Probing Non-Canonical A*C Base Pairs in DNA using SERS

Raman spectroscopy probes the vibrational modes of a molecule. In recent years, surface-enhanced Raman spectra (SERS) of oligonucleotides on gold or silver nanoparticles have yielded significantly stronger signals. Raman spectra of DNA are high throughput, quantitative, and label-free and show distinct features created by vibrational modes such as ring deformation, backbone bending, and hydrogen bond stretching. Here we are using gold nanoparticles to probe various structural changes in a short helical DNA designed to mimic SL1 of coronavirus and SL of U6 snRNA. Phosphate buffers containing 1 M KCl or 10 mM magnesium chloride were utilized at two different pH (5.5 and 7). Differences in peak intensity are being observed between canonically paired helical DNA and DNA of similar composition with modifications containing non-canonical A*C base pair. We are comparing ion binding, pH-related, and temperature-variable conditions to observe changes in DNA structures.Copyright © 2023 The American Society for Biochemistry and Molecular Biology, Inc.

The Potential Impact of Ayurvedic Traditional Bhasma on SARS-CoV-2-Induced Pathogenesis

The mass casualties caused by the delta variant and the wave of the newer "Omicron" variant of SARS-COV-2 in India have brought about great concern among healthcare officials. The government and healthcare agencies are seeking effective strategies to counter the pandemic. The application of nanotechnology and repurposing of drugs are reported as promising approaches in the management of COVID-19 disease. It has also immensely boomed the search for productive, re-liable, cost-effective, and bio-assimilable alternative solutions. Since ancient times, the traditional-ly employed Ayurvedic bhasmas have been used for diverse infectious diseases, which are now employed as nanomedicine that could be applied for managing COVID-19-related health anomalies. Like currently engineered metal nanoparticles (NPs), the bhasma nanoparticles (BNPs) are also packed with unique physicochemical properties, including multi-elemental nanocrystalline compo-sition, size, shape, dissolution, surface charge, hydrophobicity, and multi-pathway regulatory as well as modulatory effects. Because of these conformational and configurational-based physico-chemical advantages, Bhasma NPs may have promising potential to manage the COVID-19 pandemic and reduce the incidence of pneumonia-like common lung infections in children as well as age-related inflammatory diseases via immunomodulatory, anti-inflammatory, antiviral, and adju-vant-related properties.Copyright © 2023 Bentham Science Publishers.

Assessment of different laboratory tests for the diagnosis of novel coronavirus infections

Rapid diagnosis of coronavirus disease 2019 (COVID-19)-infected patients is urgent in making decisions on public health measures. There are different types of diagnostic tests, such as quantitative PCR assay, antibody, and antigen-based and CRISPR-based tests, which detect genetic materials, viral proteins, or human antibodies in clinical samples. However, the proper test should be highly sensitive, quick, and affordable to address this life-threatening situation. This review article highlights the advantages and disadvantages of each test and compares its different features, such as sensitivity, specificity, and limit of detection to reach a reliable conclusion. Moreover, the FDA- authorized kits and studies' approaches toward these have been compared to provide a better perspective to the researchers.Copyright © 2022 Lippincott Williams and Wilkins. All rights reserved.

AuNP-Coated Cotton as VOC Sensor for Disease Detection from Breath

The COVID-19 pandemic outbreak, declared in March 2020, has led to several behavioral changes in the general population, such as social distancing and mask usage among others. Furthermore, the sanitary emergency has stressed health system weaknesses in terms of disease prevention, diagnosis, and cure. Thus, smart technologies allowing for early and quick detection of diseases are called for. In this framework, the development of point-of-care devices can provide new solutions for sanitary emergencies management. This work focuses on the development of useful tools for early disease diagnosis based on nanomaterials on cotton substrates, to obtain a low-cost and easy-to-use detector of breath volatiles as disease markers. Specifically, we report encouraging experimental results concerning acetone detection through impedance measurements. Such findings can pave the way to the implementation of VOCs (Volatile Organic Compounds) sensors into smart and user friendly diagnostic devices. © 2023, The Author(s), under exclusive license to Springer Nature Switzerland AG.

Fluorophore-encapsulated nanobeads for on-site, rapid, and sensitive lateral flow assay.

Since December 2019, the rapid and sensitive detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has become a priority for public health. Although the lateral flow assay (LFA) sensor has emerged as a rapid and on-site SARS-CoV-2 detection technique, the conventional approach of using gold nanoparticles for the signaling probe had limitations in increasing the sensitivity of the sensor. Herein, our newly suggested methodology to improve the performance of the LFA system could amplify the sensor signal with a facile fabrication method by concentrating fluorescent organic molecules. A large Stokes shift fluorophore (single benzene) was encapsulated into polystyrene nanobeads to enhance the fluorescence intensity of the probe for LFA sensor, which was detected on the test line with a longpass filter under ultraviolet light irradiation. This approach provides comparatively high sensitivity with the limit of detection of 1 ng mL-1 for the SARS-CoV-2 spike protein and a fast detection process, which takes less than 20 min. Furthermore, our sensor showed higher performance than gold nanoparticle-based commercial rapid diagnostics test kits in clinical tests, proving that this approach is more suitable and reliable for the sensitive and rapid detection of viruses, bacteria, and other hazardous materials.

