Oligodeoxynucleotide Synthesis Under Non-Nucleophilic Deprotection Conditions.

This protocol describes a method for the incorporation of sensitive functional groups into oligodeoxynucleotides (ODNs). The nucleophile-sensitive epigenetic N4-acetyldeoxycytosine (4acC) DNA modification is used as an example, but other sensitive groups can also be incorporated, e.g., alkyl halide, α-haloamide, alkyl ester, aryl ester, thioester, and chloropurine groups, all of which are unstable under the basic and nucleophilic deprotection and cleavage conditions used in standard ODN synthesis methods. The method uses a 1,3-dithian-2-yl-methoxycarbonyl (Dmoc) group that carries a methyl group at the carbon of the methoxy moiety (meDmoc) for the protection of exo-amines of nucleobases. The growing ODN is anchored to a solid support via a Dmoc linker. With these protecting and linking strategies, ODN deprotection and cleavage are achieved without using any strong bases and nucleophiles. Instead, they can be carried out under nearly neutral non-nucleophilic oxidative conditions. To increase the length of ODNs that can be synthesized using the meDmoc method, the protocol also describes the synthesis of a PEGylated Dmoc (pDmoc) phosphoramidite. With some of the nucleotides being incorporated with pDmoc-CE phosphoramidite, the growing ODN on the solid support carries PEG moieties and becomes more soluble, thus enabling longer ODN synthesis. The ODN synthesis method described in this protocol is expected to make many sensitive ODNs that are difficult to synthesize accessible to researchers in multiple areas, such as epigenetics, nanopore sequencing, nucleic acid-protein interactions, antisense drug development, DNA alkylation carcinogenesis, and DNA nanotechnology. © 2024 Wiley Periodicals LLC. Basic Protocol: Sensitive ODN synthesis Support Protocol 1: Synthesis of meDmoc-CE phosphoramidites Support Protocol 2: Synthesis of a pDmoc-CE phosphoramidite.

Exploring the multifaceted effects of Interleukin-1 in lung cancer: From tumor development to immune modulation.

Lung cancer, acknowledged as one of the most fatal cancers globally, faces limited treatment options on an international scale. The success of clinical treatment is impeded by challenges such as late diagnosis, restricted treatment alternatives, relapse, and the emergence of drug resistance. This predicament has led to a saturation point in lung cancer treatment, prompting a rapid shift in focus towards the tumor microenvironment (TME) as a pivotal area in cancer research. Within the TME, Interleukin-1 (IL-1) is abundantly present, originating from immune cells, tissue stromal cells, and tumor cells. IL-1's induction of pro-inflammatory mediators and chemokines establishes an inflammatory milieu influencing tumor occurrence, development, and the interaction between tumors and the host immune system. Notably, IL-1 expression in the TME exhibits characteristics such as staging, tissue specificity, and functional pluripotency. This comprehensive review aims to delve into the impact of IL-1 on lung cancer, encompassing aspects of occurrence, invasion, metastasis, immunosuppression, and immune surveillance. The ultimate goal is to propose a novel treatment approach, considering the intricate dynamics of IL-1 within the TME.

PEGylated Dmoc phosphoramidites for sensitive oligodeoxynucleotide synthesis.

Sensitive oligodeoxynucleotides (ODNs) can be synthesized using Dmoc phosphoramidites, but only short ODNs were demonstrated. Here, we report the synthesis of much longer ODNs, which was made possible by the use of PEGylated Dmoc (pDmoc) phosphoramidites. The longer ODNs synthesized include those containing the sensitive 4acC epigenetic modification recently discovered in nature.

Oligonucleotide synthesis under mild deprotection conditions.

Over a hundred non-canonical nucleotides have been found in DNA and RNA. Many of them are sensitive toward nucleophiles. Because known oligonucleotide synthesis technologies require nucleophilic conditions for deprotection, currently there is no suitable technology for their synthesis. The recently disclosed method regarding the use of 1,3-dithian-2-yl-methyl (Dim) for phosphate protection and 1,3-dithian-2-yl-methoxycarbonyl (Dmoc) for amino protection can solve the problem. With Dim-Dmoc protection, oligodeoxynucleotide (ODN) deprotection can be achieved with NaIO4 followed by aniline. Some sensitive groups have been determined to be stable under these conditions. Besides serving as a base, aniline also serves as a nucleophilic scavenger, which prevents deprotection side products from reacting with ODN. For this reason, excess aniline is needed. Here, we report the use of alkyl Dim (aDim) and alkyl Dmoc (aDmoc) for ODN synthesis. With aDim-aDmoc protection, deprotection is achieved with NaIO4 followed by K2CO3. No nucleophilic scavenger such as aniline is needed. Over 10 ODNs including one containing the highly sensitive N4-acetylcytidine were synthesized. Work on extending the method for sensitive RNA synthesis is in progress.

Effects of Epitranscriptomic RNA Modifications on the Catalytic Activity of the SARS-CoV-2 Replication Complex.

