Nucleoside alpha-thiotriphosphates, polymerases and the exonuclease III analysis of oligonucleotides containing phosphorothioate linkages

Bacterial exonuclease III expands its enzymatic activities on single-stranded DNA

Bacterial exonuclease III (ExoIII), widely acknowledged for specifically targeting double-stranded DNA (dsDNA), has been documented as a DNA repair-associated nuclease with apurinic/apyrimidinic (AP)-endonuclease and 3'→5' exonuclease activities. Due to these enzymatic properties, ExoIII has been broadly applied in molecular biosensors. Here, we demonstrate that ExoIII (Escherichia coli) possesses highly active enzymatic activities on ssDNA. By using a range of ssDNA fluorescence-quenching reporters and fluorophore-labeled probes coupled with mass spectrometry analysis, we found ExoIII cleaved the ssDNA at 5'-bond of phosphodiester from 3' to 5' end by both exonuclease and endonuclease activities. Additional point mutation analysis identified the critical residues for the ssDNase action of ExoIII and suggested the activity shared the same active center with the dsDNA-targeted activities of ExoIII. Notably, ExoIII could also digest the dsDNA structures containing 3'-end ssDNA. Considering most ExoIII-assisted molecular biosensors require the involvement of single-stranded DNA (ssDNA) or nucleic acid aptamer containing ssDNA, the activity will lead to low efficiency or false positive outcome. Our study revealed the multi-enzymatic activity and the underlying molecular mechanism of ExoIII on ssDNA, illuminating novel insights for understanding its biological roles in DNA repair and the rational design of ExoIII-ssDNA involved diagnostics.

Modern approaches to therapeutic oligonucleotide manufacturing

Therapeutic oligonucleotides are a powerful drug modality with the potential to treat many diseases. The rapidly growing number of therapies that have been approved and that are in advanced clinical trials will place unprecedented demands on our capacity to manufacture oligonucleotides at scale. Existing methods based on solid-phase phosphoramidite chemistry are limited by their scalability and sustainability, and new approaches are urgently needed to deliver the multiton quantities of oligonucleotides that are required for therapeutic applications. The chemistry community has risen to the challenge by rethinking strategies for oligonucleotide production. Advances in chemical synthesis, biocatalysis, and process engineering technologies are leading to increasingly efficient and selective routes to oligonucleotide sequences. We review these developments, along with remaining challenges and opportunities for innovations that will allow the sustainable manufacture of diverse oligonucleotide products.

An exonuclease-resistant chain-terminating nucleotide analogue targeting the SARS-CoV-2 replicase complex

Nucleotide analogues (NA) are currently employed for treatment of several viral diseases, including COVID-19. NA prodrugs are intracellularly activated to the 5'-triphosphate form. They are incorporated into the viral RNA by the viral polymerase (SARS-CoV-2 nsp12), terminating or corrupting RNA synthesis. For Coronaviruses, natural resistance to NAs is provided by a viral 3'-to-5' exonuclease heterodimer nsp14/nsp10, which can remove terminal analogues. Here, we show that the replacement of the α-phosphate of Bemnifosbuvir 5'-triphosphate form (AT-9010) by an α-thiophosphate renders it resistant to excision. The resulting α-thiotriphosphate, AT-9052, exists as two epimers (RP/SP). Through co-crystallization and activity assays, we show that the Sp isomer is preferentially used as a substrate by nucleotide diphosphate kinase (NDPK), and by SARS-CoV-2 nsp12, where its incorporation causes immediate chain-termination. The same -Sp isomer, once incorporated by nsp12, is also totally resistant to the excision by nsp10/nsp14 complex. However, unlike AT-9010, AT-9052-RP/SP no longer inhibits the N-terminal nucleotidylation domain of nsp12. We conclude that AT-9052-Sp exhibits a unique mechanism of action against SARS-CoV-2. Moreover, the thio modification provides a general approach to rescue existing NAs whose activity is hampered by coronavirus proofreading capacity.

