiqal al-sahih (the accepted transition) and al-Intiqal al-fasid (the damaged transition). Study concludes that DNA synthesizer as conversion agent within SMOs production process can be considered permissible (Halal), while synthetic spider silk is also permissible (Halal) as the raw material is considered pure and its transition process had completely occurred in Shariah, nonetheless humanized pig organ is impermissible (Haram) as the raw material and its recipient organism are impermissible (Haram) and its transition process had not completely occurred in Shariah, except for emergency (darurah) case with some provisions.

DNA Fragment Enrichment for High-Throughput Sequencing

Application of oligonucleotides, mainly obtained using new generation DNA synthesizers (microarray DNA synthesizers), for the enrichment of targeted genomic fragments are described. Methods of molecular hybridization, polymerase chain reaction and CRISPR-based methods for targets enrichment are considered. Examples of the practical use of the developed methods for research and diagnostic purposes are given.

The Long and Winding Road: On-Demand DNA Synthesis in High Demand

The Long and Winding Road: On-Demand DNA Synthesis in High Demand

The construction of oligonucleotide-cycloastragenol and the renoprotective effect study.

Traditional Chinese Medicine (TCM) provides unique therapeutic effects for many diseases with identified efficacy during long practice. Astragalus Membranaceus (AM) is the Chinese herbal applied for kidney injury in the clinic, but it remains challenging to further enhance the efficacy. Cycloastragenol (CAG) is the ingredient isolated from AM with poor water solubility, which has shown a renoprotective effect. Herein we designed and synthesized the corresponding solid-phase module of CAG, from which CAG as a pharmaceutical element was incorporated into oligonucleotides (ON) as an ON-CAG conjugate in a programmable way by a DNA synthesizer. Cell viability study demonstrated that ON-CAG conjugate remains similar renoprotective effect as that of CAG, which efficiently recovers the activity of HK-2 cells pretreated with cisplatin. Similarly, in the renal cells treated with the conjugate, the biomarkers of kidney injury such as KIM-1 and IL-18 are downregulated, and cytokines are reduced as treated with anti-inflammatory agents. Overall, we have managed to incorporate a hydrophobic ingredient of TCM into ON and demonstrate the oligonucleotide synthesis technology as a unique approach for the mechanism study of TCM, which may facilitate the discovery of new therapeutics based on TCM.

Synthesis of Phosphorodiamidate Morpholino Oligonucleotides Using Trityl and Fmoc Chemistry in an Automated Oligo Synthesizer.

Phosphorodiamidate morpholino oligonucleotides (PMOs) constitute 3 out of the 11 FDA-approved oligonucleotide-based drugs in the last 6 years. PMOs can effectively silence disease-causing genes and modify splicing. However, PMO synthesis has remained challenging for a variety of reasons: inefficient deprotection and coupling methods and instability of monomers. Here, we report the development of a suitable combination of resin supports, deblocking and coupling reagents for synthesizing PMOs using either trityl or Fmoc-protected chlorophosphoramidate monomers. The synthesized PMOs using both the methods on a solid support have been validated for gene silencing in a zebrafish model. The protocol was successfully transferred into an automated DNA synthesizer to make several sequences of PMOs, demonstrating for the first time the adaptation of regular PMOs in a commercial DNA synthesizer. Moreover, PMOs with longer than 20-mer sequences, including FDA-approved Eteplirsen (30-mer), were achieved in >20% overall yield that is superior to previous reports. Hybridization study shows that PMOs exhibit a higher binding affinity toward complementary DNA relative to the DNA/DNA duplex (>6 °C). Additionally, the introduction of Fmoc chemistry into PMOs opens up the possibility for PMO synthesis in commercial peptide synthesizers for future development.

Secondary Structure Libraries for Artificial Evolution Experiments.

