Molecular dynamics simulation as a promising approach for computational study of liquid crystal-based aptasensors.

As a potent computational methodology, molecular dynamics (MD) simulation provides advantageous knowledge about biological compounds from the molecular viewpoint. In particular, MD simulation gives exact information about aptamer strands, such as the short synthetic oligomers, their orientation, binding sites, folding-unfolding state, and conformational re-arrangement. Also, the effect of the different chemicals and biochemicals as the components of aptamer-based sensors (aptasensors) on the aptamer-target interaction can be investigated by MD simulation. Liquid crystals (LCs) as soft substances with characteristics of both solid anisotropy and liquid fluidity are new candidates for designing label-free aptasensors. To now, diverse aptasensors have been developed experimentally based on the optical anisotropy, fluidity, and long-range orientational order of LCs. Here, we represent a computational model of an LC-based aptasensor through a detailed MD simulation study. The different parameters are defined and studied to achieve a comprehensive understanding of the computational design of the LC-based aptasensor, including the density of LCs, their orientation angle, and lognormal distribution in the absence and presence of aptamer strands, both aptamer and target molecules with various concentrations, and interfering substance. As a case study, the tobramycin antibiotic is considered the target molecule for the computational model of the LC-based aptasensor.Communicated by Ramaswamy H. Sarma.

A Simple Aptamer-Based Nanoconjugate Assay for Diagnosis of Chronic Myeloid Leukemia.

Chronic myeloid leukemia (CML) as a bone marrow stem cell clonal disease appears from the proliferation of granulocyte cells at all stages of maturation. If the disease diagnosis is not early, patients enter the blastic phase, which decreases their survival rate to 3-6 months. It implies the significance of the early diagnosis of CML. In this study, we introduce a simple array for diagnosis of the K562 cells as the human immortalized myeloid leukemia cell line. The developed aptamer-based biosensor (aptasensor) includes the T2-KK1B10 aptamer strands attached to the surface of mesoporous silica nanoparticles (MSNPs) with the cavities accumulated from rhodamine B and coated by both Ca2+ ions and ATP aptamer. The aptamer-based nanoconjugate can enter the K562 cells through the complexation of the T2-KK1B10 aptamer with the cells. The ATP in the cells and low level of intracellular Ca2+ ion release both the aptamer and ion from the surface of the MSNPs. The liberated rhodamine B results in an increased fluorescence intensity. Fluorescence microscope imaging and flow cytometry histogram display a strong fluorescence emission for the K562 cells (CML cells) exposed to the nanoconjugate in comparison with that for MCF-7 cells. The aptasensor possesses good performance in the blood samples with the advantages of high sensitivity, rapidness, and cost-effectiveness, making it an appropriate tool for the diagnosis of CML disease.

Strong and selective interactions of palmatine with G-rich sequences in TRF2 promoter; experimental and computational studies.

G-rich sequences have the potential to fold into G-quadruplexes (GQs). G-quadruplexes, particularly those positioned in the regulatory regions of proto-oncogenes, have recently garnered attention in anti-cancer drug design. A thermal FRET assay was employed to conduct preliminary screening of various alkaloids, aiming to identify stronger interactions with a specific set of G-rich double-labeled oligonucleotides in both K + and Na + buffers. These oligonucleotides were derived from regions associated with Kit, Myc, Ceb, Bcl2, human telomeres, and potential G-quadruplex forming sequences found in the Nrf2 and Trf2 promoters. Palmatine generally increased the stability of different G-rich sequences into their folded GQ structures, more or less in a concentration dependent manner. The thermal stability and interaction of palmatine was further studied using transition FRET (t-FRET), CD and UV-visible spectroscopy and molecular dynamics simulation methods. Palmatine showed the strongest interaction with T RF2 in both K+ and Na+ buffers even at equimolar concentration ratio. T-FRET studies revealed that palmatine has the potential to disrupt double-strand formation by the T RF2 sequence in the presence of its complementary strand. Palmatine exhibits a stronger interaction with G-rich strand DNA, promoting its folding into G-quadruplex structures. It is noteworthy that palmatine exhibits the strongest interaction with T RF2, which is the shortest sequence among the G-rich oligonucleotides studied, featuring only one nucleotide for two of its loops. Palmatine represents a suitable structure for drug design to develop more specific ligands targeting G-quadruplexes. Whether palmatine can also affect the expression of the T RF2 gene requires further studies.Communicated by Ramaswamy H. Sarma.