SARS-CoV-2 causes individualized symptoms. Many reasons have been given. We propose that an individual's epitranscriptomic system could be responsible as well. The viral RNA genome can be subject to epitranscriptomic modifications, which can be different for different individuals, and thus epitranscriptomics can affect many events including RNA replication differently. In this context, we studied the effects of modifications including pseudouridine (Ψ), 5-methylcytosine (m5 C), N6-methyladenosine (m6 A), N1-methyladenosine (m1 A) and N3-methylcytosine (m3 C) on the activity of SARS-CoV-2 replication complex (SC2RC). We found that Ψ, m5 C, m6 A and m3 C had little effect, whereas m1 A inhibited the enzyme. Both m1 A and m3 C disrupt canonical base pairing, but they had different effects. The fact that m1 A inhibits SC2RC implies that the modification can be difficult to detect. This fact also implies that individuals with upregulated m1 A including cancer, obesity and diabetes patients might have milder symptoms. However, this contradicts clinical observations. Relevant discussions are provided.

Risk factors for postoperative myasthenia gravis in patients with thymoma without myasthenia gravis: A systematic review and meta-analysis.

Introduction: According to the principle, thymomas combined with myasthenia gravis (MG) require surgical treatment. However, patients with non-MG thymoma rarely develop MG and early- or late-onset MG after surgery is called postoperative MG (PMG). Our study used a meta-analysis to examine the incidence of PMG and risk factors. Methods: Relevant studies were searched for in the PubMed, EMBASE, Web of Science, CNKI,and Wanfang databases. Investigations that directly or indirectly analyzed the risk factors for PMG development in patients with non-MG thymoma were included in this study. Furthermore, risk ratios (RR) with 95% confidence intervals (CI) were pooled using meta-analysis, and fixed-effects or random-effects models were used depending on the heterogeneity of the included studies. Results: Thirteen cohorts containing 2,448 patients that met the inclusion criteria were included. Metaanalysis revealed that the incidence of PMG in preoperative patients with non-MG thymoma was 8%. Preoperative seropositive acetylcholine receptor antibody (AChR-Ab) (RR = 5.53, 95% CI 2.36 - 12.96, P<0.001), open thymectomy (RR =1.84, 95% CI 1.39 - 2.43, P<0.001), non-R0 resection (RR = 1.87, 95% CI 1.36 - 2.54, P<0.001), world health organization (WHO) type B (RR =1.80, 95% CI 1.07 - 3.04, P= 0.028), and postoperative inflammation (RR = 1.63, 95% CI 1.26 - 2.12, P<0.001) were the risk factors for PMG in patients with thymoma. Masaoka stage (P = 0.151) and sex (P = 0.777) were not significantly associated with PMG. Discussion: Patients with thymoma but without MG had a high probability of developing PMG. Although the incidence of PMG was very low, thymectomy could not completely prevent the occurrence of MG. Preoperative seropositive AChR-Ab level, open thymectomy, non-R0 resection, WHO type B, and postoperative inflammation were risk factors for PMG. Systematic Review Registration: https://www.crd.york.ac.uk/PROSPERO/, identifier CRD42022360002.

Long oligodeoxynucleotides: chemical synthesis, isolation via catching-by-polymerization, verification via sequencing, and gene expression demonstration.

Long oligodeoxynucleotides (ODNs) are segments of DNAs having over one hundred nucleotides (nt). They are typically assembled using enzymatic methods such as PCR and ligation from shorter 20 to 60 nt ODNs produced by automated de novo chemical synthesis. While these methods have made many projects in areas such as synthetic biology and protein engineering possible, they have various drawbacks. For example, they cannot produce genes and genomes with long repeats and have difficulty to produce sequences containing stable secondary structures. Here, we report a direct de novo chemical synthesis of 400 nt ODNs, and their isolation from the complex reaction mixture using the catching-by-polymerization (CBP) method. To determine the authenticity of the ODNs, 399 and 401 nt ODNs were synthesized and purified with CBP. The two were joined together using Gibson assembly to give the 800 nt green fluorescent protein (GFP) gene construct. The sequence of the construct was verified via Sanger sequencing. To demonstrate the potential use of the long ODN synthesis method, the GFP gene was expressed in E. coli. The long ODN synthesis and isolation method presented here provides a pathway to the production of genes and genomes containing long repeats or stable secondary structures that cannot be produced or are highly challenging to produce using existing technologies.

The anticancer effects of curcumin and clinical research progress on its effects on esophageal cancer.

Esophageal cancer (EC) is a common tumor of the gastrointestinal system and a major threat to human health. The etiology and incidence of EC vary depending on the type of pathology. Owing to the unique physiological structure of the esophagus and the poor biological behavior of EC, the treatment modalities available are limited, and the prognosis of patients is relatively poor. Curcumin is a type of natural phytochemical belonging to the class of phenolic compounds. It exerts favorable anticancer effects on various cancers. A growing body of evidence indicates that curcumin suppresses tumor development and progression by inhibiting tumor cell proliferation, invasion, and migration, thus inducing apoptosis, regulating microRNA expression, reversing multidrug resistance, and inducing sensitivity to the therapeutic effect of chemoradiotherapy. Multiple cellular molecules, growth factors, and genes encoding proteins participating in different signaling pathways interact with each other to contribute to the complex and orderly anticancer effect. The efficacy and safety of curcumin have been established in preclinical studies for EC and clinical trials for other cancers. However, the low bioavailability of curcumin limits its clinical application. Therefore, the modification of curcumin analogs, the combination of curcumin with other drugs or therapies, and the use of novel nanocarriers have been widely investigated to improve the clinical effects of curcumin in EC.

