Label-free peptide aptamer based impedimetric biosensor for highly sensitive detection of TNT with a ternary assembly layer

Immobilization of DNA on nanostructured gold and silver substrates via alkanethiolate linkers: The influence of linker length

Various single-stranded DNA (ssDNA) chains were attached to nanostructured gold and silver surfaces highly active in surface-enhanced Raman scattering (SERS) spectroscopy. The DNA was attached to the metal surface using alkanethiol linkers with 6 or 3 carbon atoms in the chain, and then the metal surface was sealed with HS-(CH2)n-OH alkanethiols having the same number of carbon atoms in the chain as one of the linkers. The immobilized ssDNA was then hybridized with complementary ssDNA, which induced significant changes in the conformation of the chains of chemisorbed ω-substituted alkanethiols. For the first time, it has been investigated how the length of the alkanethiol chain through which the capture ssDNA is attached to the metal surface affects the DNA hybridization-induced changes in the measured SERS spectra. We found that the differences between the SERS spectra of the DNA layers recorded before and after hybridization were much larger when thiols with 6 carbon atoms in the chain were used as linking and sealing compounds than when compounds with 3 carbon atoms in the chains were used. This means that, in SERS DNA sensors based on the rearrangement of linking layers, using C6 linkers should make it easier than C3 linkers to observe the rearrangement based on SERS measurements. The properties of the monolayers formed from the compounds used to seal the metal surfaces with immobilized DNA chains (6-mercaptohexanol and 3-mercaptopropanol) were also analyzed. It was found that monolayers on silver generally form faster, but are less stable, than those formed on gold.

Molecular Origami: Designing Functional Molecules of the Future

In the field of chemical biology, DNA origami has been actively researched. This technique, which involves folding DNA strands like origami to assemble them into desired shapes, has made it possible to create complex nanometer-sized structures, marking a major breakthrough in nanotechnology. On the other hand, controlling the folding mechanisms and folded structures of proteins or shorter peptides has been challenging. However, recent advances in techniques such as protein origami, peptide origami, and de novo design peptides have made it possible to construct various nanoscale structures and create functional molecules. These approaches suggest the emergence of new molecular design principles, which can be termed "molecular origami". In this review, we provide an overview of recent research trends in protein/peptide origami and DNA/RNA origami and explore potential future applications of molecular origami technologies in electrochemical biosensors.

Computational analysis of spike protein of SARS-CoV-2 (Omicron variant) for development of peptide-based therapeutics and diagnostics

In the last few years, the worldwide population has suffered from the SARS-CoV-2 pandemic. The WHO dashboard indicated that around 504,079,039 people were infected and 6,204,155 died from COVID-19 caused by different variants of SARS-CoV-2. Recently, a new variant of SARS-CoV-2 (B.1.1.529) was reported by South Africa known as Omicron. The high transmissibility rate and resistance towards available anti-SARS-CoV-2 drugs/vaccines/monoclonal antibodies, make Omicron a variant of concern. Because of various mutations in spike protein, available diagnostic and therapeutic treatments are not reliable. Therefore, the present study explored the development of some therapeutic peptides that can inhibit the SARS-CoV-2 virus interaction with host ACE2 receptors and can also be used for diagnostic purposes. The screened linear B cell epitopes derived from receptor-binding domain of spike protein of Omicron variant were evaluated as peptide inhibitor/vaccine candidates through different bioinformatics tools including molecular docking and simulation to analyze the interaction between Omicron peptide and human ACE2 receptor. Overall, in-silico studies revealed that Omicron peptides OP1-P12, OP14, OP20, OP23, OP24, OP25, OP26, OP27, OP28, OP29, and OP30 have the potential to inhibit Omicron interaction with ACE2 receptor. Moreover, Omicron peptides OP20, OP22, OP23, OP24, OP25, OP26, OP27, and OP30 have shown potential antigenic and immunogenic properties that can be used in design and development vaccines against Omicron. Although the in-silico validation was performed by comparative analysis with the control peptide inhibitor, further validation through wet lab experimentation is required before its use as therapeutic peptides.Communicated by Ramaswamy H. Sarma.