Reducing the assemblies of amyloid-beta multimers by sodium dodecyl sulfate surfactant at concentrations lower than critical micelle concentration: molecular dynamics simulation exploration.

Amyloid-ß peptide, the predominant proteinaceous component of senile plaques, is responsible for the incidence of Alzheimer's disease (AD), an age-associated neurodegenerative disorder. Specifically, the amyloid-ß(1-42) (Aß1-42) isoform, known for its high toxicity, is the predominant biomarker for the preliminary diagnosis of AD. The aggregation of the Aß1-42 peptides can be affected by the components of the cellular medium through changing their structures and molecular interactions. In this study, we investigated the effect of sodium dodecyl sulfate (SDS) at much lower concentrations than the critical micelle concentration (CMC) on Aß1-42 aggregation. For this purpose, we studied mono-, di-, tri- and tetramers of Aß1-42 peptide in two different concentrations of SDS molecules (10 and 40 molecules) using a 300 ns molecular dynamics simulation for each system. The distance between the center of mass (COM) of Aß1-42 peptides confirms that an increase in the number of SDS molecules decreases their aggregation probability due to greater interaction with SDS molecules. Besides, the less compactness parameter reveals the reduced aggregation probability of Aß1-42 peptides. Based on the energetic FEL landscapes, SDS molecules with the concentration closer to the CMC are an effective inhibitory agent to prevent the formation of Aß1-42 fibrils. Also, the aggregation direction of the peptide pairs can be predicted by determining the direction of the accumulation-deterrent forces.Communicated by Ramaswamy H. Sarma.

Robust tag-free aptasensor for monitoring of tobramycin: Architecting of rolling circle amplification and fluorescence synergism.

With the unpredictable risks on human health and ecological safety, tobramycin (TOB) as an extensively applied antibiotic has embraced global concern. Herein, a label-free fluorescent aptasensor was developed that opened up an innovative sensing strategy for monitoring trace TOB levels. Based on the rolling circle amplification (RCA) process, a giant DNA building was established by the catalytic action of T4 DNA ligase and Phi 29 DNA polymerase with the cooperation of the specific aptamer as a primer skeleton. By having the role of signal amplifier template, the RCA product with the G-quadruplex sequence duplications was decorated by a high number of the thioflavin T (ThT) fluorescent dyes. The aptasensor with good selectivity toward TOB achieved a detection limit as low as 150 pM. Thanks to its accurate target quantification, ease of operation, economic manufacture, as well as high potency for real-time and point-of-care testing, the represented aptasensor is superb for clinical application and food safety control.

A simple and robust aptasensor assembled on surfactant-mediated liquid crystal interface for ultrasensitive detection of mycotoxin.

Here, a simple aptasensing approach is represented to sensitively detect ochratoxin A (OTA) as one of the most perilous mycotoxins with carcinogenic, nephrotoxic, teratogenic, and immunosuppressive sequels on human health. The aptasensor is based on the alteration in the orientational order of liquid crystal (LC) molecules at the surfactant-arranged interface. Homeotropic alignment of LCs is achieved by the interaction of the surfactant tail with LCs. By perturbing the alignment of LCs due to the electrostatic interaction of the aptamer strand with the surfactant head, a colorful polarized view of the aptasensor substrate is induced drastically. While OTA causes the re-orientation of LCs to a vertical state by forming an OTA-aptamer complex that induces darkness of the substrate. This study shows that the length of the aptamer strand impacts the efficiency of the aptasensor; longer strand results in the greater disruption of LCs, and therefore, increases the aptasensor sensitivity. Hence, the aptasensor can determine OTA in the linear concentration range of 0.1 fM-1 pM as low as 0.021 fM. The aptasensor is capable to monitor OTA in grape juice, coffee drink, corn, and human serum real samples. The proposed LC-based aptasensor provides a cost-effective, easy-to-carry, operator-independent, and user-friendly array with great potential to develop portable sensing gadgets for food quality control and health care monitoring.