Stereocontrolled access to thioisosteres of nucleoside di- and triphosphates

Nucleoside diphosphates and triphosphates impact nearly every aspect of biochemistry; however, the use of such compounds as tools or medicinal leads for nucleotide-dependent enzymes and receptors is hampered by their rapid in vivo metabolism. Although a successful strategy to address the instability of the monophosphate moiety in oligonucleotide therapeutics has been accomplished by their isosteric replacement with phosphorothioates, no practical methods exist to rapidly and controllably access stereopure di- and triphosphate thioisosteres of both natural and unnatural nucleosides. Here we show how a modular, reagent-based platform can enable the stereocontrolled and scalable synthesis of a library of such molecules. This operationally simple approach provides access to pure stereoisomers of nucleoside α-thiodiphosphates and α-thiotriphosphates, as well as symmetrical or unsymmetrical dinucleoside thiodiphosphates and thiotriphosphates (including RNA cap reagents). We demonstrate that ligand-receptor interactions can be dramatically influenced by P-stereochemistry, showing that such thioisosteric replacements can have profound effects on the potency and stability of lead candidates.

Exonuclease III Can Efficiently Cleave Linear Single-Stranded DNA: Reshaping Its Experimental Applications in Biosensors

Exonuclease III (Exo III) has been generally used as a double-stranded DNA (dsDNA)-specific exonuclease that does not degrade single-stranded DNA (ssDNA). Here, we demonstrate that Exo III at concentrations above 0.1 unit/μL can efficiently digest linear ssDNA. Moreover, the dsDNA specificity of Exo III is the foundation of many DNA target recycling amplification (TRA) assays. We demonstrate that with 0.3 and 0.5 unit/μL Exo III, the degradation of an ssDNA probe, free or fixed on a solid surface, was not discernibly different, regardless of the presence or absence of target ssDNA, indicating that Exo III concentration is critical in TRA assays. The study has expanded the Exo III substrate scope from dsDNA to both dsDNA and ssDNA, which will reshape its experimental applications.

Interfering with nucleotide excision by the coronavirus 3'-to-5' exoribonuclease

Some of the most efficacious antiviral therapeutics are ribonucleos(t)ide analogs. The presence of a 3'-to-5' proofreading exoribonuclease (ExoN) in coronaviruses diminishes the potency of many ribonucleotide analogs. The ability to interfere with ExoN activity will create new possibilities for control of SARS-CoV-2 infection. ExoN is formed by a 1:1 complex of nsp14 and nsp10 proteins. We have purified and characterized ExoN using a robust, quantitative system that reveals determinants of specificity and efficiency of hydrolysis. Double-stranded RNA is preferred over single-stranded RNA. Nucleotide excision is distributive, with only one or two nucleotides hydrolyzed in a single binding event. The composition of the terminal basepair modulates excision. A stalled SARS-CoV-2 replicase in complex with either correctly or incorrectly terminated products prevents excision, suggesting that a mispaired end is insufficient to displace the replicase. Finally, we have discovered several modifications to the 3'-RNA terminus that interfere with or block ExoN-catalyzed excision. While a 3'-OH facilitates hydrolysis of a nucleotide with a normal ribose configuration, this substituent is not required for a nucleotide with a planar ribose configuration such as that present in the antiviral nucleotide produced by viperin. Design of ExoN-resistant, antiviral ribonucleotides should be feasible.

Interfering with nucleotide excision by the coronavirus 3'-to-5' exoribonuclease

Some of the most efficacious antiviral therapeutics are ribonucleos(t)ide analogs. The presence of a 3'-to-5' proofreading exoribonuclease (ExoN) in coronaviruses diminishes the potency of many ribonucleotide analogs. The ability to interfere with ExoN activity will create new possibilities for control of SARS-CoV-2 infection. ExoN is formed by a 1:1 complex of nsp14 and nsp10 proteins. We have purified and characterized ExoN using a robust, quantitative system that reveals determinants of specificity and efficiency of hydrolysis. Double-stranded RNA is preferred over single-stranded RNA. Nucleotide excision is distributive, with only one or two nucleotides hydrolyzed in a single binding event. The composition of the terminal basepair modulates excision. A stalled SARS-CoV-2 replicase in complex with either correctly or incorrectly terminated products prevents excision, suggesting that a mispaired end is insufficient to displace the replicase. Finally, we have discovered several modifications to the 3'-RNA terminus that interfere with or block ExoN-catalyzed excision. While a 3'-OH facilitates hydrolysis of a nucleotide with a normal ribose configuration, this substituent is not required for a nucleotide with a planar ribose configuration such as that present in the antiviral nucleotide produced by viperin. Design of ExoN-resistant, antiviral ribonucleotides should be feasible.

