Phosphorothioate Oligonucleotides Research Articles

Detection of the phosphorothioate oligonucleotide fomivirsen using a ligase detection reaction with polymerase chain reaction.

This study aimed to develop a simple and sensitive detection method for fomivirsen, a 21-nucleotide phosphorothioate oligonucleotide used as a nucleic acid medicine, using a ligase detection reaction. A ligation probe was designed to hybridize with fomivirsen and polymerase chain reaction (PCR) primers, with a deoxyuridine part between the primer binding sites. The probe was ligated to a circular product by Taq DNA ligase, and the resulting product was converted to a linear form through the removal of the uracil base using uracil DNA glycosylase. The linear product was then quantified using real-time PCR. The developed method could detect 0.025-6.4nM of fomivirsen in water and HeLa genomic DNA solutions and 0.6-160nM of fomivirsen in mouse serum in combination with an extraction method based on alkalinization and neutralization. This method could be useful for not only detecting fomivirsen but also other functional oligonucleotides composed of phosphorothioate oligonucleotides. In summary, this study presents a practical and effective approach to the detection of the nucleic acid medicine fomivirsen.

Abstract 3252: Anti-tumor effect of the combination of a lipid nanoparticle suspension of an AKT-1 antisense oligonucleotide (WGI-0301) with tyrosine kinase inhibitors in an orthotopic murine tumor model

Abstract Background: Archexin is a fully phosphorothioated 20-mer antisense oligonucleotide, complementary to AKT-1 mRNA, which leads to the inhibition of translation and the downstream pathway activities of AKT-1 mRNA. WGI-0301 is a proprietary lipid nanoparticle formulation (QTsomeTM) of Archexin designed to enhance delivery. A phase I clinical study of WGI-0301 as monotherapy in patients with advanced solid tumors is currently ongoing in the U.S. Given the limited efficacy of TKIs compared to immunotherapy and growing incidence resistance, WGI-0301 combined with TKIs may augment the therapeutic response to TKIs by enhancing angiogenic blockade, inhibiting AKT-1, and overcome resistance. Methods: The anti-tumor effect of combining WGI-0301 with Lenvatinib/Sorafenib/Cabozantinib was assessed using a Hep3B-Luciferase orthotopic mouse tumor model. We divided sixty-four female Balb/c nude mice into groups (8 mice per group), including vehicle control, WGI-0301 (8 mg/kg), Lenvatinib (10 mg/kg), Sorafenib (20 mg/kg), Cabozantinib (20 mg/kg), WGI-0301+Lenvatinib (8+10 mg/kg), WGI-0301+Sorafenib (8+20 mg/kg), and WGI-0301+Cabozantinib (8+20 mg/kg). We administered treatments via tail vein injection (vehicle/WGI-0301, QW4 weeks) or oral administration (Lenvatinib/Sorafenib/Cabozantinib, QD28 days). We monitored body weight twice weekly and measured tumor burden using bioluminescence with an IVIS (Lumina III) imaging system twice weekly as well. Treatment was suspended between Day 29 and Day 70 for survival observation. Results: The tumor growth inhibition (TGI) rates of the combination of WGI-0301 with Lenvatinib/Sorafenib/Cabozantinib were 66.05%, 86.81%, and 75.89%, respectively. These values were higher than those of the Lenvatinib/Sorafenib/Cabozantinib single drug group with TGI rate of 50.84%, 55.68%, and 47.84%. The tumor bioluminescence signal intensities of the two drugs combination (56.74*108, 22.28*108, and 40.40*108 photon/s) were slightly lower than that of the Lenvatinib/Sorafenib/Cabozantinib single drug group (81.97*108, 73.95*108, and 86.96*108 photon/s). The median survival time was 35.0, 46.0, 55.5, and 51.5 days in the vehicle, WGI-0301+Lenvatinib, WGI-0301+Sorafenib and WGI-0301+Cabozantinib, respectively. The median survival time of Sorafenib, the two-drug combinations were 55.5, 55.5, 58.0, and 53.5 days, which was significantly prolonged compared to the vehicle in the mice bearing the Hep3B-luc orthotopic tumor model. No severe adverse effects were observed in the drug combination groups. Conclusion: The combination of WGI-0301 with TKIs demonstrated superior anti-tumor efficacy over TKI monotherapy in the absence of substantial increase in toxicity. This finding warrants further robust clinical investigation in patients with advanced HCC. Citation Format: Fengyang Xie, Tao Lin, Chao Wang, Jia Wei, Robert J. Lee, Ben Zhao, Yuxin Angela Men. Anti-tumor effect of the combination of a lipid nanoparticle suspension of an AKT-1 antisense oligonucleotide (WGI-0301) with tyrosine kinase inhibitors in an orthotopic murine tumor model [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 3252.