A simple tag-free fluorometric aptasensing assay for sensitive detection of kanamycin.

A novel label-free and enzyme-free fluorescence aptasensing assay that uses Sybr Green I (SGI) as the signal indicator for the kanamycin determination was designed. An aptamer-complementary strand (Apt/CP) conjugate was formed, which provided the intercalation sites for SGI and, therefore, a considerable fluorescent signal. The introduction of the target led to the separation of Apt from CP due to the high affinity of Apt toward kanamycin. Hence, the suitable intercalation gaps reduced, which resulted in a decrease in the generated fluorescent signal. Under optimized conditions, a broad linear concentration range from 0.05 µM to 20 µM and a limit of detection of 11.76 nM were obtained, confirming the ability of the fabricated aptasensor for sensitive and specific kanamycin detection in real samples such as milk and human serum. The aptasensing method has the potential to be extensively employed in the food industry and veterinary science due to its simplicity, sensitivity, user-friendly, and capability of on-site detection of kanamycin.

A fluorescent aptasensor for quantification of cocaine mediated by signal amplification characteristics of UiO-66/AuNPs nanocomposite.

Due to the detrimental effects of cocaine on the human body such as organ damage, paranoia, immunodeficiency, cardiovascular disease, blood pressure, and stress, it is highly required to develop sensing approaches for its rapid and facile determination. Based on the signal enhancement capability of the UiO-66/AuNPs nanocomposite and acting as a capture agent, we designed a cost-effective fluorescent aptasensor for cocaine detection. The cocaine presence in the sample would cause a considerable escalation in the quenching of the fluorescence signal. The aptasensor achieved the linear response range over 0.5 µM-20 µM with a low detection limit of 0.178 µM. The selectivity of the designed aptasensing assay was successfully confirmed by examining several analgesic drugs. The aptasensor was employed for cocaine determination in human serum as the real samples. This method has a substantial benefit the for development of a low-cost and facile tool in medicine and forensic science.

Exonuclease-based aptasensors: Promising for food safety and diagnostic aims.

As of today's requirement, developing cost-effective smart sensing tools with ultrahigh sensitivity for food safety insurance is of special importance. For this purpose, aptamer-based biosensors (aptasensors) powered by the superiorities of the recycling signal amplification strategies have been expanded especially. Target recycling supported by enzymes is an appealing approach for implementing signal amplification. As the supreme biocatalyst enzymes, exonucleases can inaugurate signal improvement by involving a single target in a process would result in appreciable repeating cycles of the cleavage of the phosphodiester bonds between the building blocks of the nucleic acid strands, and also, their terminals. Although there are diverse substances for catalyzing amplification strategies, including nanoparticles, carbon-based nanocomposites, and quantum dots (QDs), exonucleases are of superiority over them by simplifying the amplification process with no need for the complicated pre-treatment processes. The outstanding selectivity and great sensitivity of the aptasensors tuned by amplification potency of exonucleases nominate them as the promising sensing tools for label-free, ease-of-use, cost-effective, and real-time diagnosis of diverse targets. Here, we summarize the achievements and perspectives in the scientific branch of aptasensor design for the qualitative monitoring of diverse targets by cooperation of exonucleases with the conspicuous potential for the signal amplification. Finally, some results are expressed to provide a comprehensive viewpoint for developing novel nuclease-based aptasensors in the future.

A tag-free fluorescent aptasensor for tobramycin detection using a hybridization of three aptamer strands and SYBR Green I dye.

In this study, a sensitive fluorescent method is designed to detect tobramycin (TOB) drug applying a hybrid structure of three aptamer strands and SYBR Green I (SGI) fluorescent dye as the bioreceptor segment and signal indicator, respectively. The preferential binding of the aptamers to TOB resulted in the collapse of the hybridized aptamer skeleton to the single strands. So, the intercalation of SGI molecules reduced that quenched the fluorescence response. The aptasensing assay provided the superior target specificity with a detection limit (LOD) of 0.153 pM and a wide linear dynamic range over 0.5 pM-300 µM. The aptasensor could successfully quantify TOB in human serum samples. The tag-free sensor with the remarkable advantages of simplicity, easy-to-use, cost-effectiveness, and high sensitivity is superior to be applicable for clinical samples.

