Short Molecules Research Articles

Aptamers: Promising Reagents in Biomedicine Application.

Nucleic acid aptamers, often termed "chemical antibodies," are short, single-stranded DNA or RNA molecules, which are selected by SELEX. In addition to their high specificity and affinity comparable to traditional antibodies, aptamers have numerous unique advantages such as wider identification of targets, none or low batch-to-batch variations, versatile chemical modifications, rapid mass production, and lack of immunogenicity. These characteristics make aptamers a promising recognition probe for scientific research or even clinical application. Aptamer-functionalized nanomaterials are now emerged as a promising drug delivery system for various diseases with decreased side-effects and improved efficacy. In this review, the technological strategies for generating high-affinity and biostable aptamers are introduced. Moreover, the development of aptamers for their application in biomedicine including aptamer-based biosensors, aptamer-drug conjugates and aptamer functionalized nanomaterials is comprehensively summarized.

Non-Coding Ribonucleic Acids as Diagnostic and Therapeutic Targets in Cardiac Fibrosis.

Cardiac fibrosis is a crucial juncture following cardiac injury and a precursor for many clinical heart disease manifestations. Epigenetic modulators, particularly non-coding RNAs (ncRNAs), are gaining prominence as diagnostic and therapeutic tools. miRNAs are short linear RNA molecules involved in post-transcriptional regulation; lncRNAs and circRNAs are RNA sequences greater than 200 nucleotides that also play roles in regulating gene expression through a variety of mechanisms including miRNA sponging, direct interaction with mRNA, providing protein scaffolding, and encoding their own products. NcRNAs have the capacity to regulate one another and form sophisticated regulatory networks. The individual roles and disease relevance of miRNAs, lncRNAs, and circRNAs to cardiac fibrosis have been increasingly well described, though the complexity of their interrelationships, regulatory dynamics, and context-specific roles needs further elucidation. This review provides an overview of select ncRNAs relevant in cardiac fibrosis as a surrogate for many cardiac disease states with a focus on crosstalk and regulatory networks, variable actions among different disease states, and the clinical implications thereof. Further, the clinical feasibility of diagnostic and therapeutic applications as well as the strategies underway to advance ncRNA theranostics is explored.

Clinical Insights into MicroRNAs in Depression: Bridging Molecular Discoveries and Therapeutic Potential.

Depression is a major contributor to the overall global burden of disease. The discovery of biomarkers for diagnosis or prediction of treatment responses and as therapeutic agents is a current priority. Previous studies have demonstrated the importance of short RNA molecules in the etiology of depression. The most extensively researched of these are microRNAs, a major component of cellular gene regulation and function. MicroRNAs function in a temporal and tissue-specific manner to regulate and modify the post-transcriptional expression of target mRNAs. They can also be shuttled as cargo of extracellular vesicles between the brain and the blood, thus informing about relevant mechanisms in the CNS through the periphery. In fact, studies have already shown that microRNAs identified peripherally are dysregulated in the pathological phenotypes seen in depression. Our article aims to review the existing evidence on microRNA dysregulation in depression and to summarize and evaluate the growing body of evidence for the use of microRNAs as a target for diagnostics and RNA-based therapies.

Considering Context-Specific microRNAs in Ischemic Stroke with Three "W": Where, When, and What.

MicroRNAs are short non-coding RNA molecules that function as critical regulators of various biological processes through negative regulation of gene expression post-transcriptionally. Recent studies have indicated that microRNAs are potential biomarkers for ischemic stroke. In this review, we first illustrate the pathogenesis of ischemic stroke and demonstrate the biogenesis and transportation of microRNAs from cells. We then discuss several promising microRNA biomarkers in ischemic stroke in a context-specific manner from three dimensions: biofluids selection for microRNA extraction (Where), the timing of sample collection after ischemic stroke onset (When), and the clinical application of the differential-expressed microRNAs during stroke pathophysiology (What). We show that microRNAs have the utilities in ischemic stroke diagnosis, risk stratification, subtype classification, prognosis prediction, and treatment response monitoring. However, there are also obstacles in microRNA biomarker research, and this review will discuss the possible ways to improve microRNA biomarkers. Overall, microRNAs have the potential to assist clinical treatment, and developing microRNA panels for clinical application is worthwhile.