Hydrophilic interaction liquid chromatography with mass spectrometry for the separation and identification of antisense oligonucleotides impurities and nusinersen metabolites

With the development of therapeutic oligonucleotides for antisense and gene therapies, the demand for analytical methods also increases. For the analysis of complex samples, for example plasma samples, where the use of mass detection is essential, hydrophilic interaction liquid chromatography is a suitable choice. The aim of the present work was to develop a method for separation and identification of the oligonucleotide impurities and metabolites by hydrophilic interaction liquid chromatography.First of all, the effects of different chromatographic conditions (e.g. pH of the aqueous part of the mobile phase, buffer concentration, column temperature) on the retention and separation of phosphorothioate oligonucleotides standards on the amide stationary phase were investigated. A set of model oligonucleotides containing a fully modified 21mer and its typical impurities (shortmers and oligonucleotides with different number of thiophosphate modifications) was used. The results showed that the concentration of the salt in the mobile phase as well as its pH, are the most influential parameters with regard to peak shape and separation.The knowledge gained was applied to the analysis of an unpurified 18mer oligonucleotides, analogues of the drug nusinersen used for the treatment of spinal muscular atrophy. The successful separation and identification of twenty-six and twenty-eight impurities was performed with the developed HILIC method. The method was applied to analysis of nusinersen metabolites of serum samples of patients treated with Spinraza.

A robust method using reducing inorganic salts for preventing the desulfurization of phosphorothioate oligonucleotides during the cleavage and deprotection step

The phosphorothioate (PS) linkage has been widely utilized in oligonucleotide therapeutics because it dramatically enhances the nuclease resistance of oligonucleotides. Although PS-modified oligonucleotides are easily synthesized using the phosphoramidite method, they are partially desulfurized during the cleavage and deprotection (C&D) step. The separation and purification of these desulfurized oligonucleotides are quite difficult because they have physical properties similar to those of their intact counterparts. Therefore, the suppression of desulfurization is important for oligonucleotide manufacturing. In this study, we developed a robust C&D method that avoids desulfurization by adding reducing inorganic salts such as NaI and Na2S2O3 to the reaction solutions. This new C&D method has potential application for manufacturing high-quality oligonucleotide therapeutics.

Ion-pair reversed-phase and hydrophilic interaction chromatography methods for analysis of phosphorothioate oligonucleotides

In this study we investigated the separation of a 25 mer fully phosphorothioated oligonucleotide from its truncated n-1 (24 mer) species and selected phosphodiester 25 mer impurities using ion-pair reversed-phase chromatography. The hydrophobicity of ion-pairing agents (alkylamines) impacts n-1 separation selectivity. 25 mer impurities with single and double phosphodiester bonds eluted prior to the parent phosphorothioate oligonucleotide in the same region as 24 mer impurities, which complicated the chromatographic separation. An alternative technique, hydrophilic interaction chromatography, provided a different retention pattern; 24 mer n-1 impurities eluted prior to the 25 mer, while the phosphodiester impurities eluted after the full-length oligonucleotide. This enabled an improved chromatographic separation of the truncated and phosphodiester impurities from the phosphorothioate oligonucleotide of interest.