A comprehensive computer simulation insight into inhibitory mechanisms of EGCG and NQTrp ligands on amyloid-beta assemblies as the Alzheimer's disease insignia.

Amyloid-ß peptide with predominant presence in the senile plaques is the most common agent for Alzheimer's disease (AD) incidence. Assembly of the amyloid-ß(1-42) (Aß1-42) isoform is known as the main reason for the AD appearance. Epigallocatechin gallate (EGCG) and 1,4-naphthoquinone-2-yl-L-tryptophan (NQTrp) are two small molecules that inhibit the formation of the Aß1-42 fibrils. The present study provides molecular insight to clarify the inhibitory mechanisms of the EGCG and NQTrp ligands on the Aß1-42 assemblies by using molecular dynamics (MD) simulation. Hence, nine different Aß1-42-containing systems including the monomer, dimer, and hexamer of Aß1-42 considering each of them in a media with no ligands, in the presence of one EGCG ligand, and in the presence of one EGCG ligand were studied with a simulation time of 1 µs for each system. The precise investigation of the peptide-ligand distance, conformational factor (Pi), solvent accessible surface area (SASA), dictionary of secondary structure (DSSP), and Lys28-Ala42 salt bridge analyses confirmed that the hydroxyl-rich structure of the EGCG ligand applied its inhibitory effect on the aggregation of the peptides indirectly by involving water molecules. While the hydroxyl-free structure of the NQTrp ligand exposed its inhibitory effect through a direct interaction with the Aß1-42 peptides. Besides, reduced density gradient (RDG) analysis clarified the hydrogen bonding interactions as the dominant ones for the peptide-EGCG systems, and also, steric and van der Waals interactions for the peptide-NQTrp systems.Communicated by Ramaswamy H. Sarma.

Polyphenol-loaded bacterial cellulose nanofiber as a green indicator for fish spoilage.

Seafood products as a source of vitamins, minerals, and polyunsaturated fatty acids represent an important component of the human diet. However, they are susceptible to spoilage even under appropriate storage conditions, making it indispensable to develop freshness indicators. In this study, we introduce a green user-friendly pH indicator film for the naked-eye monitoring of fish spoilage. The pH indicator was prepared by successful loading of a mixture of anthocyanin and curcumin on bacterial cellulose (BC) nanofiber substrate. BC nanofiber with the advantages of biocompatibility, biodegradability, high purity, and superior mechanical strength was promising for generating pH-sensing arrays. The Fourier transform infrared (FT-IR) analysis proved the incorporation of anthocyanin and curcumin into the BC skeleton. Besides, the scanning electron microscopy (SEM) results clarified the morphology of the modified film by anthocyanin and curcumin. The pH indicator film was still stable after preserving for 60 days at different temperatures. The curcumin-anthocyanin loaded nanofiber indicated a distinct color change after spoilage by its exposure to fish meat in a transparent plastic package. Hence, the modified film by the anthocyanin-curcumin mixture is potent for the naked-eye monitoring of meat spoilage.

Nano-gold mediated aptasensor for colorimetric monitoring of acrylamide: Smartphone readout strategy for on-site food control.

A simple aptasensor is embedded in the internal surface of a micropipette tip as the aptasensor substrate for the label-free monitoring of acrylamide. The aptasensor is based on the formation of the triple-helix molecular switch (THMS) structure of the DNA strands that induces the salt-enforced aggregation of gold nanoparticles (AuNPs). A smartphone imaging readout-based strategy is applied to quantify acrylamide. The developed aptasensor is novel for the naked-eye monitoring of the target through the color change of the solution inside the micropipette tip. The colorimetric aptasensor detects acrylamide in the concentration range of 0.05-200 nmol L-1 and at the trace level of 0.038 nmol L-1 with the comparable selectivity. The aptasensor can successfully quantify acrylamide in the chips, coffee, and bread samples with recoveries range from 92 to 102 %. The designed aptasensor paves an efficient device for the portable, on-site, facile, and real-time target sensing, superior for food safety control.

Aptamer-based Biosensors: Promising Sensing Technology for Diabetes Diagnosis in Biological Fluids.