Aptamers based targeted drug delivery system: A newer trend in cancer treatment therapy

The investigation of targeted drug delivery systems as a way to improve therapeutic efficacy while minimizing adverse effects is a result of the development of novel cancer treatment strategies. This subject explores the exciting field of aptamer-based targeted drug delivery systems for the treatment of cancer. Short single-stranded DNA or RNA molecules called aptamers have a remarkable capacity to bind to particular target molecules with high specificity and affinity. Aptamers have drawn attention as excellent possibilities for creating targeted drug delivery systems by taking use of their special characteristic. The applications, choice, and modification of aptamers to precisely identify cancer-associated biomarkers, such as receptors overexpressed on cancer cells, are covered in detail in this topic. Additionally, it emphasizes various techniques for aptamer-drug conjugation optimization which ensure effective carrier delivery and regulated drug release inside the tumor microenvironment. It is investigated if aptamer-based systems have the ability to overcome problems such drug resistance, heterogeneity, and insufficient drug penetration within solid tumors.In conclusion, this article illuminates how aptamer-based targeted drug delivery systems have transformed the world of cancer treatment. It advances knowledge of these systems and their potential to transform cancer treatment by providing insights into design principles, delivery systems, and therapeutic results.

Genomic origin, fragmentomics, and transcriptional properties of long cell-free DNA molecules in human plasma.

Recent studies have revealed an unexplored population of long cell-free DNA (cfDNA) molecules in human plasma using long-read sequencing technologies. However, the biological properties of long cfDNA molecules (>500 bp) remain largely unknown. To this end, we have investigated the origins of long cfDNA molecules from different genomic elements. Analysis of plasma cfDNA using long-read sequencing reveals an uneven distribution of long molecules from across the genome. Long cfDNA molecules show overrepresentation in euchromatic regions of the genome, in sharp contrast to short DNA molecules. We observe a stronger relationship between the abundance of long molecules and mRNA gene expression levels, compared with short molecules (Pearson's r = 0.71 vs. -0.14). Moreover, long and short molecules show distinct fragmentation patterns surrounding CpG sites. Leveraging the cleavage preferences surrounding CpG sites, the combined cleavage ratios of long and short molecules can differentiate patients with hepatocellular carcinoma (HCC) from non-HCC subjects (AUC = 0.87). We also investigated knockout mice in which selected nuclease genes had been inactivated in comparison with wild-type mice. The proportion of long molecules originating from transcription start sites are lower in Dffb-deficient mice but higher in Dnase1l3-deficient mice compared with that of wild-type mice. This work thus provides new insights into the biological properties and potential clinical applications of long cfDNA molecules.

Size counting analysis of short nucleic acid molecules using high-resolution hydrogel-interfaced glass nanopore

Size counting analysis of short nucleic acid molecules using high-resolution hydrogel-interfaced glass nanopore

A comparative study of grain quality and physicochemical properties of premium japonica rice from three typical production regions.

Grain quality indicates rice commodity value. This research compared grain quality and physicochemical properties of premium japonica rice from three production regions, Yangtze River downstream of China (YRDCN), Northeast region of China (NECN) and Japan. Results showed that there were distinct quality and physicochemical characteristics variance among the three groups of japonica rice, while CVs of most quality parameters from low to high was Japan, YRDCN and NECN. YRDCN rice presented obvious lower apparent amylose content (AAC) and ratio of each chain-length sections of amylopectin, and showed higher protein contents especially glutelin and ratio in short and intermediate amylopectin molecules. Among three rice groups, YRDCN rice presented weaker appearance, whereas did not show inferior cooking and eating properties, which was primarily linked to lower AAC. Rice AAC and starch fine structure significantly correlated with pasting parameters, swelling power and solubility, while protein content had close relation with taste analyzer parameters. Results of this study indicated improvement direction for japonica rice of YRDCN, and also provided reference for consumers' rice purchasing selection in accordance with individual taste preference.