Recent advances in the peptide-based biosensor designs

Biosensors have rapidly emerged as a high-sensitivity and convenient detection method. Among various types of biosensors, optical and electrochemical are the most commonly used. Conventionally, antibodies have been employed to ensure specific interaction between the transmission material and analytes. However, there has been increasing recognition of peptides as a promising recognition element for biosensor development in recent years. The use of peptides as recognition elements provides high level of specificity, sensitivity, and stability for the detection process. The combination of peptide designs and optical or electrochemical detection methods has significantly improved biosensor efficacy. These advancements present opportunities for developing biosensors with diverse functions that can be used to lay a strong scientific foundation for the development of personalized medicine and various other fields. This paper reviews the recent advancements in the development and application of peptide-based optical and electrochemical biosensors, as well as their prospects as a sensor type.

A highly sensitive and selective detection of 2,4,6-trinitrotoluene (TNT) using a peptide-functionalized silicon nanowire array sensor

A highly sensitive and specific detection of 2,4,6-trinitrotoluene (TNT), a typical nitrated aromatic explosive, was demonstrated by a silicon nanowire (SiNW) array sensor. The SiNW array devices were self-assembled and functionalized with the anti-TNT peptide to obtain unique sensitivity toward TNT. Also, the effect of the biointerfacing linker's chemistry and Debye screening with varied ionic strength of phosphate buffer solution (PBS) on TNT binding response signals were investigated. The optimization of the peptide-functionalized SiNW array sensor showed high sensitivity for TNT with a detection limit of 0.2 fM, the highest sensitivity reported to date. These initial promising results may help accelerate the development of portable sensors for femtomolar level TNT detection.

Rational Design of Functional Peptide-Gold Hybrid Nanomaterials for Molecular Interactions

Gold nanoparticles (AuNPs) have been extensively used for decades in biosensing-related development due to outstanding optical properties. Peptides, as newly realized functional biomolecules, are promising candidates of replacing antibodies, receptors, and substrates for specific molecular interactions. Both peptides and AuNPs are robust and easily synthesized at relatively low cost. Hence, peptide-AuNP-based bio-nano-technological approaches have drawn increasing interest, especially in the field of molecular targeting, cell imaging, drug delivery, and therapy. Many excellent works in these areas have been reported: demonstrating novel ideas, exploring new targets, and facilitating advanced diagnostic and therapeutic technologies. Importantly, some of them also have been employed to address real practical problems, especially in remote and less privileged areas. This contribution focuses on the application of peptide-gold hybrid nanomaterials for various molecular interactions, especially in biosensing/diagnostics and cell targeting/imaging, as well as for the development of highly active antimicrobial/antifouling coating strategies. Rationally designed peptide-gold nanomaterials with functional properties are discussed along with future challenges and opportunities.

An electrochemical impedimetric sensing platform based on a peptide aptamer identified by high-throughput molecular docking for sensitive l-arginine detection

As a primary building block for protein synthesis, l-arginine (l-Arg) is also a precursor for the synthesis of important metabolites, and is involved in various physiological and pathophysiological processes. l-Arg is a potential biomarker in clinical diagnosis and nutritional status assessment, making it valuable to quantify and monitor this biomolecule. In this study, peptide aptamers that specifically interact with l-Arg were identified by high-throughput molecular docking, and the binding capacities between the synthesized peptide aptamers and l-Arg were then measured by isothermal titration calorimetry. We hypothesized that the peptide aptamer with the greatest binding capacity could be used as the recognition element in a biosensor. A chemosynthetic peptide aptamer modified with mercaptan and spacer units (thioctic acid-GGGG-FGHIHEGY) was thus used to construct label-free electrochemical impedimetric biosensors for l-Arg based on gold electrodes. The optimum biosensor showed good sensitivity to l-Arg with a linear range of 0.1 pM-0.1 mM, and the calculated limit of detection (three times the signal-to-noise ratio) was 0.01 pM. Interference studies and assays of diluted serum samples were also carried out, and satisfactory results obtained. In conclusion, a potential method of peptide aptamer screening and biosensor fabrication for detecting small biological molecules was demonstrated.