Diabetes is a chronic disease state in which the pancreas fails to secrete sufficient insulin, resulting in an elevation of blood glucose levels. As one of the most prevalent diseases worldwide, diabetes is recognized as a global health concern that, if undiagnosed or untreated, can lead to serious and life-threatening complications, such as kidney failure, cardiovascular disease and diabetic retinopathy. Despite progress in the diagnosis of diabetes, limitations still exist with current analytical techniques, and, therefore, the development of precise sensing devices for on-site, real-time detection of diabetes is needed. Biosensors have contributed significantly to the field of diabetes healthcare, due to their cost-effectiveness, portability, ease of use, and rapid assay time. Recently, there has been a preference for the utilization of aptamers over antibodies in designing biosensors. Aptasensors, biosensors made with aptamers, offer potential in the diagnosis of diabetes. Aptamers, due to having lower molecular weight, low price, and stability over a wide temperature range and pH range, their in vitro synthesis, and the ability to refold after being removed from denaturing conditions compared to antibodies, have some distinctive characteristics as well as diverse types, such as optical FNA-based biosensors, colorimetric biosensors, fluorescent biosensors and electrochemical FNA-based biosensors. With this in mind, we highlight the recent developments and novel perspectives in the field of aptasensor design to quantitatively monitor diabetes biomarkers. Finally, some results are highlighted to offer a basis for the future design of aptasensor kits for diabetes diagnosis.

A label-free liquid crystal-assisted aptasensor for trace level detection of tobramycin in milk and chicken egg samples.

Developed herein is an aptasensing array based on liquid crystal (LC) for monitoring of tobramycin (TOB) antibiotic. The direction of LC molecules from vertical to a random status was induced by the conformational changes of the specific aptamer due to its selective interaction with the target. The dark view of the aptasensing platform changed to colorful through observation by a polarized light microscope that clarifies the TOB presence. The aptasensor is especially able to determine TOB in the linear concentration range of 0.005-600 pM with a limit of detection (LOD) as 0.0021 pM. The TOB values can be determined successfully in the milk and chicken egg samples that highlights the potential applicability of the designed aptasensor. The proposed sensing approach is facile, operator-independent, label-free, and ultra-sensitive, making it novel for developing real-time portable sensing devices for future.

An ultrasensitive detection platform for cocaine: Aptasensing strategy in capillary tube.

Cocaine as a detrimental addictive drug threats human health through inducing heart problem, blood pressure, anxiety, immunodeficiency, paranoia, and organ damage. Thus, the quantification of cocaine in the biological samples by a simple, high specificity, and fast method is highly urgent to decrease the harmful effect of the misuse of this drug. In this study, we constructed a novel fluorescent aptasensor by combining the fluorescein (FAM)-modified specific aptamer and AuNPs in a capillary tube as the sensing substrate for the first time. The presence of cocaine recovered the fluorescence response of the aptasensor through interaction with the aptamer and differentiation of the aptamer@AuNPs complex. By fluorescence microscopy imaging of the aptasensor substrate and its quantitative analysis, a remarkable linear range from 100 pM to 600 µM and the ultra-low limit of detection (LOD) as 0.31 pM were achieved for the target detection. Cocaine was successfully quantified in the real samples (human serum and urine) by using the aptasensor. The aptasensor is simple, easy-to-use, favorable applicability, and cost-effective; and to the best of our knowledge, it is the first use of the capillary tube as a sensing platform just by using about 3 µl of the samples. It is also an easy-to-carry tool, promising for the on-site target detection. Besides, it can be a portable device for monitoring cocaine by using a handheld single-beam fluorescence microscope. It can be an appropriate detection tool in forensic science and medicine.

CRISPR/Cas-engineered technology: Innovative approach for biosensor development.