Characterization of cooperative PS-oligo activation of human TLR9

Single-stranded phosphorothioate oligonucleotides (PS-oligos) can activate TLR9, leading to an innate immune response. This can occur with PS-oligos containing unmethylated CpG sites, the canonical motif, or PS-oligos that do not contain those motifs (non-CpG). Structural evidence shows that TLR9 contains two PS-oligo binding sites, and recent data suggest that synergistic cooperative activation of TLR9 can be achieved by adding two separate PS-oligos to cells, each engaging with a separate site on TLR9 to enhance TLR9 activation as a pair. Here, we demonstrate and characterize this cooperativity phenomenon using PS-oligos in human cell lines, and we introduce several novel PS-oligo pairs (CpG and non-CpG pairs) that show cooperative activation. Indeed, we find that cooperative PS-oligos likely bind at different sites on TLR9. Interestingly, we find that PS-oligos that generate little TLR9 activation on their own can prime TLR9 to be activated by other PS-oligos. Finally, we determine that previous models of TLR9 activation cannot be used to fully explain data from systems using human TLR9 and PS-oligos. Overall, we reveal new details of TLR9 activation, but we also find that more work needs to be done to determine where certain PS-oligos are binding to TLR9.

Stereo-Controlled Liquid Phase Synthesis of Phosphorothioate Oligonucleotides on a Soluble Support.

5'-O-(2-Methoxyisopropyl) (MIP)-protected 2'-deoxynucleosides as chiral P(V)-building blocks, based on the limonene-derived oxathiaphospholane sulfide, were synthesized and used for the assembly of di-, tri-, and tetranucleotide phosphorothioates on a tetrapodal pentaerythritol-derived soluble support. The synthesis cycle consisted of two reactions and two precipitations: (1) the coupling under basic conditions, followed by neutralization and precipitation and (2) an acid catalyzed 5'-O-deacetalization, followed by neutralization and precipitation. The simple P(V) chemistry together with the facile 5'-O-MIP deprotection proved efficient in the liquid phase oligonucleotide synthesis (LPOS). Ammonolysis released nearly homogeneous Rp or Sp phosphorothioate diastereomers in ca. 80% yield/synthesis cycle.

Inhibitory Effect of Phosphorothioate Oligonucleotide Complementary to G6PD mRNA on Murine Melanoma.

In terms of the incidence among all tumors, skin cancer is on top, with the most deadly among them being melanoma. The search for new therapeutic agents to combat melanoma is very relevant. In our opinion, antisense oligonucleotides (ASO) aimed at suppressing the genes responsible for their viability in cancer cells give hope for treatment, which makes it possible to eliminate cancer cells near the tumor site both before and after surgery. In this article, we describe how Skeen-11 phosphorothioate oligonucleotide significantly decreased the proliferative activity of murine melanoma cells. Injections of Skeen-11 also inhibited tumor growth in mice with inoculated melanoma. A toxicity study showed no side effects with dose adjustments. The results show that the use of ASO Skeen-11 in vivo reduced the tumor size within 7 days, reduced the number of mitoses in the tumor cells, and increased the amount of necrosis compared with the control group.

Abstract 701: Evaluation of an AKT-1 antisense oligonucleotide in combination with Lenvatinib and Everolimus in Renca-luciferase syngeneic orthotopic murine tumor model