Clinical Uses of Fructooligosaccharides for Gastrointestinal health in the Pediatric Population

Fructooligosaccharides (FOS) are non-digestible carbohydrates that are one of the major classes of bifidogenic oligosaccharides. Studies find that prebiotics such as FOS display health benefits pertaining to but not restricted to the gastrointestinal tract of an infant. This review article aims to discuss the therapeutic potential of FOS for different pediatric gut conditions. FOS in varying concentration has been found to prevent constipation and soften stools; reduce the incidence and severity of diarrhoea; alleviate GI discomfort symptoms such as vomiting and regurgitation. Infants and children seem to tolerate both short and long chain FOS molecules well. Although FOS is beneficial for infant and child health, there is still a need for rigorous clinical trials and long term follow up studies to understand if FOS supplemented in infancy can confer long term effects in adulthood.

Force-induced unzipping of DNA in the presence of solvent molecules

The melting of double-stranded DNA (dsDNA) in the presence of solvent molecules is a fundamental process with significant implications for understanding the thermal and mechanical behavior of DNA and its interactions with the surrounding environment. The solvents play an essential role in the structural transformation of DNA subjected to a pulling force. In this study, we simulate the thermal and force induced denaturation of dsDNA and elucidate the solvent dependent melting behavior, identifying key factors that influence the stability of DNA melting in presence of solvent molecules. Using a statistical model, we first find the melting profile of short heterogeneous DNA molecules in the presence of solvent molecules in Force ensemble. We also investigate the effect of solvent's strengths on the melting profile of DNA. In the force ensemble, we consider two homogeneous DNA chains and apply the force on different locations along the chain in the presence of solvent molecules. Different pathways manifest the melting of the molecule in both ensembles, and we found several interesting features of melting DNA in a constant force ensemble, such as lower critical force when the chain is pulled from the base pair close to a solvent molecule. The results provide new insights into the force-induced unzipping of DNA and could be used to develop new methods for controlling the unzipping process. By providing a better understanding of melting and unzipping of dsDNA in the presence of solvent molecules, this study provides valuable guidelines for predicting DNA thermodynamic quantities and for designing DNA nanostructures.

Understanding molecular mechanisms and miRNA-based targets in diabetes foot ulcers.

In today's culture, obesity and overweight are serious issues that have an impact on how quickly diabetes develops and how it causes complications. For the development of more effective therapies, it is crucial to understand the molecular mechanisms underlying the chronic problems of diabetes. The most prominent effects of diabetes are microvascular abnormalities such as retinopathy, nephropathy, and neuropathy, especially diabetes foot ulcers, as well as macrovascular abnormalities such as heart disease and atherosclerosis. MicroRNAs (miRNAs), which are highly conserved endogenous short non-coding RNA molecules, have been implicated in several physiological functions recently, including the earliest stages of the disease. By binding to particular messenger RNAs (mRNAs), which cause mRNA degradation, translation inhibition, or even gene activation, it primarily regulates posttranscriptional gene expression. These molecules exhibit considerable potential as diagnostic biomarkers for disease and are interesting treatment targets. This review will provide an overview of the latest findings on the key functions that miRNAs role in diabetes and its complications, with an emphasis on the various stages of diabetic wound healing.

Co-regulation strategy dominated by double short molecules permitting the regrowth of quantum dots for efficient deep-blue perovskite light-emitting diodes

Recently, blue perovskite quantum dots (PeQDs) have garnered considerable attention for use in full-color optoelectronic displays. However, the large specific surface area caused by the small particle size of blue PeQDs results in high defect state density, which severely limits their optical pursuit. To address this issue, a co-regulation strategy using double short-chain molecules of tetraoctylammonium fluoride and tetraethylammonium perfluorooctanesulfonate is proposed to enhance the regrowth of blue CsxRb1−xPb(ClyBr1−y)3 PeQDs. Long-chain insulated oleylamine and oleic acid ligands, which restrict the growth of PeQDs, are substantially replaced using short-chain ligands with higher adsorption energy. This replacement promotes PeQDs to regrow considerably from ∼8 to ∼18 nm, and the defect-state density decreases by 3–5 times. Consequently, highly efficient blue PeQDs with a photoluminescent quantum yield of unity are obtained. Moreover, the PeQDs exhibit lower insulating ligand density and improved charge injection property. As a result, the synthesized deep-blue PeQD light-emitting diodes (PeQLEDs) exhibit a maximum external quantum efficiency of 5.7% at the CIE coordinate of (0.148, 0.032). According to the International Telecommunication Union Radiocommunication Sector television standard (Rec. 2100), the obtained PeQLEDs are state-of-the-art among colloidal deep-blue PeQDs. This study provides a novel strategy to improve the optical performance of deep-blue PeQLEDs and paves the way for developing high-end wide color-gamut displays.

