Role Of Nucleic Acids Research Articles

The amount of DNA and RNA in primary cancer cells and their metastases

Considering the significant impact of oncopathology on global morbidity and mortality, as well as changes in its prevalence and typology, research into the molecular-genetic mechanisms of oncogenesis and metastasis, particularly the role of nucleic acids, becomes crucial. The aim of this study is to determine the content of DNA and RNA in cells of primary cancer and its metastases through microspectrophotometric analysis of malignant cells collected from 30 patients with primary and metastatic oncological processes. The following methods were employed: microspectrophotometric analysis using the automated complex “Protva-PM11-DVK-3m,” staining of histological specimens with halo cyanin-chrome alum, the discrete statistics method, frequency and cluster analysis, and the bibliographic method. Changes in the concentration of nucleic acids in the cells of primary and metastatic tumors were identified during the study. The changes did not always correlate with each other, indicating morphofunctional polymorphism in tumor cell populations. A trend towards a decrease in nuclear RNA concentration and an increase in cytoplasmic RNA concentration in metastases were observed, suggesting alterations in metabolic and synthetic processes in cells and a decrease in their differentiation degree.

Roles of Nucleic Acids in Protein Folding, Aggregation, and Disease.

The role of nucleic acids in protein folding and aggregation is an area of continued research, with relevance to understanding both basic biological processes and disease. In this review, we provide an overview of the trajectory of research on both nucleic acids as chaperones and their roles in several protein misfolding diseases. We highlight key questions that remain on the biophysical and biochemical specifics of how nucleic acids have large effects on multiple proteins' folding and aggregation behavior and how this pertains to multiple protein misfolding diseases.

Structural characterization and functional insights into the type II secretion system of the poly-extremophile Deinococcus radiodurans

The extremophile bacterium D. radiodurans boasts a distinctive cell envelope characterized by the regular arrangement of three protein complexes. Among these, the Type II Secretion System (T2SS) stands out as a pivotal structural component. We used cryo-electron microscopy to reveal unique features, such as an unconventional protein belt (DR_1364) around the main secretin (GspD), and a cap (DR_0940) found to be a separated subunit rather than integrated with GspD. Furthermore, a novel region at the N-terminus of the GspD constitutes an additional second gate, supplementing the one typically found in the outer membrane region. This T2SS was found to contribute to envelope integrity, while also playing a role in nucleic acid and nutrient trafficking. Studies on intact cell envelopes show a consistent T2SS structure repetition, highlighting its significance within the cellular framework.

Immunomodulation with Nucleic Acid Nanodevices.

The precise regulation of interactions of specific immunological components is crucial for controllable immunomodulation, yet it remains a great challenge. With the assistance of advanced computer design, programmable nucleic acid nanotechnology enables the customization of synthetic nucleic acid nanodevices with unprecedented geometrical and functional precision, which have shown promising potential for precise immunoengineering. Notably, the inherently immunologic functions of nucleic acids endow these nucleic acid-based assemblies with innate advantages in immunomodulatory engagement. In this review, the roles of nucleic acids in innate immunity are discussed, focusing on the definition, immunologic modularity, and enhanced bioavailability of structural nucleic acid nanodevices. In light of this, molecular programming and precise organization of functional modules with nucleic acid nanodevices for immunomodulation are emphatically reviewed. At last, the present challenges and future perspectives of nucleic acid nanodevices for immunomodulation are discussed.

Biointerface Engineering with Nucleic Acid Materials for Biosensing Applications

AbstractMolecular recognition at the biointerface plays a critical role in sensing molecular interactions (e.g., DNA hybridization) and extracellular changes, which can directly affect the detection performance of biosensors (e.g., sensitivity, specificity, and response dynamics). However, conventional sensing biointerfaces show low molecular recognition efficiency due to limited target accessibility. Engineering sensing biointerfaces to regulate the orientation, spacing, and density of surface‐confined molecular probes offer an effective approach to improve molecular recognition at interfaces. Over the last decades, biointerface engineering with nucleic acid materials has advanced the fundamental understanding of DNA hybridization kinetics and facilitated the design of improved biosensing platforms for monitoring cellular activities and diagnosing relevant diseases. This review summarizes the recent progress in nucleic acid‐based biointerface engineering. The development of nucleic acid materials that can be applied to specific diagnostic applications is briefly introduced. Then the roles of nucleic acids in tailoring the properties of nanosurfaces, cell surfaces, and macroscopic surfaces are discussed and their biosensing applications are comprehensively highlighted. Finally, future challenges and perspectives of emerging technologies and applications in the field are presented.

