Identification of ssDNA aptamers specific to clinical isolates of Streptococcus mutans strains with different cariogenicity

Aptamer decorated emodin nanoparticles-assisted delivery of dermcidin-derived peptide DCD-1L: Photoactive bio-theragnostic agent for Enterococcus faecalis biofilm destruction

BACKGROUND

Despite the high success rate of root canal treatment, failures are observed in a broad range of cases. Therefore, the need for novel approaches with the development of new generations of antimicrobial agents and intracellular drug delivery systems as adjunctive therapy is undeniable. In this study, we investigated the antimicrobial effects of antimicrobial photodynamic therapy (aPDT) using dermcidin‑derived peptide DCD‑1L loaded onto aptamer-functionalized emodin nanoparticles (Apt@EmoNp-DCD-1L) against Enterococcus faecalis as one of the most common bacteria involved in recurrent root canal treatment failures.

MATERIALS AND METHODS

Following preparation of EmoNp-DCD-1L, the binding of selected labeled Apt to EmoNp-DCD-1L was performed, followed by the specificity of Apt@EmoNp-DCD-1L to E. faecalis was determined. The antimicrobial potential of aPDT was then assessed after the determination of the minimum inhibitory concentration (MIC) of Apt@EmoNp-DCD-1L. The molecular docking analysis was conducted to evaluate the potential binding modes of EmoNp to the proteins involved in E. faecalis pathogenesis. Eventually, the anti-virulence capacity of Apt@EmoNp-DCD-1L-mediated aPDT was investigated via quantitative real-time PCR (qRT-PCR) assay following measurement of intracellular reactive oxygen species (ROS) generation.

RESULTS

The binding specificity of Apt@EmoNp-DCD-1L to E. faecalis was confirmed by flow cytometry. The results showed that the cell viability of E. faecalis exposed to aPDT groups employing the sub-MIC doses of Apt@EmoNp-DCD-1L (7.8 and 15.6 µM) was significantly reduced compared to the control group (P < 0.05). Also, Apt@EmoNp-DCD-1L in combination with a blue laser light was capable of enhancing the anti-biofilm activity of aPDT against E. faecalis biofilm. Data obtained from the qRT-PCR analysis showed significant downregulation in the expression level of genes involved in bacterial biofilm formation after exposure to aPDT (P < 0.05).

CONCLUSIONS

This in vitro study highlights that aPDT with the minimum concentration of Apt@EmoNp-DCD-1L can be considered as a targeted bio-theragnostic agent for the detection and elimination of E. faecalis in the dispersed and biofilm states.

DNA-aptamer-nanographene oxide as a targeted bio-theragnostic system in antimicrobial photodynamic therapy against Porphyromonas gingivalis

The aim of this study was to design and evaluate the specificity of a targeted bio-theragnostic system based on DNA-aptamer-nanographene oxide (NGO) against Porphyromonas gingivalis during antimicrobial photodynamic therapy (aPDT). Following synthesis and confirmation of NGO, the binding of selected labeled DNA-aptamer to NGO was performed and its hemolytic activity, cytotoxic effect, and release times were evaluated. The specificity of DNA-aptamer-NGO to P. gingivalis was determined. The antimicrobial effect, anti-biofilm potency, and anti-metabolic activity of aPDT were then assessed after the determination of the bacteriostatic and bactericidal concentrations of DNA-aptamer-NGO against P. gingivalis. Eventually, the apoptotic effect and anti-virulence capacity of aPDT based on DNA-aptamer-NGO were investigated. The results showed that NGO with a flaky, scale-like, and layered structure in non-cytotoxic DNA-aptamer-NGO has a continuous release in the weak-acid environment within a period of 240 h. The binding specificity of DNA-aptamer-NGO to P. gingivalis was confirmed by flow cytometry. When irradiated, non-hemolytic DNA-aptamer-NGO were photoactivated, generated ROS, and led to a significant decrease in the cell viability of P. gingivalis (P < 0.05). Also, the data indicated that DNA-aptamer-NGO-mediated aPDT led to a remarkable reduction of biofilms and metabolic activity of P. gingivalis compared to the control group (P < 0.05). In addition, the number of apoptotic cells increased slightly (P > 0.05) and the expression level of genes involved in bacterial biofilm formation and response to oxidative stress changed significantly after exposure to aPDT. It is concluded that aPDT using DNA-aptamer-NGO as a targeted bio-theragnostic system is a promising approach to detect and eliminate P. gingivalis as one of the main bacteria involved in periodontitis in periopathogenic complex in real-time and in situ.