Abstract Background: The combination of 18mg Lenvatinib and 5mg Everolimus per day is used in the clinic for advanced renal cancer patients. However, due to the severe side effects of Lenvatinib, the dose is often reduced to 12mg. Archexin, a fully phosphorothioated 20-mer antisense oligonucleotide, inhibits AKT-1 mRNA translation and inhibits tumor growth. Combination of Archexin with reduced-dosed Lenvatinib and Everolimus may reduce adverse reactions while enhancing therapeutic efficacy. Methods: First, Lenvatinib and Everolimus monotherapies were evaluated for antitumor efficacy in an orthotopic Renca-luciferase syngeneic model. 45 mice were randomly divided into 9 groups (5 in each group), vehicle control, Lenvatinib (5, 10, 20, and 30 mg/kg) and Everolimus (0.2, 0.5, 1, 2, and 4 mg/kg) via daily oral administration for 20 days. Next, we investigated the anti-tumor effect of the two- and three-drug combination. 35 mice were randomly divided into 7 groups (5 in each group), including vehicle control, Lenvatinib/Everolimus combinations (5+0.2, 10+0.2 and 10+0.5 mg/kg) and Archexin/Lenvatinib/Everolimus combinations (60+5+0.2, 60+10+0.2 and 60+10+0.5 mg/kg) via tail vein injection (vehicle/Archexin, Q3D*6 times) or oral administration (Lenvatinib and Everolimus, QD*18 days). Body weight was monitored daily. Tumor burden was measured by bioluminescence through whole-body fluorescence images, performed twice a week. Results: The results showed that Everolimus inhibited tumor growth in a dose-dependent manner. Partial response was observed in mice treated with varying doses of Lenvatinib(TGIs: 57.94%,76.65% and 60.22%), and no significant dose-effect correlation was found. The dose of Lenvatinib and Everolimus that partially inhibited the orthotopic tumor growth had also been identified and selected for subsequent study investigating drug combinations. The drugs combination study showed that three drug combinations (Archexin/Lenvatinib/Everolimus) had superior efficacy compared to the Lenvatinib and Everolimus combination. The fluorescence signal intensities (Lg10) of the three-drug combination were significantly lower than that of the two-drug combination group with P value <0.05. No severe adverse effects were observed in the three drug combinations group. Conclusion: Three drugs combination of Archexin, Lenvatinib and Everolimus, demonstrated superior anti-tumor efficacy compared to the two-drug combination currently used in the clinic. This finding suggests the three-drug combination warrant investigation in the clinical trial in the patients with advanced renal cancer. Citation Format: Fengyang Xie, Jia Wei, Lan Deng, Chao Wang, Ben Zhao, Robert J. Lee, Yuxin Angela Men. Evaluation of an AKT-1 antisense oligonucleotide in combination with Lenvatinib and Everolimus in Renca-luciferase syngeneic orthotopic murine tumor model [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 701.

Establishing stereochemical comparability in phosphorothioate oligonucleotides with nuclease P1 digestion coupled with LCMS analysis.

Stereochemical comparability is critical for ensuring manufacturing consistency in therapeutic phosphorothioate oligonucleotides. Currently, analytical methods for this assessment are limited. We hereby report on a novel protocol capable of detecting a stereochemistry change in a single phosphorothioate linkage by employing nuclease P1 digestion of the oligonucleotide with subsequent LCMS analysis of the resulting fragments. The method proves valuable for establishing stereochemical comparability and for ensuring manufacturing consistency of oligonucleotide therapeutics.

A simple and green solid phase extraction method for oligonucleotides using adsorbent with amino and carboxylic moieties

The study aimed to use a material with amino and carboxylic moieties to extract unmodified and phosphorothioate oligonucleotides. The charge of amine and carboxyl groups at the surface has changed with the change in pH of the adsorption (pH 4.5) and desorption solution (pH 9.5). Thus, both the binding and elution of the oligonucleotides were based on electrostatic interactions, and the procedure required only 10 mM ammonium acetate, with the change of pH depending on the extraction step. The developed procedure was successfully applied to extract oligonucleotides from aqueous solutions and serum samples. The method is simple and fast, providing good reproducibility (SD between 1 and 4%) and relatively high oligonucleotide recovery (81–98% for standards, 60–71% for diluted serum samples, and 80–92 for LLE serum extracts). Moreover, only environmentally friendly solvents were used.

Potential of RH5 Antisense on Plasmodium falciparum Proliferation Abatement.