Effect of supplemental dietary zinc on the growth, body composition and anti-oxidant enzymes of coho salmon (Oncorhynchus kisutch) alevins

Zinc (Zn) is a trace element in the animal body, which plays a vital regulatory role in nucleic acid, protein synthesis and anti-oxidative enzymes activities. Therefore, this study was designed to elucidate the role of dietary Zn on growth performance, whole body and vertebral Zn concentrations, the total hepatic anti-oxidative enzymes and alkaline phosphatase (AKP) activities in coho salmon (Oncorhynchus kisutch) alevins. Triplicate groups of alevins (initial body weight: 0.38 ± 0.02 g) were fed dietary treatments containing 13.4, 28.6, 38.5, 44.3, 56.6 and 65.7 mg/kg Zn level, respectively for 12 weeks. Fish were held in 18 tanks (80cm × 60cm × 60 cm, water volume 240-L, 100 fish/tank). At the ending of experiment, the sampling procedure was implemented after 24 h of fasting. The results showed that dietary Zn treatment higher than 44.3 mg/kg significantly increased the specific growth rate (SGR) (P < .05). Zn concentrations in whole-body and vertebrae were increased as dietary Zn concentrations increased from 38.5–65.7 mg/kg (P < 0.01), compared to dietary Zn contents 13.4 and 28.6 mg/kg. The hepatic superoxide dismutase (T-SOD), catalase (CAT) and AKP enzymes activities were increased, however, malondialdehyde (MDA) enzyme activity was decreased as dietary Zn concentrations increased from 28.6–65.7 mg/kg (P < .01). There were no significant differences (P > .05) in whole-body moisture, crude protein, crude lipid and ash in all the dietary treatments. These results indicated proper dietary Zn supplementation improved SGR and anti-oxidative enzyme activities. Based on the results analysis of SGR, Zn contents in whole-body and vertebrate and liver T-SOD and AKP activities, the optimal dietary Zn levels for coho salmon alevins were estimated to be 54.0, 59.3, 54.5, 59.8 and 53.8 mg/kg, respectively.

DNA Facilitates Oligomerization and Prevents Aggregation via DNA Networks

Previous studies have shown that nucleic acids can nucleate protein aggregation in disease-related proteins, but in other cases, they can act as molecular chaperones that prevent protein aggregation, even under extreme conditions. In this study, we describe the link between these two behaviors through a combination of electron microscopy and aggregation kinetics. We find that two different proteins become soluble under harsh conditions through oligomerization with DNA. These DNA/protein oligomers form “networks,” which increase the speed of oligomerization. The cases of DNA both increasing and preventing protein aggregation are observed to stem from this enhanced oligomerization. This observation raises interesting questions about the role of nucleic acids in aggregate formation in disease states.

Liquid-liquid phase separation and fibrillation of the prion protein modulated by a high-affinity DNA aptamer.

Structural conversion of cellular prion protein (PrPC) into scrapie PrP (PrPSc) and subsequent aggregation are key events associated with the onset of transmissible spongiform encephalopathies (TSEs). Experimental evidence supports the role of nucleic acids (NAs) in assisting this conversion. Here, we asked whether PrP undergoes liquid-liquid phase separation (LLPS) and if this process is modulated by NAs. To this end, two 25-mer DNA aptamers, A1 and A2, were selected against the globular domain of recombinant murine PrP (rPrP90-231) using SELEX methodology. Multiparametric structural analysis of these aptamers revealed that A1 adopts a hairpin conformation. Aptamer binding caused partial unfolding of rPrP90-231 and modulated its ability to undergo LLPS and fibrillate. In fact, although free rPrP90-231 phase separated into large droplets, aptamer binding increased the number of droplets but noticeably reduced their size. Strikingly, a modified A1 aptamer that does not adopt a hairpin structure induced formation of amyloid fibrils on the surface of the droplets. We show here that PrP undergoes LLPS, and that the PrP interaction with NAs modulates phase separation and promotes PrP fibrillation in a NA structure and concentration-dependent manner. These results shed new light on the roles of NAs in PrP misfolding and TSEs.

ATR Inhibition Potentiates the Radiation-induced Inflammatory Tumor Microenvironment.