On-site and real-time clinical monitoring have been progressed dramatically by integrating biosensor science with portable digital electronic technology. Clustered regularly interspaced short palindromic repeats (CRISPR) with association of RNA-guided nucleases (CrRNA-Cas enzymes) have achieved novel CRISPR/Cas biosensing science as a promising revolutionized diagnostic technology for portable and on-site healthcare monitoring and diagnostics. Among several available CRISPR/Cas systems, CRISPR/Cas12a and CRISPR/Cas13a conjugates are utilized broadly in biosensor design, because of their capability to cleave both target and non-target sequences. With the advantages of portability, cost-effectiveness, facile operation, high durability, and reproducibility, CRISPR/Cas-based biosensing techniques are a perfect choice for designing ultra-sensitive point-of-care diagnostic devices with amplified response signals. In the present review, we summarize the advances in the CRISPR/Cas-based biosensors with the focus on healthcare and diagnostic purposes. The cooperation of nanomaterial engineering with CRISPR/Cas biosensors is also represented to attain a promising viewpoint for offering novel user-friendly test kits for announcing ultra-low levels of diverse targets in the future.

A fluorescence imaging-supported aptasensor for sensitive monitoring of cadmium pollutant in diverse samples: A critical role of metal organic frameworks.

Water pollution, as the remarkable environmental remediation issue, is a today worldwide concern. Cadmium ion (Cd2+) as a hazardous water pollutant is seriously detrimental to human health, food safety, and ecological areas. Hence, we successfully designed a simple detection array for monitoring of ultra-low levels of Cd2+ ion by combining the advantages of aptamer as a high sensitive and selective sensing probe and zeolitic imidazolate framework-8 (ZIF-8) as a superior fluorescence quenching inducer. To have a portable and on-site detection assay, the aptamer biosensing array (aptasensor) was designed by using a paper-supported substrate. The basis of the designed paper-supported aptasensor was the specific complexation of Cd2+ with the aptamer strand, adsorption of fluorescein-labeled complementary (FAM-CP) strand on the ZIF-8 surface, and fluorescence quenching of FAM molecule after the leakage of the injected target solution on the sample zone of the paper substrate to the detection part. A linear relationship was obtained between the Mean Gray Value index, as a criterion for the fluorescence quenching, and the Cd2+ concentration in the range of 0.1-120 pM with a detection limit of 0.076 pM. The aptasensor could detect Cd2+ in the diverse real sample, including tap water, milk, coffee, and human blood serum.

Metal organic frameworks as advanced functional materials for aptasensor design.

BACKGROUND: Advancement in coordination chemistry has achieved an impressive development of metal organic frameworks (MOFs) as the supramolecular hybrid materials, comprising harmonized metal nodes with organic ligands. Scope and approach: MOFs offer the unique properties of easy synthesis, nanoscale structure, adjustable size and morphology, high porosity, large surface area, supreme chemical tunability and stability, and biocompatibility. The features provide an exceptional opportunity for the widely usage of MOFs in the different scientific fields, e.g. biomedicine, electrocatalysis, food safety, energy storage, environmental surveillance, and biosensing platforms. The synergistic incorporation of the aptamer advantages and the superiorities of MOFs attains the novel MOF-based aptasensors. The excellent selectivity and sensitivity of the MOF-based aptasensors nominate them as efficient lab-on-chip tools for cost-effective, label-free, portable, and real-time monitoring of diverse targets. KEY FINDINGS AND CONCLUSIONS: Here, we review the achievements in the sensor design by cooperation of MOF motifs and aptamers with the conspicuous potential of determining the targets. Finally, some results are expressed that provide a valuable viewpoint for developing the novel MOF-based test strips in the future.

An ultra-sensitive dual-responsive aptasensor with combination of liquid crystal and intercalating dye molecules: A food toxin case study.

Herein, a label-free aptasensor was designed through forming a double-stranded DNA skeleton on the glass substrate for ultrasensitive quantification of ochratoxin A (OTA) as a case study. The function fundament of the dual-responsive aptasensor was the perturbation of the vertical alignment of the liquid crystals (LCs) and intercalation of the SYBR Green I (SGI) dye molecules between the base pairs of the double-stranded DNA structure. The presence of OTA decomposed the double-stranded structure of DNA by releasing the OTA-specific aptamer from the sensing platform that induced an apparent alteration of the optical and fluorescent responses. The aptasensor specifically detected the ultra-low levels of OTA as 47.0E-9 pM (0.047 aM) and 34.0E-3 pM (34 fM) based on the polarized and fluorescent responses, respectively. The aptasensor monitored OTA in the coffee and grape drink samples. The aptasensor provides promising insight for manufacturing real-time, cost-effective, and portable sensing devices for food control usage.