Methods of artificial evolution such as SELEX and in vitro selection have made it possible to isolate RNA and DNA motifs with a wide range of functions from large random sequence libraries. Once the primary sequence of a functional motif is known, the sequence space around it can be comprehensively explored using a combination of random mutagenesis and selection. However, methods to explore the sequence space of a secondary structure are not as well characterized. Here we address this question by describing a method to construct libraries in a single synthesis which are enriched for sequences with the potential to form a specific secondary structure, such as that of an aptamer, ribozyme, or deoxyribozyme. Although interactions such as base pairs cannot be encoded in a library using conventional DNA synthesizers, it is possible to modulate the probability that two positions will have the potential to pair by biasing the nucleotide composition at these positions. Here we show how to maximize this probability for each of the possible ways to encode a pair (in this study defined as A-U or U-A or C-G or G-C or G.U or U.G). We then use these optimized coding schemes to calculate the number of different variants of model stems and secondary structures expected to occur in a library for a series of structures in which the number of pairs and the extent of conservation of unpaired positions is systematically varied. Our calculations reveal a tradeoff between maximizing the probability of forming a pair and maximizing the number of possible variants of a desired secondary structure that can occur in the library. They also indicate that the optimal coding strategy for a library depends on the complexity of the motif being characterized. Because this approach provides a simple way to generate libraries enriched for sequences with the potential to form a specific secondary structure, we anticipate that it should be useful for the optimization and structural characterization of functional nucleic acid motifs.

Observation of Z-DNA Structure via the Synthesis of Oligonucleotide DNA Containing 8-Trifluoromethyl-2-Deoxyguanosine.

This article contains detailed synthetic protocols for the preparation of DNA oligonucleotides containing 8-trifluoromethyl-2'-deoxyguanosine (CF3 dG) and their application to observe Z-DNA structure in vitro and in living HeLa cells. First, using a catalytic system consisting of FeSO4 , H2 SO4 , and H2 O2 in DMSO, we achieved a one-step synthesis of CF3 dG through a radical reaction between deoxyguanosine (dG) and CF3 I, with a yield of 45%. We then obtained the 3'-phosphoramidite of CF3 dG through a routine three-step procedure. Next, we employed the CF3 dG phosphoramidite monomer in the synthesis of oligonucleotides on a solid-phase DNA synthesizer. Finally, we used the CF3 dG-modified DNA oligonucleotides to observe Z-DNA structure in vitro and in living HeLa cells through 19 F NMR spectroscopy. © 2021 Wiley Periodicals LLC. Basic Protocol 1: Synthesis of CF3 dG phosphoramidites Basic Protocol 2: Preparation of CF3 dG-modified DNA oligonucleotides Basic Protocol 3: Evaluation of CF3 dG stabilization of Z-DNA structure by CD spectroscopy Basic Protocol 4: Investigation of Z-DNA structure in vitro and in HeLa cells with CF3 dG-modified DNA oligonucleotides and 19 F NMR spectroscopy.

Programmable Repurposing of Existing Drugs as Pharmaceutical Elements for the Construction of Aptamer-Drug Conjugates.

Converting marketed drug molecules into phosphoramidites may present a potential strategy to facilitate the development of aptamer-drug conjugates (ApDCs) by a DNA synthesizer in a programmable way; however, quite limited methods were reported. Herein, we demonstrated a general approach by repurposing camptothecin (CPT) species. Commonly used inactive ingredients in pharmaceuticals are investigated and selected as a bonding moiety, from which 2-mercaptoethoxy ethanol and thioglycerol were efficiently incorporated with CPT to give the precursors. Cell viability and molecular docking results of the precursors supported that incorporation of the bonding moiety would not interrupt the inhibitory activity. Therefore, corresponding phosphoramidites were prepared as pharmaceutical elements, and a series of ApDCs were constructed automatically by solid-phase synthesis. Biological studies revealed that CPT elements could be specifically delivered to HCT116 cells by an aptamer and released inside cells. This kind of programmable repurposing may take advantage of established safety data and efficacy of existing drugs resulting in a faster development of ApDCs.

A novel class of polymeric fluorescent dyes assembled using a DNA synthesizer.

In the pursuit of a novel class of fluorescent dyes we have developed a programmable polymer system that enables the rational design and control of macromolecular constructs through simple control of polymer primary sequence. These polymers are assembled using standard phosphoramidite chemistry on a DNA synthesizer which allows for extremely rapid prototyping and enables many permutations due to the large selection of phosphoramidite monomers presently available on the market. This programmability to some extent allows us to control the interactions/spacing of payload molecules distributed along the designed polymeric backbone. Control of molecular architecture using this technology has allowed us to address the long-standing technical issue of contact quenching between fluorescent dyes offering new possibilities in the life sciences arena. Much like peptidic sequences coding for enzymes, cofactors, and receptors (all needing control of tertiary structure for proper function via primary sequence) our programmable system approaches a similar endpoint using a phosphate based polymeric backbone assembled in a completely automated fashion. Using this novel technology, we have efficiently synthesized several types of fluorescent dyes and demonstrated the programmability in molecule design, including the increases in brightness of the fluorescence emission.