The application of antibody-aptamer hybrid biosensors in clinical diagnostics and environmental analysis

The growing number of various diseases and the increase of environmental contamination are the causes for the development of novel methods for their detection. The possibility of the application of affinity-based biosensors for such purposes seems particularly promising as they provide high selectivity and low detection limits. Recently, the usage of hybrid antibody-aptamer sandwich constructs was shown to be more advantageous in terms of working parameters in comparison to aptamer-based and immune-based biosensors. This review is focused on the usage of hybrid antibody-aptamer receptor layers for the determination of clinically and environmentally important target molecules. In this work, antibodies and aptamer molecules are characterized and the methods of their immobilization as well as analytical signal generation are shown. This is followed by the critical presentation of examples of hybrid sandwich biosensors that have been elaborated in the past 12 years.

What Electrochemical Biosensors Can Do for Forensic Science? Unique Features and Applications

This article critically discusses the latest advances in the use of voltammetric, amperometric, potentiometric, and impedimetric biosensors for forensic analysis. Highlighted examples that show the advantages of these tools to develop methods capable of detecting very small concentrations of analytes and provide selective determinations through analytical responses, without significant interferences from other components of the samples, are presented and discussed, thus stressing the great versatility and utility of electrochemical biosensors in this growing research field. To illustrate this, the determination of substances with forensic relevance by using electrochemical biosensors reported in the last five years (2015–2019) are reviewed. The different configurations of enzyme or affinity biosensors used to solve analytical problems related to forensic practice, with special attention to applications in complex samples, are considered. Main prospects, challenges to focus, such as the fabrication of devices for rapid analysis of target analytes directly on-site at the crime scene, or their widespread use and successful applications to complex samples of interest in forensic analysis, and future efforts, are also briefly discussed.

Targeted delivery of doxorubicin to cancer cells by a cruciform DNA nanostructure composed of AS1411 and FOXM1 aptamers

OBJECTIVES

Here, a novel cruciform DNA nanostructure was developed for targeted delivery of doxorubicin (Dox), as an anticancer agent, to lung (A549 cells) and breast (4T1 cells) cancer cells. The cruciform DNA nanostructure consisted of AS1411 aptamer as targeting agent and Forkhead Box Protein M1(FOXM1) aptamer as therapeutic agent.

METHODS

MTT assay, fluorescence imaging, flow cytometry analysis, and in vivoantitumor efficacy were performed to evaluate the function of the Dox-DNA nanostructure complex.

RESULTS

The presented delivery system benefited from tumor targeting, high stability in serum and simple construction. The Dox-DNA nanostructure complex showed a noticeable higher internalization degree into A549 and 4T1 cells (target), overexpressing nucleolin on their cell membranes, compared to CHO cells (nontarget, nucleolin negative). Moreover, the results of MTT assay exhibited that Dox-DNA nanostructure complex significantly decreased cell viability in A549 and 4T1 cells compared to CHO cells, which significantly preserved their viability. Besides, Dox-DNA nanostructure complex significantly reduced tumor growth in tumor-bearing mice in comparison with Dox and DNA nanostructure treatments.

CONCLUSION

These findings confirmed that synergistic combination of FOXM1 aptamer and Dox into Dox-DNA nanostructure complex enhanced antitumor effectiveness and reduced toxicity toward nontarget cells, opening up new insights in cancer treatment.

DNA Nanotechnology-Enabled Interfacial Engineering for Biosensor Development

Biosensors represent biomimetic analytical tools for addressing increasing needs in medical diagnosis, environmental monitoring, security, and biodefense. Nevertheless, widespread real-world applications of biosensors remain challenging due to limitations of performance, including sensitivity, specificity, speed, and reproducibility. In this review, we present a DNA nanotechnology-enabled interfacial engineering approach for improving the performance of biosensors. We first introduce the main challenges of the biosensing interfaces, especially under the context of controlling the DNA interfacial assembly. We then summarize recent progress in DNA nanotechnology and efforts to harness DNA nanostructures to engineer various biological interfaces, with a particular focus on the use of framework nucleic acids. We also discuss the implementation of biosensors to detect physiologically relevant nucleic acids, proteins, small molecules, ions, and other biomarkers. This review highlights promising applications of DNA nanotechnology in interfacial engineering for biosensors and related areas.