Determination of optical density (OD) of oligodeoxynucleotide from HPLC peak area.

Oligodeoxynucleotides (ODNs) are typically purified and analysed with HPLC equipped with a UV-Vis detector. Quantities of ODNs are usually determined using a UV-Vis spectrometer separately after HPLC, and are reported as optical density at 260 nm (OD260). Here, we describe a method for direct determination of OD260 of ODNs using the area of the peaks in HPLC profiles. It is expected that the method will save significant time for researchers in the area of nucleic acid research, and minimize the loss of oligonucleotide samples.

Stepwise PEG synthesis featuring deprotection and coupling in one pot.

The stepwise synthesis of monodisperse polyethylene glycols (PEGs) and their derivatives usually involves using an acid-labile protecting group such as DMTr and coupling the two PEG moieties together under basic Williamson ether formation conditions. Using this approach, each elongation of PEG is achieved in three steps - deprotection, deprotonation and coupling - in two pots. Here, we report a more convenient approach for PEG synthesis featuring the use of a base-labile protecting group such as the phenethyl group. Using this approach, each elongation of PEG can be achieved in two steps - deprotection and coupling - in only one pot. The deprotonation step, and the isolation and purification of the intermediate product after deprotection using existing approaches are no longer needed when the one-pot approach is used. Because the stepwise PEG synthesis usually requires multiple PEG elongation cycles, the new PEG synthesis method is expected to significantly lower PEG synthesis cost.

Downregulated Recycling Process but Not De Novo Synthesis of Glutathione Limits Antioxidant Capacity of Erythrocytes in Hypoxia.

Red blood cells (RBCs) are susceptible to sustained free radical damage during circulation, while the changes of antioxidant capacity and regulatory mechanism of RBCs under different oxygen gradients remain unclear. Here, we investigated the changes of oxidative damage and antioxidant capacity of RBCs in different oxygen gradients and identified the underlying mechanisms using an in vitro model of the hypoxanthine/xanthine oxidase (HX/XO) system. In the present study, we reported that the hypoxic RBCs showed much higher oxidative stress injury and lower antioxidant capacity compared with normoxic RBCs. In addition, we found that the disturbance of the recycling process, but not de novo synthesis of glutathione (GSH), accounted for the significantly decreased antioxidant capacity of hypoxic RBCs compared to normoxic RBCs. We further elucidated the underlying molecular mechanism by which oxidative phosphorylation of Band 3 blocked the hexose monophosphate pathway (HMP) and decreased NADPH production aggravating the dysfunction of GSH synthesis in hypoxic RBCs under oxidative conditions.

Linear Oligosulfoxides: Synthesis and Solubility Studies.

Synthesis of three linear oligosulfoxides containing up to six sulfoxide groups was achieved by multiple SN2 reactions between an alkanethiol and alkyl tosylate to give a linear oligosulfide followed by oxidation of the oligosulfide with sodium periodate to give an oligosulfoxide. The challenge of complete avoidance of partial oxidation and over oxidation was easily overcome using the sodium periodate oxidation conditions. Although sulfoxide is a highly polar functional group, the oligosulfoxides were found to have limited solubility in many solvents including DMSO and water, which disobeys the "like dissolves like" rule. The surprising solubility pattern of oligosulfoxides was discussed in the context of the drastically different solubility patterns of polyethylene glycol (PEG), poly(butylene oxide), and poly(methylene oxide). According to a dissolution model, solubility properties of linear oligomers including the oligosulfoxides and PEGs may be heavily affected by their conformations and the suitability of their conformations in water for maximizing attractive interactions between them and water. Based on these hypotheses, the limited solubility of the present oligosulfoxides may not imply the low solubility of similar molecules.

Sensitive Oligodeoxynucleotide Synthesis Using Dim and Dmoc as Protecting Groups.

In traditional oligodeoxynucleotide (ODN) synthesis, phosphate groups are protected with the 2-cyanoethyl group, and amino groups are protected with acyl groups. At the end of ODN synthesis, deprotection is achieved with strong bases and nucleophiles. Therefore, traditional technologies are not suitable for the synthesis of ODNs containing sensitive functionalities. To address the problem, we report the use of Dim and Dmoc groups, which are based on the 1,3-dithian-2-yl-methyl function, for phosphate and amine protection for the solid phase ODN synthesis. Using the new Dim-Dmoc protection, deprotection was achieved under mild oxidative conditions without using any strong bases and nucleophiles. As a result, the new technology is suitable for the synthesis of ODNs containing sensitive functions. To demonstrate feasibility, seven 20-mer ODNs including four that contain sensitive ester and alkyl chloride groups were synthesized, purified with RP HPLC, and characterized with MALDI-TOF MS and enzyme digestion essays. High purity ODNs were obtained.