Infections by Plasmodium falciparum, are becoming increasingly difficult to treat. Therefore, there is an urgent need for novel antimalarial agents' discovery against infection. In present study, we described a 2'-O-Methyl gapmer phosphorothioate oligonucleotide antisense targeting translation initiation region of 3D7 strain RH5 gene. The study was conducted in Pasteur Institute of Iran in 2020. ODNs effects were measured by microscopic examination and real time RT-PCR. For microscopy, microplates were charged with 2'-OMe ODNs at different dilutions. Unsynchronized parasites were added to a total of 0.4 ml (0.4% parasitemia, 5% red blood cells), and slides were prepared. Proportion of infected cells was measured by counting at least 500 red blood cells. RH5 genes start codon regions selected as conserved region besed on alignment results. Gap-RH5-As which was complementary to sequence surrounding AUG RH5 start codon significantly reduced parasite growth (>90% at 50 nM) compared to sense sequence control (Gap-RH5-Se) (17%), (P<0.001). RH5 transcripts were dramatically reduced after exposed to ODNs at a concentration of 5-500 nM for 48 h. Gemnosis delivery of a chimeric gapmer PS-ODN with 2'-OMe modifications at both sides had high antisense activity at low concentrations (10-100 nM) and shown a good efficiency to reach to target mRNA in human RBCs. Anti-parasite effect was correlated to reduction of target gene mRNA level. In addition, 2'-OMe ODNs free delivery is an effective way and does not need any carrier molecules or particles.

Kinetics of DNA strand transfer between polymerase and proofreading exonuclease active sites regulates error correction during high-fidelity replication

We show that T7 DNA polymerase (pol) and exonuclease (exo) domains contribute to selective error correction during DNA replication by regulating bidirectional strand transfer between the two active sites. To explore the kinetic basis for selective removal of mismatches, we used a fluorescent cytosine analog (1,3-diaza-2-oxophenoxazine) to monitor the kinetics of DNA transfer between the exo and pol sites. We globally fit stopped-flow fluorescence and base excision kinetic data and compared results obtained with ssDNA versus duplex DNA to resolve how DNA transfer governs exo specificity. We performed parallel studies using hydrolysis-resistant phosphorothioate oligonucleotides to monitor DNA transfer to the exo site without hydrolysis. ssDNA binds to the exo site at the diffusion limit (109M-1 s-1, Kd = 40 nM) followed by fast hydrolysis of the 3'-terminal nucleotide (>5000s-1). Analysis using duplex DNA with a 3'-terminal mismatch or a buried mismatch exposed a unique intermediate state between pol and exo active sites and revealed that transfer via the intermediate to the exo site is stimulated by free nucleoside triphosphates. Transfer from the exo site back to the pol site after cleavage is fast and efficient. We propose a model to explain why buried mismatches are removed faster than single 3'-terminal mismatches and thereby provide an additional opportunity for error correction. Our data provide the first comprehensive model to explain how DNA transfer from pol to exo active sites and back again after base excision allow efficient selective mismatch removal during DNA replication to improve fidelity by more than 1000-fold.

Separation of phosphorothioate oligonucleotide impurities by WAX HPLC under high organic content elution conditions

The separation of impurities in phosphorothioate diester (PS) oligonucleotides is complicated by (1) the presence of a very large number of diastereoisomers, e.g., 219 for a 20-mer oligonucleotide, (2) peak broadening due to the hydrophobic character of the sulfur atom, and (3) the chemical similarity of the impurities to the parent oligonucleotide and each other. Further difficulties arise due to the chemical nature of oligonucleotides, which display a complex mixture of ionic, hydrophobic, H-bonding, and other functionalities. To minimize hydrophobic interactions and peak broadening due to the PS modification, we have developed a novel method that combines a weak anion exchange (WAX) column with a mobile phase elution system designed to maximize separation by a single ionic/electrostatic interaction. We found that although chaotropes are helpful, the most significant beneficial effect of the hydrophilic WAX column is that high-organic, low-salt mobile phase is required for product elution. Separations are also benefitted by pH gradient effects on stationary phase electrostatic potential and analyte ionization. An extraordinary degree of separation is achieved by the new WAX method in comparison to SAX (strong anion exchange) chromatography. For the first time, the extent of deamination of PS oligonucleotides is directly determined by a chromatography-only method. The approach, representative results, and the mechanisms of separation are discussed.