Stepwise Strategy for One-Pot Synthesis of Single-Stranded DNA Rings from Multiple Short Fragments.

Cyclic rings of single-stranded (ss) DNA have various unique properties, but wider applications have been hampered by their poor availability. This paper reports a convenient one-pot method in which these rings are efficiently synthesized by using T4 DNA ligase through convergent cyclization of easily available short DNA fragments. The key to the present method is to separate all the splint oligonucleotides into several sets, and add each set sequentially at an appropriate interval to the solutions containing all the short DNA fragments. Compared with simple one-pot strategies involving simultaneous addition of all the splints at the beginning of the reaction, both the selectivity and the yields of target ssDNA rings are greatly improved. This convergent method is especially useful for preparing large-sized rings that are otherwise hard to obtain. By starting from six short DNA fragments (71-82 nt), prepared by a DNA synthesizer, a ssDNA ring of 452-nt size was synthesized in 35 mol % yield and in high selectivity. Satisfactorily pure DNA rings were obtainable simply by treating the crude products with exonuclease.

Evaluation of the Base‐Pairing Properties of 5‐(5‐Indolylethynyl) and 5‐(5‐Indolyl)‐2′‐deoxyuridine Modified Triplex and Duplex

AbstractIndole was conjugated to deoxyuridine either directly or via ethynyl linkage to synthesize two new DNA monomers. Due to the high reactivity of indole toward electrophilic substitution reactions, unwanted iodination was observed during the oxidation step with iodine oxidizer in automated DNA synthesizer leading to an additional oligonucleotide having extra 126 mass unit beside the desired oligonucleotide. On the other hand, using CSO oxidizer ensured the formation of the wanted oligonucleotide. Oligonucleotide synthesis was confirmed by MALDI‐TOF‐MS analysis. Polypyrimidine strands containing non‐iodinated indole nucleoside were able to form parallel triplexes, antiparallel RNA and DNA duplexes. The thermal denaturation experiments showed higher triplex stabilization for 5‐(5‐indolylethynyl)‐2′‐deoxyuridine over 5‐(5‐indolyl)‐2′‐deoxyuridine as the triple bond allows twisting to put the indole into a proper position within the triplex encouraging better π‐π stacking.

Biased photo cleavage of N1-/N6-nitrobenzyl from 2’-hydroxyethyl-adenosine and their DNA/RNA Caged-analogues

The protection and deprotection of functional groups are critical steps during the synthesis of complex molecules. The chemo-selective and regio-selective protection-deprotection under mild conditions are always preferred. The photolabile protecting groups have such qualities. For example, o-nitrobenzyl is a versatile photolabile protecting group of amine, alcohol, and carboxylic acid. This report describes the regio-selective N-nitrobenzylation of 2′-tethered-adenosine nucleoside analogue with o-nitrobenzyl bromide, as resultant two new protected nucleosides such as 2′-hydroxylethyl-NBn1A/2′-hydroxylethyl-NBn6A are prepared. Importantly, N-nitrobezylation occurs only at adenine residue, though it is protected. This analogue has a free tethered hydroxyl group at 2′-position and remained unaffected with nitrobenzylation. Furthers, these analogues are incorporated into DNA/RNA oligonucleotides using DNA synthesizer. This report also demonstrates the photocleavage of those nitrobenzyl groups in a regio-specific manner by UV-light (λ365nm). The nitrobenyl of only NBn6A derivatives are cleavable regio-specifically with UV-light. Surprisingly, unusual chemical cleavage of nitrobenzyl of NBn1A-DNA/RNA has found during oligo syntheses. Also, the isomerization of NBn1A-DNA into NBn6A-DNA occurs. Thus only NBn6A derivatives are caged-adenosine analogues. Hence 2′-tethered-NBn6A/-NBn1A derivatives are potential analogues for regulating the biochemical activities with light.

Synthesis of Phosphoramidite Monomers Equipped with Complementary Bases for Solid-Phase DNA Oligomerization.

We describe the preparation of two monomers that bear complementary nucleobases at the edges (guanine-2'-deoxycytidine and 2-aminoadenine-2'-deoxyuridine) and that are conveniently protected and activated for solid-phase automated DNA synthesis. We report the optimized synthetic routes leading to the four nucleobase derivatives involved, their cross-coupling reactions into dinucleobase-containing monomers, and their oligomerization in the DNA synthesizer.