RNA Oncological Therapeutics: Intracellular Hairpin RNA Assembly Enables MicroRNA-Triggered Anticancer Functionality.

RNA therapeutics are of global interest because of their versatility in targeting a variety of intracellular and extracellular biomolecules. In that context, long double-stranded RNA (dsRNA) has been studied as an antitumor agent that activates the immune response. However, its performance is constrained by poor cancer selectivity and cell-penetration ability. Here, we designed and synthesized an oncolytic RNA hairpin pair (oHP) that was selectively cytotoxic toward cancer cells expressing abundant oncogenic microRNA-21 (miR-21). Although the structure of each hairpin RNA was thermodynamically metastable, catalytic miR-21 input triggered it to open to generate a long nicked dsRNA. We demonstrated that oHP functioned as a cytotoxic amplifier of information in the presence of miR-21 in various cancer cells and tumor-bearing mice. This work represents the first example of the use of short RNA molecules as build-up-type anticancer agents that are triggered by an oncogenic miRNA.

Potential clinical application of microRNAs in bladder cancer.

Bladder cancer (BC) is the tenth most prevalent malignancy globally, presenting significant clinical and societal challenges because of its high incidence, rapid progression, and frequent recurrence. Presently, cystoscopy and urine cytology serve as the established diagnostic methods for BC. However, their efficacy is limited by their invasive nature and low sensitivity. Therefore, the development of highly specific biomarkers and effective non-invasive detection strategies is imperative for achieving a precise and timely diagnosis of BC, as well as for facilitating an optimal tumor treatment and an improved prognosis. microRNAs (miRNAs), short noncoding RNA molecules spanning around 20-25 nucleotides, are implicated in the regulation of diverse carcinogenic pathways. Substantially altered miRNAs form robust functional regulatory networks that exert a notable influence on the tumorigenesis and progression of BC. Investigations into aberrant miRNAs derived from blood, urine, or extracellular vesicles indicate their potential roles as diagnostic biomarkers and prognostic indicators in BC, enabling miRNAs to monitor the progression and predict the recurrence of the disease. Simultaneously, the investigation centered on miRNA as a potential therapeutic agent presents a novel approach for the treatment of BC. This review comprehensively analyzes biological roles of miRNAs in tumorigenesis and progression, and systematically summarizes their potential as diagnostic and prognostic biomarkers, as well as therapeutic targets for BC. Additionally, we evaluate the progress made in laboratory techniques within this field and discuss the prospects.

Protocol for Testing the Effects of ssDNA Aptamer in HeLa and MCF-7.

Conventional approaches for treating tumors encompass chemotherapy, radiotherapy, and surgery. However, these methods come with their limitations when applied in clinical practice. Aptamers are often referred to as "chemical antibodies" and consist of short DNA or RNA molecules, designed to bind to a wide range of targets, including proteins or nucleic acid structures. They exhibit strong affinities and remarkable specificity for their target molecules, making them capable of functioning as therapeutic agents to directly impede tumor cell proliferation. This approach helps minimize the harm to normal cells, thus reducing toxicity through decreased side effects. Here we report the procedure to develop ssDNA aptamer and investigate its ability to inhibit cancer cell proliferation in HeLa and MCF-7 cancer cell lines.

Exploring MicroRNA biogenesis, applications and bioinformatics analysis in livestock: A comprehensive review.