Structures of annexin A2-PS DNA complexes show dominance of hydrophobic interactions in phosphorothioate binding.

The introduction of phosphorothioate (PS) linkages to the backbone of therapeutic nucleic acids substantially increases their stability and potency. It also affects their interactions with cellular proteins, but the molecular mechanisms that underlie this effect are poorly understood. Here, we report structural and biochemical studies of interactions between annexin A2, a protein that does not possess any known canonical DNA binding domains, and phosphorothioate-modified antisense oligonucleotides. We show that a unique mode of hydrophobic interactions between a sulfur atom of the phosphorothioate group and lysine and arginine residues account for the enhanced affinity of modified nucleic acid for the protein. Our results demonstrate that this mechanism of interaction is observed not only for nucleic acid-binding proteins but can also account for the association of PS oligonucleotides with other proteins. Using the anomalous diffraction of sulfur, we showed that preference for phosphorothioate stereoisomers is determined by the hydrophobic environment around the PS linkage that comes not only from protein but also from additional structural features within the ASO such as 5-Me groups on cytosine nucleobases.

Phosphorothioate oligonucleotides separation in ion-pairing reversed-phase liquid chromatography: effect of temperature

Analysis of diastereomers of phosphorothioate oligonucleotides in ion-pairing reversed-phase liquid chromatography is affected not only by the character and concentration of ion-pairing system, but also by the separation temperature. In this work, eight ion-pairing systems at two concentrations buffered with acetic acid were used with octadecyl column to investigate the effects of temperature (in the range from 20 °C to 90 °C) on retention, diastereomeric separation, resolution of mers of different length and resolution of oligonucleotides with different number of phosphorothioate linkages. It was observed that elevated temperature suppresses the diastereomeric separation and oligonucleotide peaks become narrower. This improves the resolution of n and n-1 mers at elevated temperature. Plots of ln k (k = retention factor) versus reciprocal absolute temperature show that for 100 mM ion-pairing systems the increase in temperature does not lead to simple decrease in oligonucleotides retention as generally observed in reversed-phase liquid chromatography. The aim of this work is to improve chromatographic method for analysis of phosphorothioate oligonucleotides.

NAT10 and DDX21 Proteins Interact with RNase H1 and Affect the Performance of Phosphorothioate Oligonucleotides.

RNase H1-dependent phosphorothioate oligonucleotides (PS-ASOs) have been developed to treat various diseases through specific degradation of target RNAs. Although many factors or features of RNA and PS-ASOs have been demonstrated to affect antisense activity of PS-ASOs, little is known regarding the roles of RNase H1-associated proteins in PS-ASO performance. In this study, we report that two nucleolar proteins, NAT10 and DDX21, interact with RNase H1 and affect the potency and safety of PS-ASOs. The interactions of these two proteins with RNase H1 were determined using BioID proximity labeling in cells and confirmed biochemically. Reduction of NAT10 and DDX21 decreased PS-ASO activity in cells, and purified NAT10 and DDX21 proteins enhanced RNase H1 cleavage rates, indicating that these two proteins facilitate RNase H1 endoribonuclease activity. Consistently, reduction of these proteins increased the levels of R-loops, and impaired pre-rRNA processing. In addition, reduction of the two proteins increased the cytotoxicity of toxic PS-ASOs, and treatment of toxic PS-ASOs also altered the localization of these proteins. Together, this study shows for the first time that NAT10 and DDX21 interact with RNase H1 protein and enhance its enzymatic activity, contributing to the potency and safety of PS-ASOs.