Recent advances in the exonuclease III-assisted target signal amplification strategy for nucleic acid detection

The detection of nucleic acids has become significantly important in molecular diagnostics, gene therapy, mutation analysis, forensic investigations and biomedical development, and so on. In recent years, exonuclease III (Exo III) as an enzyme in the 3'-5' exonuclease family has evolved as a frequently used technique for signal amplification of low level DNA target detection. Different from the traditional target amplification strategies, the Exo III-assisted amplification strategy has been used for target DNA detection through directly amplifying the amounts of signal reagents. The Exo III-assisted amplification strategy has its unique advantages and characters, because the character of non-specific recognition of Exo III can overcome the limitation of a target-to-probe ratio of 1 : 1 in the traditional nucleic acid hybridization assay and acquire higher sensitivity. In this review, we selectively discuss the recent advances in the Exo III-assisted amplification strategy, including the amplification strategy integrated with nanomaterials, biosensors, hairpin probes and other nucleic acid detection methods. We also discuss the strengths and limitations of each strategy and methods to overcome the limitations.

Towards the enzymatic synthesis of phosphorothioate containing LNA oligonucleotides

Therapeutic oligonucleotides require the addition of multiple chemical modifications to the nucleosidic scaffold in order to improve their drug delivery efficiency, cell penetration capacity, biological stability, and pharmacokinetic properties. This chemical modification pattern is often accompanied by a synthetic burden and by limitations in sequence length. Here, we have synthesized a nucleoside triphosphate analog bearing two simultaneous modifications at the level of the sugar (LNA) and the backbone (thiophosphate) and have tested its compatibility with enzymatic DNA synthesis which could abrogate some of these synthetic limitations. While this novel analog is not as well tolerated by polymerases compared to the corresponding α-thio-dTTP or LNA-TTP, α -thio-LNA-TTP can readily be used for enzymatic synthesis on universal templates for the introduction of phosphorothioated LNA nucleotides.

A hairpin-mediated nicking enzymatic signal amplification for nucleic acids detection

A novel signal amplification to detect nucleic acid, called hairpin-mediated nicking enzymatic signal amplification (HNESA), is developed. This method overcomes the limitation of conventional nicking enzymatic signal amplification (NESA) that the target must contain the nicking endonuclease recognition site by using a hairpin probe containing the nicking endonuclease recognition site as an intermediary. Nucleic acid with any sequence can be amplified by HNESA which substantially improves the substrate-scope of traditional NESA. HNESA could detect nucleic acids (ssDNA and RNA) with a detection limit of 8.3 pM at 55 °C. As low as 68 fM could also be detected by integrating HNESA and strand-displacement amplification (SDA). More importantly, HNESA is quite efficient in distinguish single base mismatched sequences. HNESA has potential application for nucleic acid detection in complex biological samples. Therefore, HNESA with high sensitivity and ultrahigh selectivity, should be a promising tool for nucleic acid research, especially for single nucleotide polymorphism (SNP) detection.

Increasing cell-free gene expression yields from linear templates in Escherichia coli and Vibrio natriegens extracts by using DNA-binding proteins

In crude extract-based cell-free protein synthesis (CFPS), DNA templates are transcribed and translated into functional proteins. Although linear expression templates (LETs) are less laborious and expensive to generate, plasmid templates are often desired over polymerase chain reaction-generated LETs due to increased stability and protection against exonucleases present in the extract of the reaction. Here we demonstrate that addition of a double stranded DNA-binding protein to the CFPS reaction, termed single-chain Cro protein (scCro), achieves terminal protection of LETs. This CroP-LET (scCro-based protection of LET) method effectively increases superfolder green fluorescent protein (sfGFP) expression levels from LETs in Escherichia coli CFPS reactions by sixfold. Our yields are comparable to other strategies that provide chemical and enzymatic DNA stabilization in E. coli CFPS. Notably, we also report that the CroP-LET method successfully enhanced yields in CFPS platforms derived from nonmodel organisms. Our results show that CroP-LET increased sfGFP yields by 18-fold in the Vibrio natriegens CFPS platform. With the fast-expanding applications of CFPS platforms, this method provides a practical and generalizable solution to protect linear expression DNA templates.