Aptamers against Pathogenic Bacteria: Selection Strategies and Apta-assay/Aptasensor Application for Food Safety

Pathogenic bacteria are primarily kinds of detrimental agents that cause mankind illness via contaminated food with traits of multiple types, universality, and low content. In view of the detection demands for rapidity, aptamer recognition factors emerged as a substitution for antibodies, which are short single strands of nucleic acid selected via in vitro. They display certain superiorities over antibodies, such as preferable stability, liable modification, and cost-efficiency. Taking advantage of the situation, numerous aptamers against pathogenic bacteria have been successfully selected and applied, yet there are still restrictions on commercial availability. In this review, the strategies/approaches to key sections in pathogen aptamers SELEX and post-SELEX are summarized and sorted out. Recently, optical, electrochemical, and piezoelectric aptamer-based assays or sensors dedicated to pathogen detection have been critically reviewed. Ultimately, the existing challenges and future trends in this field are proposed to further promote development prospects.

Lactoferrin: A Nutraceutical with Activity against Colorectal Cancer

Homeostasis in the human body results from the tight regulation of several events, since too little inflammation disrupts the process of tissue repair and remodeling, whereas too much exerts a collateral effect by causing tissue damage with life-threatening consequences. In some clinical conditions, such as inflammatory bowel disease (IBD), inflammation functions as a double-edged sword by either enabling or inhibiting cancer development and progression. Generally, cancer develops through evasion mechanisms that regulate cell growth, causing a high rate of uncontrolled proliferation, and mechanisms for evading cell death, such as apoptosis. Moreover, chronic inflammation is a factor that contributes to colorectal cancer (CRC), as observed in individuals with IBD; all these conditions favor an increased rate of angiogenesis and eventual metastasis. Lactoferrin (Lf) is a mammalian iron-binding multifunctional glycoprotein regarded as a natural compound that up- and downregulates both humoral and cellular components of immunity involved in regulating the inflammatory response and maintaining gut homeostasis. Human and bovine Lf share high sequence homology and have very similar antimicrobial, anti-inflammatory, and immunomodulatory activities. Bovine Lf from milk is considered a safe molecule and is commercially available in large quantities. This review mainly focuses on the regulatory effects of orally administered bovine Lf on the inflammatory response associated with CRC; this approach indicates that CRC is one of the most frequently diagnosed cancers and affects the intestinal tract with high clinical and epidemiologic relevance. Thus, this review may provide foundations for the potential use of bovine Lf alone or as a natural adjunct agent to increase the effectiveness and reduce the side effects of anticancer chemotherapy.

Investigating the anti-streptococcal biofilm effect of ssDNA aptamer-silver nanoparticles complex on a titanium-based substrate

Streptococcus mutans is a commensal and opportunistic pathogen that causes several diseases by forming a biofilm in humans and animals in many areas such as nasopharyngeal, cardiac valves, lungs, and oral cavity. Biofilms are very important in prosthetic infections associated with medical implants. The use of nanoparticles is one of the evolving fields in biofilm targeting. Silver nanoparticles can be used for biofilm targeting due to their inherent antimicrobial properties. Hybridization of nanoparticles with small molecules increases their biological properties and makes them multifunctional. The present investigation aimed to design an appropriate silver nanoparticles–aptamer complex that binds to the surface receptors of streptococcal strains. For this reason, silver nanoparticles with particle sizes in a range of 50 to 70 nm were synthesized and connected to a designed aptamer with a streptavidin–biotin linker. Then, the effect of the complex was investigated on the S. mutans biofilm formed on the surface of a medical-grade titanium substrate. The silver nanoparticles–aptamer complex at a concentration of 100 μg mL⁻¹ after 48 h inhibited 43% of the biofilm formation and degraded 63% of the formed biofilm. Also, the cell availability reached 96% and the complex was stable in cell medium culture for 360 min. It was concluded that this complex could be a good candidate for removing the formed biofilms on the surface of titanium implants.

Silver nanoparticles attached to the specific aptamer forStreptococcus mutans, can significantly remove the biofilm of this bacterium attached to the surface of the titanium implant.