ATR inhibitors (ATRi) are in early phase clinical trials and have been shown to sensitize to chemotherapy and radiotherapy preclinically. Limited data have been published about the effect of these drugs on the tumor microenvironment.Experimental Design: We used an immunocompetent mouse model of HPV-driven malignancies to investigate the ATR inhibitor AZD6738 in combination with fractionated radiation (RT). Gene expression analysis and flow cytometry were performed posttherapy. Significant radiosensitization to RT by ATRi was observed alongside a marked increase in immune cell infiltration. We identified increased numbers of CD3+ and NK cells, but most of this infiltrate was composed of myeloid cells. ATRi plus radiation produced a gene expression signature matching a type I/II IFN response, with upregulation of genes playing a role in nucleic acid sensing. Increased MHC I levels were observed on tumor cells, with transcript-level data indicating increased antigen processing and presentation within the tumor. Significant modulation of cytokine gene expression (particularly CCL2, CCL5, and CXCL10) was found in vivo, with in vitro data indicating CCL3, CCL5, and CXCL10 are produced from tumor cells after ATRi + RT. We show that DNA damage by ATRi and RT leads to an IFN response through activation of nucleic acid-sensing pathways. This triggers increased antigen presentation and innate immune cell infiltration. Further understanding of the effect of this combination on the immune response may allow modulation of these effects to maximize tumor control through antitumor immunity.

Pattern Recognition Receptors and Control of Innate Immunity: Role of Nucleic Acids.

The innate immune system protects against infectious microbes by the recognition of pathogen- associated molecular patterns, which serve to detect pathogens on the host cell surface or in endosomes by pattern recognition receptors such as Toll-like receptors, nucleotide-binding oligomerization domain-containing protein-1-like receptors, mannose-receptor, or retinoic acid-inducible gene-1- like receptors that initiate proper host defense mechanisms. In addition to pathogen-associated molecular patterns, a series of endogenous danger-associated molecular patterns, such as nucleic acids, are recognized by pattern recognition receptors, which serve as body´s own alarm signals under sterile conditions, such as ischemic injuries, trauma, tumors, tissue transplants, or autoimmune diseases. Thus, exogenous as well as endogenous nucleic acids can function as "alarmins" to alert the body about danger or disease by triggering inflammation, dendritic cell maturation, and stimulate the immune response resulting in the release of cytokines, which in turn can augment the local inflammatory environment. Moreover, danger-associated molecular patterns such as nucleic acids can act as cofactor in the activation of pattern recognition receptors in situations of cellular stress or upon infection leading to a massive amplification of the inflammatory response. As a consequence, acute and also chronic inflammatory diseases such as rheumatoid arthritis, cancer, or atherosclerosis may depend on such perpetuated proinflammatory responses involving activities of nucleic acids. As antagonists, RNase1 or DNase administration or nucleic acid complexing agents may result in a significant blockade of the outcome of particular pathological situations and in considerable tissue protection.

Further the liquid biopsy: Gathering pieces of the puzzle of genometastasis theory

Metastasis is the major cause of mortality in cancer disease and still constitutes one of the most controversial mechanism, not yet fully understood. What is almost beyond doubt is that circulatory system is crucial for cancer propagation. Regarding this system, much attention has been recently paid to liquid biopsy. This technique is aimed to detect circulating tumor cells (CTCs) and circulating nucleic acids so it can be used as a tool for diagnostic, prognostic and follow-up of patients. Whereas CTCs tend to be scarce in serum and plasma from cancer patient, abundant circulating nucleic acids can be detected in the same location. This fact, together with the genetic origin of cancer, stands out the relevance of circulating nucleic acids and shed light into the role of nucleic acids as drivers of metastasis, a recently discovered phenomenon called Genometastasis. This innovative theory supports the transfer of oncogenes from cancer cells to normal and susceptible cells located in distant target organs through circulatory system. What is more, many biological processes haven been described to deliver and secrete circulating nucleic acids into the circulation which can allow such horizontal transfer of oncogenes. In this review, we focus not only on these mechanisms but also we demonstrate its putative role in cancer propagation and give insights about possible therapeutic strategies based on this theory. Our objective is to demonstrate how findings about cell-to-cell communications and previous results can agree with this unprecedented theory.

Identification of nucleases related to nutrient mobilization in senescing cotyledons from French bean