Improvement of chemo- and stereoselectivity for phosphorothioate oligonucleotides in capillary electrophoresis by addition of cyclodextrins

Phosphorothioate (PS) modification is one of the most widely used oligonucleotide chemical alterations in the oligonucleotide backbone. It has proven to be crucial in the field of therapeutic oligonucleotides regarding the optimization of their physicochemical and biological properties. In this study, a capillary electrophoresis (CE) method with an acidic background electrolyte (BGE) containing a combination of β- and γ-cyclodextrins derivatives as chiral selectors is proposed for the diastereomeric separation of 5-mer oligonucleotides containing 0, 1, 2, or 3 phosphorothioate linkages (5´-TCGTG-3´). The effects of the BGE pH, organic modifier addition, and type of cyclodextrin (CD) on chemo- and stereoselectivity and resolution were studied. A mixture of 25 mM (2-hydroxy-3-N,N,N-trimethylamino)propyl-γ-CD and 10 mM carboxymethyl-β-cyclodextrin in a pH 3 buffer was found to be the most appropriate system for the qualitative evaluation of the short oligonucleotides investigated. These phosphorothioate oligonucleotides were separated with high efficiency in less than 11 min with no capillary treatment. The suggested approach can be the basis for purity testing of this new generation of therapeutics.

Phosphorothioate oligonucleotides separation in ion-pairing reversed-phase liquid chromatography: Effect of ion-pairing system

Ion-pairing reversed-phase liquid chromatography was utilized for the analysis of native and phosphorothioate oligonucleotides of the identical sequence but different amount and position of phosphorothioate modifications. The effects of ion-pairing amines nature (alkyl chain length, hydrophobicity) and concentration on retention, n/n-1 resolution, and diastereomeric separation of phosphorothioate oligonucleotides were investigated using octadecyl column. Eight different ion-pairing agents at two concentrations (10 mM and 100 mM) buffered with acetic acid were investigated. The resolution of n and n-1 mers oligonucleotides improved with hydrophobicity and concentration of ion-pairing amines. Ion-pairing amines with moderate hydrophobicity were most successful in suppressing diastereomeric resolution. However, a partial separation of phosphorothioate oligonucleotide diastereomers was observed with all ion-pairing systems, which resulted in wider peaks compared to phosphorodiester oligonucleotides of the same sequence. This phenomenon complicates the n and n-1 mers separation of oligonucleotides with high degree of phosphorothioate modifications. Separation of oligonucleotides with different number of phosphorothioate modifications was observed, which may be useful for therapeutic oligonucleotide analysis. The aim of the work was to identify the ion-pairing systems useful for chromatographic characterization of phosphorothioate oligonucleotides.

Developing predictive hybridization models for phosphorothioate oligonucleotides using high-resolution melting.

The ability to predict nucleic acid hybridization energies has been greatly enabling for many applications, but predictive models require painstaking experimentation, which may limit expansion to non-natural nucleic acid analogues and chemistries. We have assessed the utility of dye-based, high-resolution melting (HRM) as an alternative to UV-Vis determinations of hyperchromicity in order to more quickly acquire parameters for duplex stability prediction. The HRM-derived model for phosphodiester (PO) DNA can make comparable predictions to previously established models. Using HRM, it proved possible to develop predictive models for DNA duplexes containing phosphorothioate (PS) linkages, and we found that hybridization stability could be predicted as a function of sequence and backbone composition for a variety of duplexes, including PS:PS, PS:PO, and partially modified backbones. Individual phosphorothioate modifications destabilize helices by around 0.12 kcal/mol on average. Finally, we applied these models to the design of a catalytic hairpin assembly circuit, an enzyme-free amplification method used for nucleic acid-based molecular detection. Changes in PS circuit behavior were consistent with model predictions, further supporting the addition of HRM modeling and parameters for PS oligonucleotides to the rational design of nucleic acid hybridization.