Small non-coding RNAs called microRNAs (miRNAs) control the expression of genes post-transcriptionally. Their correlation with commercial economic traits including milk, meat and egg production, as well as their effective role in animal productivity, fertility, embryo survival and disease resistance, make them significant in livestock research. The miRNAs exhibit distinct spatial and temporal expression patterns, offering insights into their functional roles within cells and tissues. Aberrant miRNA production can disrupt vital cellular processes and genetic networks, contributing to conditions like metabolic disorders and viral diseases. These short RNA molecules are present in extracellular fluids, displaying remarkable stability against RNA degradation enzymes and extreme environmental conditions. miRNAspreservation is facilitated through packaging in lipid vesicles or complex formation with RNA-binding proteins. Numerous studies have illuminated the roles of miRNAs in diverse physiological processes, including embryonic stem cell differentiation, haematopoietic stem cell proliferation and differentiation and the coordinated development of organ systems. The integration of miRNA profiling, next-generation sequencing and bioinformatics analysis paves the way for transformative advancements in livestock research and industry. The present review underscores the applications of miRNAs in livestock, showcasing their potential to improve breeding strategies, diagnose diseases and enhance our understanding of fundamental biological processes.

Multimodal layer-by-layer nanoparticles: a breakthrough in gene and drug delivery for osteosarcoma.

Osteosarcoma is one of the most common primary malignant bone tumours in children and adolescents, frequently arising from mesenchymal tissue in the distal femur. It is highly aggressive, often metastasising to the lungs. Current treatments, which include surgery combined with neoadjuvant chemotherapy and radiotherapy, are often unsatisfactory due to the inability of surgery to control metastasis and the side effects and drug resistance associated with chemotherapy. Thus, there is an urgent need for new treatment technologies. This study explored the use of nanoparticles for gene and drug delivery in osteosarcoma treatment. The nanoparticles were composed of biodegradable and biocompatible polymers, chitosan and PLGA, and were loaded with miRNA-34a, a short RNA molecule that functions as a tumour suppressor by inducing cell cycle arrest and apoptosis in osteosarcoma cells. Recognising that the co-delivery of multiple drugs can enhance treatment efficacy while reducing systemic toxicity and drug resistance, three additional classes of nanoparticles were developed by adding doxorubicin and resveratrol to the chitosan-PLGA-miRNA-34a core. A layer-by-layer technique was employed to create a bilayer nanocoating using pectin and chitosan as polyelectrolytes, for encapsulating the therapeutic payloads. The manufactured nanoparticles were tested on U2OS and Saos-2 cells to assess cell viability, metabolic activity, and morphology before and after treatment. Cells were treated in both two-dimensional cultures and three-dimensional osteosarcoma spheroids, creating a biomimetic cellular model. Increased apoptotic activity and disruption of cellular functions were primarily observed with nanoparticles co-delivering miRNA-34a and drugs, particularly those functionalised with the LbL nanocoating, as confirmed by PCR analysis.

Bacteriophage-encoded 24B_1 molecule resembles herpesviral microRNAs and plays a crucial role in the development of both the virus and its host.

The 24B_1 small non-coding RNA molecule has been identified in Escherichia coli after induction of Shiga toxin-converting bacteriophage Φ24B. In this work, we focused on its direct role during phage and bacterial host development. We observed that in many aspects, this phage sRNA resembles herpesviral microRNAs. Similar to microRNAs, the mature 24B_1 is a short molecule, consisting of just 20 nucleotides. It is generated by cleaving the 80-nt long precursor transcript, and likely it undergoes a multi-step maturation process in which the Hfq protein plays an important role, as confirmed by demonstration of its binding to the 24B_1 precursor, but not to the 24B_1 mature form. Moreover, 24B_1 plays a significant role in maintaining the prophage state and reprogramming the host's energy metabolism. We proved that overproduction of this molecule causes the opposite physiological effects to the mutant devoid of the 24B_1 gene, and thus, favors the lysogenic pathway. Furthermore, the 24B_1 overrepresentation significantly increases the efficiency of expression of phage genes coding for proteins CI, CII, and CIII which are engaged in the maintenance of the prophage. It seems that through binding to mRNA of the sdhB gene, coding for the succinate dehydrogenase subunit, the 24B_1 alters the central carbon metabolism and causes a drop in the ATP intracellular level. Interestingly, a similar effect, called the Warburg switch, is caused by herpesviral microRNAs and it is observed in cancer cells. The advantage of the Warburg effect is still unclear, however, it was proposed that the metabolism of cancer cells, and all rapidly dividing cells, is adopted to convert nutrients such as glucose and glutamine faster and more efficiently into biomass. The availability of essential building blocks, such as nucleotides, amino acids, and lipids, is crucial for effective cell proliferation which in turn is essential for the prophage and its host to stay in the lysogenic state.