The knowledge about the physiological function of plant nucleases is scarce besides that they have been involved in nucleic acid degradation related with programmed cell death processes. Cotyledons provide a suitable system to investigate this process and the changes associated to nutrient mobilization. Nuclease activities have been determined in French bean seedlings. The total nuclease activity in French bean cotyledons is lower than in embryonic axes; however, several nucleases were detected by in-gel nuclease activity assays with extracts from cotyledons of French bean and ssDNA as substrate. The nuclease activities induced during cotyledon senescence showed higher activity at neutral than at acidic pH. Five different nuclease genes belonging to S1/P1 family have been identified in French bean genome database named PVN1 to PVN5. Their relative expression in cotyledons has been determined from the start of imbibition to senescence, and three genes from this family showed expression in cotyledons. PVN1 was expressed during early stages of seedlings development, whereas PVN4 and PVN5 were expressed during cotyledons senescence. The removal of epicotyl in French bean seedlings resulted in a decrease in the activity and in the expression of the genes associated with the cotyledons senescence process, i.e. PVN4 and PVN5. At the same time, the mobilization of reserves in those cotyledons was slowed down. In the same way, the deficit in phosphate and nitrate during seedlings development led to an acceleration of induction of these genes at the same time that reserves were utilized early on the time. Therefore, the induction of PVN4 and PVN5, the two S1 nuclease genes involved in the process of cotyledon senescence, is related to nutrient mobilization, supporting a possible role for nucleic acids in nutrient recycling during cotyledon senescence.

Getting to PTI of bacterial RNAs: Triggering plant innate immunity by extracellular RNAs from bacteria

ABSTRACTDefense against diverse biotic and abiotic stresses requires the plant to distinguish between self and non-self signaling molecules. Pathogen/microbe-associated molecular patterns (PAMPs/MAMPs) are pivotal for triggering innate immunity in plants. Unlike in animals and humans, the precise roles of nucleic acids in plant innate immunity are unclear. We therefore investigated the effects of infiltration of total Pseudomonas syringae pv. tomato DC3000 (Pto DC3000) RNAs into Arabidopsis plants. The pathogen population was 10-fold lower in bacterial RNAs pre-treated Arabidopsis plants than in the control. Bacterial RNAs purity was confirmed by physical (sonication) and chemical (RNase A and proteinase K digestion) methods. The perception of bacterial RNAs, especially rRNAs, positively regulated mitogen-activated protein kinase (MAPK) and induced a reactive oxygen species burst, callose deposition, salicylic acid (SA) and jasmonic acid (JA) signaling, and defense-related genes. Therefore, bacterial RNAs function as a new MAMP that activates plant innate immunity, providing a new paradigm for plant–microbe interactions.

Do nucleic acids moonlight as molecular chaperones?

Organisms use molecular chaperones to combat the unfolding and aggregation of proteins. While protein chaperones have been widely studied, here we demonstrate that DNA and RNA exhibit potent chaperone activity in vitro. Nucleic acids suppress the aggregation of classic chaperone substrates up to 300-fold more effectively than the protein chaperone GroEL. Additionally, RNA cooperates with the DnaK chaperone system to refold purified luciferase. Our findings reveal a possible new role for nucleic acids within the cell: that nucleic acids directly participate in maintaining proteostasis by preventing protein aggregation.

Bacterial RNAs activate innate immunity in Arabidopsis.

The common molecular patterns of microbes play a critical role in the regulation of plant innate immunity. However, little is known about the role of nucleic acids in this process in plants. We pre-infiltrated Arabidopsis leaves with total RNAs from Pseudomonas syringae pv. tomato DC3000 (Pto DC3000) and subsequently inoculated these plants with the same bacterial cells. Total Pto DC3000 RNAs pre-infiltrated into Arabidopsis leaves elicited plant immune responses against Pto DC3000. However, sheared RNAs and RNase A application failed to induce immunity, suggesting that intact bacterial RNAs function in plant innate immunity. This notion was supported by the positive regulation of superoxide anion levels, callose deposition, two mitogen-activated protein kinases and defense-related genes observed in bacterial RNA-pre-treated leaves. Intriguingly, the Pto DC3000 population was not compromised in known pattern recognition receptor mutants for chitin, flagellin and elongation factor-Tu (EF-Tu). Plant defense-related mutant analyses further revealed that bacterial RNA-elicited innate immunity was normally required for salicylic and jasmonic acid signaling. Notably, among total RNAs, the abundant bacterial RNA species 16S and 23S ribosomal RNAs were the major determinants of this response. Our findings provide evidence that bacterial RNA serves as a microbe-associated molecular pattern in plants.

The Potential Role of Nucleic Acids in Mediating Autoimmune Recognition Events: The Alpha-Omega of Innate Immunity.

The hypothesis proposed in this article suggests that in the innate immune response involving IgM moieties, nucleic acids and probably miRNAs play roles as mediators and regulators. After a discussion on how such a mechanism may operate, various diagnostic and therapeutic possibilities will be suggested.

Pathological implications of nucleic acid interactions with proteins associated with neurodegenerative diseases.