Novel Detection of Nasty Bugs, Prevention Is Better than Cure

Hospital-acquired infections (HAIs) are a growing concern around the world. They contribute to increasing mortality and morbidity rates and are an economic threat. All hospital patients have the potential to contract an HAI, but those with weakened or inferior immune systems are at highest risk. Most hospital patients will contract at least one HAI, but many will contract multiple ones. Bacteria are the most common cause of HAIs and contribute to 80-90% of all HAIs, with Staphylococcus aureus, Clostridium difficile, Escherichia coli, Acinetobacter baumannii, Pseudomonas aeruginosa and Klebsiella pneumoniae accounting for the majority. Each of these bacteria are highly resistant to antibiotics and can produce a protective film, known as a biofilm, to further prevent their eradication. It has been shown that by detecting and eradicating bacteria in the environment, infection rates can be reduced. The current methods for detecting bacteria are time consuming, non-specific, and prone to false negatives or false positives. Aptamer-based biosensors have demonstrated specific, time-efficient and simple detection, highlighting the likelihood that they could be used in a similar way to detect HAI-causing bacteria.

Recent Progress in the Identification of Aptamers Against Bacterial Origins and Their Diagnostic Applications

Aptamers have gained an increasing role as the molecular recognition element (MRE) in diagnostic assay development, since their first conception thirty years ago. The process to screen for nucleic acid-based binding elements (aptamers) was first described in 1990 by the Gold Laboratory. In the last three decades, many aptamers have been identified for a wide array of targets. In particular, the number of reports on investigating single-stranded DNA (ssDNA) aptamer applications in biosensing and diagnostic platforms have increased significantly in recent years. This review article summarizes the recent (2015 to 2020) progress of ssDNA aptamer research on bacteria, proteins, and lipids of bacterial origins that have implications for human infections. The basic process of aptamer selection, the principles of aptamer-based biosensors, and future perspectives will also be discussed.

Selection of DNA aptamers to Streptococcus pneumonia and fabrication of graphene oxide based fluorescent assay

Pneumococci are one of the leading causes of infections throughout the world causing problems mainly in children, elderly, and immune-deficient patients. In recent years antibiotic resistant Streptococcus pneumoniae strains become widespread. Therefore simple, rapid, and specific detection methods are needed for public health. In this study, DNA aptamer probes against S. pneumoniae were selected using bacterial Systematic Evolution of Ligands by Exponential Enrichment (SELEX) and these probes were integrated in to a graphene oxide (GO) based fluorescent assay. Among the tested aptamers three candidates Lyd-1, Lyd-2 and Lyd-3 showed K_d values of 844.7 ± 123.6, 1984.8 ± 347.5, and 661.8 ± 111.3 nM, respectively. These candidates showed binding affinity to S. pneumoniae and no specific binding to the bacteria used in negative selection. The binding of aptamers were showed by fluorescence spectroscopy and flow cytometry. GO based label-free fluorescent assay developed using Lyd-3 aptamer had a unique detection limit of 15 cfu mL^-1. Thus we believe that the selected aptamers and fabricated GO based assay has potential to be used in the detection of S. pneumoniae. Selected aptamers selectively bind to S. pneumonia with anti-pneumococcal potential and holds great potential to be used as molecular probes for identifying and targeting.

Nucleic acid aptamer application in diagnosis and therapy of colorectal cancer based on cell-SELEX technology

Nucleic acid aptamers are a class of high-affinity nucleic acid ligands. They serve as “chemical antibodies” since their high affinity and specificity. Nucleic acid aptamers are generated from nucleic acid random-sequence using a systematic evolution of ligands by exponential enrichment (SELEX) technology. SELEX is a process of effectively selecting aptamers from different targets. A newly developed cell-based SELEX technique has been widely used in biomarker discovery, early diagnosis and targeted cancer therapy, particular at colorectal cancer (CRC). Combined with nanostructures, nano-aptamer-drug delivery system was constructed for drug delivery. Various nanostructures functionalized with aptamers are highly efficient and has been used in CRC therapeutic applications. In the present, we introduce a cell- SELEX technique, and summarize the potential application of aptamers as biomarkers in CRC diagnosis and therapy. And some characteristics of aptamer-targeted nanocarriers in CRC have been expatiated. The challenges and perspectives for cell-SELEX are also discussed.