Aberrant miR-3135b and miR-1273g-3p expression in the peripheral blood samples of BRCA1/2 (±) ovarian cancer patients

Ovarian cancer (OC) ranks as the eighth most prevalent malignancy among women globally. The short non-coding RNA molecules, microRNAs (miRNAs) target multiple mRNAs and regulate the gene expression. Here in this study, we aimed to validate miR-3135b and miR-1273g-3p as novel biomarkers for prognostic and diagnostic factor OC. After RNA isolation, we analyzed the miR-3135b and miR-1273g-3p expression in peripheral blood samples derived from 150 OC patients. Subsequently, we compared their expression levels with 100 healthy controls. The differences of miR-3135b and miR-1273g-3p expression were detected using the Quantitative Real Time-PCR (qRT-PCR) technique following miRNA-specific cDNA synthesis pursing miRNA separation. The miR-3135b and miR-1273g-3p were higher in OC patients who tested positive for BRCA1/2 compared to BRCA-negative patients, and healthy cases. The level of miR-3135b demonstrated a roughly 4.82-fold increase in OC patients in comparison to the healthy cases, while miR-1273g-3p expression exhibited a roughly 6.77-fold increase. The receiver operating characteristic (ROC) analysis has demonstrated the potential of miR-3135b and miR-1273g-3p as markers for distinguishing between OC patients and healthy controls. The higher expressions of miR-3135b and miR-1273g-3p could be associated with OC development. Moreover, miR-3135b may have a diagnostic potential and miR-1273g-3p may have both diagnostic and prognostic potential in OC cell differentiation. The string analysis has revealed an association between miR-1273g-3p and the MDM2 gene, suggesting a potential link to tumor formation through the proteasomal degradation of the TP53 tumor suppressor gene. Additionally, the analysis indicates an association of miR-1273g-3p with CHEK1, a gene involved in checkpoint-mediated cell cycle arrest. String analysis also indicates that miR-3135b is associated with the MAPK1 gene, causing activation of the oncogenesis cascade. In conclusion, miR-1273g-3p, and miR-3135b exhibit significant potential as diagnostic markers. However, further research is needed to comprehensively investigate these miRNAs diagnostic and predictive characteristics in a larger cohort.

Dysregulated miRNAs in a canine model of haemangiosarcoma metastatic to the brain.

Haemangiosarcoma is a highly metastatic and lethal cancer of blood vessel-forming cells that commonly spreads to the brain in both humans and dogs. Dysregulations in phosphatase and tensin (PTEN) homologue have been identified in various types of cancers, including haemangiosarcoma. MicroRNAs (miRNAs) are short noncoding single-stranded RNA molecules that play a crucial role in regulating the gene expression. Some miRNAs can function as oncogenes or tumour suppressors, influencing important processes in cancer, such as angiogenesis. This study aimed to investigate whether miRNAs targeting PTEN were disrupted in canine haemangiosarcoma and its corresponding brain metastases (BM). The expression levels of miRNA-10b, miRNA-19b, miRNA-21, miRNA-141 and miRNA-494 were assessed in samples of primary canine cardiac haemangiosarcomas and their matched BM. Furthermore, the miRNA profile of the tumours was compared to samples of adjacent non-cancerous tissue and healthy control tissues. In primary cardiac haemangiosarcoma, miRNA-10b showed a significant increase in expression, while miRNA-494 and miRNA-141 exhibited downregulation. Moreover, the overexpression of miRNA-10b was retained in metastatic brain lesions. Healthy tissues demonstrated significantly different expression patterns compared to cancerous tissues. In particular, the expression of miRNA-10b was nearly undetectable in both control brain tissue and perimetastatic cerebral tissue. These findings can provide a rationale for the development of miRNA-based therapeutic strategies, aimed at selectively treating haemangiosarcoma.