Protein misfolding disorders (PMDs) refer to a group of diseases related to the misfolding of particular proteins that aggregate and deposit in the cells and tissues of humans and other mammals. The mechanisms that trigger protein misfolding and aggregation are still not fully understood. Increasing experimental evidence indicates that abnormal interactions between PMD-related proteins and nucleic acids (NAs) can induce conformational changes. Here, we discuss these protein-NA interactions and address the role of deoxyribonucleic (DNA) and ribonucleic (RNA) acid molecules in the conformational conversion of different proteins that aggregate in PMDs, such as Alzheimer's, Parkinson's, and prion diseases. Studies on the affinity, stability, and specificity of proteins involved in neurodegenerative diseases and NAs are specifically addressed. A landscape of reciprocal effects resulting from the binding of prion proteins, amyloid-β peptides, tau proteins, huntingtin, and α-synuclein are presented here to clarify the possible role of NAs, not only as encoders of genetic information but also in triggering PMDs.

ChemInform Abstract: Current Challenges in Nucleic Acid Synthesis

Our understanding of the role of nucleic acids in regulating the process of life is growing rapidly. As researchers delve deeper into the cellular activity of molecules such as microRNA, small interfering RNA, and long non-coding RNA, the oligonucleotide chemist is confronted with the challenge of synthesizing the tools needed to continue this work. Furthermore, new applications are being developed that require increasingly complicated oligonucleotide constructs. In this review, we explore the current challenges confronting oligonucleotide synthesis, describe the chemistry and the enzymology being developed in response to those challenges, and discuss future challenges as-yet unmet.

Response of older laying hens to an Escherichia coli lipopolysaccharide challenge when fed diets with or without supplemental folic acid

Folic acid plays a key role in nucleic acids and protein synthesis, and has been associated with anti-inflammatory effects in LPS-induced infections. To this end, a study was conducted to investigate the effects of dietary folic acid (FA) supplementation in older laying hens (58 to 66 wk of age) challenged with Escherichia coli lipopolysaccharide (LPS). A total of 24 Shaver White laying hens at 58 wk were fed 2 diets. The diets were wheat-soybean-based, with either 0 or 4 mg of supplemental FA per kg of diet. After 8 wk of feeding and at 66 wk, the hens were injected intravenously with 8 mg of LPS or saline per kg of BW. Four hours after injection, blood was collected and hens were euthanized to obtain spleen and cecal tonsils. The T cell subsets in the blood and the spleen (CD4+ and CD8+), total IgG, and biochemical constituents (total protein, albumin, globulin, and fibrinogen) were not influenced (P > 0.05) by dietary FA supplementation. However, LPS injection decreased (P < 0.05) biochemical constituents, CD4+, and CD8+ cells in the blood, whereas CD4+:CD8+ ratio and total IgG increased (P < 0.05), and fibrinogen was not influenced. Gene expression in the spleen and cecal tonsils was not influenced by dietary FA supplementation except a diet × challenge interaction for interleukin (IL)-8 in the spleen; IL-8 decreased in FA-fed hens that were treated with LPS. Also, FA supplementation decreased the expression of IL-8 in cecal tonsils. Relative to saline-injected hens, expression of IL-1β, interferon-γ, and IL-10 increased in the LPS-injected hens in the spleen and cecal tonsils, IL-8 increased in LPS-injected hens only in the cecal tonsils, whereas Toll-like receptor 4, IL-4, IL-17, and IL-18 increased in the LPS-injected hens only in the spleen; however, LPS decreased expression of IL-13 in the cecal tonsils. In conclusion, FA did not affect inflammatory responses in older laying hens; more studies are required to investigate possible protective effects of FA in laying hens.

CD14 is a coreceptor of Toll-like receptors 7 and 9

Recognition of pathogens by the innate immune system requires proteins that detect conserved molecular patterns. Nucleic acids are recognized by cytoplasmic sensors as well as by endosomal Toll-like receptors (TLRs). It has become evident that TLRs require additional proteins to be activated by their respective ligands. In this study, we show that CD14 (cluster of differentiation 14) constitutively interacts with the MyD88-dependent TLR7 and TLR9. CD14 was necessary for TLR7- and TLR9-dependent induction of proinflammatory cytokines in vitro and for TLR9-dependent innate immune responses in mice. CD14 associated with TLR9 stimulatory DNA in precipitation experiments and confocal imaging. The absence of CD14 led to reduced nucleic acid uptake in macrophages. Additionally, CD14 played a role in the stimulation of TLRs by viruses. Using various types of vesicular stomatitis virus, we showed that CD14 is dispensable for viral uptake but is required for the triggering of TLR-dependent cytokine responses. These data show that CD14 has a dual role in nucleic acid-mediated TLR activation: it promotes the selective uptake of nucleic acids, and it acts as a coreceptor for endosomal TLR activation.