Isothermal Nucleic Acid Amplification Techniques and Their Use in Bioanalysis

Recently, there has been a rapid progress in the development of techniques for isothermal amplification of nucleic acids as an alternative to polymerase chain reaction (PCR). The advantage of these methods is that the nucleic acids amplification can be carried out at constant temperature, unlike PCR, which requires cyclic temperature changes. Moreover, isothermal amplification can be conducted directly in living cells. This review describes the principles of isothermal amplification techniques and demonstrates their high efficiency in designing new highly sensitive detection methods of nucleic acids and enzymes involved in their modifications. The data on successful application of isothermal amplification methods for the analysis of cells and biomolecules with the use of DNA/RNA aptamers are presented.

Scalable Nanogap Sensors for Non-Redox Enzyme Assays

Clinical diagnostic assays that monitor redox enzyme activity are widely used in small, low-cost readout devices for point-of-care monitoring (e.g., a glucometer); however, monitoring non-redox enzymes in real-time using compact electronic devices remains a challenge. We address this problem by using a highly scalable nanogap sensor array to observe electrochemical signals generated by a model non-redox enzyme system, the DNA polymerase-catalyzed incorporation of four modified, redox-tagged nucleotides. Using deoxynucleoside triphosphates (dNTPs) tagged with para-aminophenyl monophosphate (pAPP) to form pAP-deoxyribonucleoside tetra-phosphates (AP-dN4Ps), incorporation of the nucleotide analogs by DNA polymerase results in the release of redox inactive pAP-triphosphates (pAPP₃) that are converted to redox active small molecules para-aminophenol (pAP) in the presence of phosphatase. In this work, cyclic enzymatic reactions that generated many copies of pAP at each base incorporation site of a DNA template in combination with the highly confined nature of the planar nanogap transducers ( z = 50 nm) produced electrochemical signals that were amplified up to 100,000×. We observed that the maximum signal level and amplification level were dependent on a combination of factors including the base structure of the incorporated nucleotide analogs, nanogap electrode materials, and electrode surface coating. In addition, electrochemical signal amplification by redox cycling in the nanogap is independent of the in-plane geometry of the transducer, thus allowing the nanogap sensors to be highly scalable. Finally, when the DNA template concentration was constrained, the DNA polymerase assay exhibited different zero-order reaction kinetics for each type of base incorporation reaction, resolving the closely related nucleotide analogs.

A universal DNAzyme-based bioluminescent sensor for label-free detection of biomolecules

We demonstrate for the first time the development of a universal DNAzyme-based bioluminescent sensor for label-free detection of various biomolecules including DNAzyme and DNA. The presence of DNAzyme may induce the cyclic cleavage of riboadenosine (rA)-containing substrates, and the subsequent digestion of the cleaved substrates by exonuclease III (Exo III) releases abundant AMPs to initiate cyclic AMP pyrophosphorylation-ATP depyrophosphorylation for the generation of an enhanced bioluminescence signal. This sensor can real-time monitor the DNAzyme activity with a detection limit of 3.16 × 10^-12 M. Moreover, the DNAzyme may be divided into two subunits for sensitive detection of target DNA. In the presence of target DNA, the two separated subunits may assemble into an active DNAzyme which can catalyze the cyclic cleavage of substrates and initiate the digestion of cleaved substrates by Exo III for the generation of an enhanced bioluminescence signal. This sensor can sensitively detect target DNA with a detection limit of 3.31 × 10^-12 M. Importantly, this bioluminescent sensor can achieve a zero-background signal, and its output signal originates from the release of AMP for the generation of self-illuminating light emission without the requirement of either the external labels or the reporting reagents.

Ultrasensitive aptamer biosensor for arsenic (III) detection based on label-free triple-helix molecular switch and fluorescence sensing platform

Arsenic ion is a well-known harmful heavy element widely existing in the environment. Arsenic pollution occurring frequently has become increasing a serious worldwide threat to human health and the environment. The development of sensitive and reliable methods to detect As³⁺ in water is of great importance to biochemical research and monitoring applications. Herein, a label-free fluorescence sensing platform was elaborately designed for As³⁺ monitoring using exonuclease III (Exo III)-assisted cascade target recycling amplification strategy. The triple-helix molecular switch was employed as the sensing element and 2-amino-5,6,7-trimethyl-1,8-naphthyridine was used as the signal indicator. The resulting biosensor is simple, ultrasensitive, and exhibits a limit of detection of 5 ng/L with high selectivity. Meanwhile, the proposed sensor is successfully applied to determination of As³⁺ in practical sample analysis (tap water, lake water and pond water). The results shown herein have important implications in the development of new fluorescent sensors for the fast, easy, and selective detection and quantification of As³⁺ in water samples. More importantly, the proposed platform can be extended to detect other heavy metal ions with newly designed triple-helix molecular switch, as well as pesticide residue, antibiotic residues, and biomarkers by using aptamer sequences.

Real-time monitoring of small biological molecules by ligation-mediated polymerase chain reaction

We develop a ligation-mediated polymerase chain reaction (PCR) for real-time detection of small biological molecules in a high-throughput format. This method is extremely sensitive with a detection limit of as low as 18.8 fM for ATP and 17.3 fM for NAD(+), and it can discriminate target molecules from their analogues as well.

A label-free double-amplification system for sensitive detection of single-stranded DNA and thrombin by liquid chromatography-mass spectrometry

A label-free double amplification system has been developed by using a ternary DNA probe containing the poly(adenine-thymine) sequence assisted by exonuclease III degradation. The method achieved more than 600-fold signal amplification and allowed sensitive detection of single-stranded DNA and thrombin at the pM level by using liquid chromatography/mass spectrometry.

Exonuclease III-aided autocatalytic DNA biosensing platform for immobilization-free and ultrasensitive electrochemical detection of nucleic acid and protein

Homogenous electrochemical biosensor has attracted substantial attention owing to its simplicity, rapid response, and improved recognition efficiency compared with heterogeneous biosensor, but the relatively low detection sensitivity and the limited detection analytes prohibit its potential applications. To address these issues, herein, a simple, rapid, isothermal, and ultrasensitive homogeneous electrochemical DNA biosensing platform for target DNA and protein detection has been developed on the basis of an exonuclease III (Exo III)-aided autocatalytic target recycling strategy. A ferrocene-labeled hairpin probe (HP1) is ingeniously designed, which contains a protruding DNA fragment at 3'-termini as the recognition unit for target DNA. Also, the DNA fragment that could be used as secondary target analogue was introduced, but it was caged in the stem region of HP1. In the presence of target DNA, its recognition with the protruding fragment of HP1 triggered the Exo III cleavage process, accompanied with the target recycling and autonomous generation of secondary target analogues. This accordingly resulted into the autonomous accumulation of ferrocene-labeled mononucleotide, inducing a distinct increase in the electrochemical signal owing to its elevated diffusivity toward indium tin oxide (ITO) electrode surface. The autocatalytic biosensing system was further extended for protein detection by advising an aptamer hairpin switch with the use of thrombin as a model analyte. The current developed autocatalytic and homogeneous strategy provided an ultrasensitive electrochemical detection of DNA and thrombin down to the 0.1 and 5 pM level, respectively, with a high selectivity. It should be further used as a general autocatalytic and homogeneous strategy toward the detection of a wide spectrum of analytes and may be associated with more analytical techniques. Thus, it holds great potential for the development of ultrasensitive biosensing platform for the applications in bioanalysis, disease diagnostics, and clinical biomedicine.

Homogeneous electrochemical aptamer-based ATP assay with signal amplification by exonuclease III assisted target recycling

A novel and homogeneous electrochemical aptamer-based adenosine triphosphate (ATP) assay was demonstrated with signal amplification by exonuclease III-assisted target recycling. A superior detection limit of 1 nM toward ATP with an excellent selectivity could be achieved.

Endonuclease V-assisted accurate cleavage of oligonucleotide probes controlled by deoxyinosine and deoxynucleoside phosphorothioate for sequencing-by-ligation

Sequencing-by-ligation (SBL) is one of the next-generation sequencing methods for massive parallel sequencing. The ligated probes used in SBL should be accurately cleaved for a better ligation in the next cycle. Here, a novel kind of oligonucleotide probe that could be accurately cleaved at the given position was proposed. Deoxynucleoside phosphorothioates were introduced into the deoxyoxanosine-containing oligonucleotide probes in order to increase the cleavage accuracy of endonuclease V on double-stranded DNA templates. The results illustrated that incorporating deoxynucleoside phosphorothioates could greatly reduce the effect of the nonsynchronous sequencing primer, and the queried bases of the DNA templates were unambiguously identified with 5 cycles of sequencing ligations. Additionally, the read length can reach up to 25 bp with high accuracy. The SBL-based method is inexpensive, has high-throughput, and is easy to operate allowing massive scale-up, miniaturization and automation.

Specific and nonhomologous isofunctional enzymes of the genetic information processing pathways as potential therapeutical targets for tritryps

Leishmania major, Trypanosoma brucei, and Trypanosoma cruzi (Tritryps) are unicellular protozoa that cause leishmaniasis, sleeping sickness and Chagas' disease, respectively. Most drugs against them were discovered through the screening of large numbers of compounds against whole parasites. Nonhomologous isofunctional enzymes (NISEs) may present good opportunities for the identification of new putative drug targets because, though sharing the same enzymatic activity, they possess different three-dimensional structures thus allowing the development of molecules against one or other isoform. From public data of the Tritryps' genomes, we reconstructed the Genetic Information Processing Pathways (GIPPs). We then used AnEnPi to look for the presence of these enzymes between Homo sapiens and Tritryps, as well as specific enzymes of the parasites. We identified three candidates (ECs 3.1.11.2 and 6.1.1.-) in these pathways that may be further studied as new therapeutic targets for drug development against these parasites.

Recognition of an expanded genetic alphabet by type-II restriction endonucleases and their application to analyze polymerase fidelity

To explore the possibility of using restriction enzymes in a synthetic biology based on artificially expanded genetic information systems (AEGIS), 24 type-II restriction endonucleases (REases) were challenged to digest DNA duplexes containing recognition sites where individual Cs and Gs were replaced by the AEGIS nucleotides Z and P [respectively, 6-amino-5-nitro-3-(1'-β-D-2'-deoxyribofuranosyl)-2(1H)-pyridone and 2-amino-8-(1'-β-D-2'-deoxyribofuranosyl)-imidazo[1,2-a]-1,3,5-triazin-4(8H)-one]. These AEGIS nucleotides implement complementary hydrogen bond donor-donor-acceptor and acceptor-acceptor-donor patterns. Results allowed us to classify type-II REases into five groups based on their performance, and to infer some specifics of their interactions with functional groups in the major and minor grooves of the target DNA. For three enzymes among these 24 where crystal structures are available (BcnI, EcoO109I and NotI), these interactions were modeled. Further, we applied a type-II REase to quantitate the fidelity polymerases challenged to maintain in a DNA duplex C:G, T:A and Z:P pairs through repetitive PCR cycles. This work thus adds tools that are able to manipulate this expanded genetic alphabet in vitro, provides some structural insights into the working of restriction enzymes, and offers some preliminary data needed to take the next step in synthetic biology to use an artificial genetic system inside of living bacterial cells.

Non-natural nucleic acids for synthetic biology

Genetic manipulation is an important facet of synthetic biology but can be complicated by undesired nuclease degradation. Incorporating non-natural nucleic acids into a gene could convey resistance to nucleases and promote expression. The compatibility of non-natural nucleosides with polymerases is reviewed with a focus on results from the past two years. Details are provided about how the different systems could be useful in synthetic biology.

[Biochemical methods for the analysis of DNA-protein interactions]

Investigation of DNA-protein interactions is fundamental to understand the mechanism underlying a variety of life processes. In this article, various types of biochemical methods in DNA-protein interaction study in vivo and in vitro at the level of DNA, protein, and the complex, respectively were briefly reviewed. Traditional assays including Nitrocellulose filter-binding assay, Footprinting, EMSA, and Southwestern blotting were summarized. In addition, chromatin immunoprecipitation techniques including nChIP, xChIP, and ChIP-on-chip, which were widely used in epigenetics, were particularly introduced.