Applications of Gold and Silver Nanoparticles in Theranostics.

Nanotechnology sculptures the current scenario of science and technology. The word nano refers 'small' which ranges from 10 to 100 nm in size. Silver and gold nanoparticles can be synthesized at nanoscale and have unique biological properties like antibacterial, antifungal, antiviral, antiparasitic, antiplatelet, anti-inflammatory, and anti-tumor activity. In this mini review, we shall discuss the various applications of silver and gold nanoparticles (AuNPs) in the field of therapy, imaging, biomedical devices and in cancer diagnosis. The usage of silver nanoparticles(AgNPs) in dentistry and dental implants, therapeutic abilities like wound dressings, silver impregnated catheters, ventricular drainage catheters, combating orthopedic infections, and osteointegration will be elaborated. Gold nanoparticles in recent years have garnered large importance in bio medical applications. They are being used in diagnosis and have recently seen a surge in therapeutics. In this mini review, we shall see about the various applications of AuNP and AgNP, and highlight their evolution in theranostics.

A portable, low-cost and high-throughput electrochemical impedance spectroscopy device for point-of-care biomarker detection

This paper presents a portable, fast and accurate electrochemical impedance spectroscopy (EIS) device with 8-well interdigitated electrode chips for biomarker detection. The design adopts low crest factor multisine signal synthesis at low frequencies (<1 kHz) and single-tone signals at high frequencies (>1 kHz), which significantly increases measurement speed without sacrificing accuracy. In addition, the low excitation amplitude of 10 mV preserves impedance linearity and protects the biosamples. The system achieved an average magnitude accuracy error of 0.30% in the frequency range of interest and it requires only 0.46 s to scan 28 frequency points from 10 Hz to 1 MHz. Experiments were conducted to test the capability to detect antibodies against SARS-CoV-2. Gold nanoparticles bound with protein G (GNP-G) were employed as the conjugated secondary antibody probe to detect anti-SARS-CoV-2 IgG in serum. A highly statistical significance (p = 7×10−6) could be found in the impedance data at 10 kHz. The impedance magnitude alteration caused by the GNP-G of the positive and negative groups were 27.2%±13.6% and 4.1%±1.7%, respectively. The results imply that the proposed system enables rapid COVID-19 antibody biomarker detection. Moreover, the EIS system and GNPs have the potential to be modified to detect other biomarkers. © 2022 The Author(s)

Recent advances of nanotechnology in COVID 19: A critical review and future perspective

The global anxiety and economic crisis causes the deadly pandemic coronavirus disease of 2019 (COVID 19) affect millions of people right now. Subsequently, this life threatened viral disease is caused due to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). However, morbidity and mortality of infected patients are due to cytokines storm syndrome associated with lung injury and multiorgan failure caused by COVID 19. Thereafter, several methodological advances have been approved by WHO and US-FDA for the detection, diagnosis and control of this wide spreadable communicable disease but still facing multi-challenges to control. Herein, we majorly emphasize the current trends and future perspectives of nano-medicinal based approaches for the delivery of anti-COVID 19 therapeutic moieties. Interestingly, Nanoparticles (NPs) loaded with drug molecules or vaccines resemble morphological features of SARS-CoV-2 in their size (60–140 nm) and shape (circular or spherical) that particularly mimics the virus facilitating strong interaction between them. Indeed, the delivery of anti-COVID 19 cargos via a nanoparticle such as Lipidic nanoparticles, Polymeric nanoparticles, Metallic nanoparticles, and Multi-functionalized nanoparticles to overcome the drawbacks of conventional approaches, specifying the site-specific targeting with reduced drug loading and toxicities, exhibit their immense potential. Additionally, nano-technological based drug delivery with their peculiar characteristics of having low immunogenicity, tunable drug release, multidrug delivery, higher selectivity and specificity, higher efficacy and tolerability switch on the novel pathway for the prevention and treatment of COVID 19. © 2022 The Author(s)

Gold Nanoparticle Enabled Localized Surface Plasmon Resonance on Unique Gold Nanomushroom Structures for On-Chip CRISPR-Cas13a Sensing.

A novel localized surface plasmon resonance (LSPR) system based on the coupling of gold nanomushrooms (AuNMs) and gold nanoparticles (AuNPs) is developed to enable a significant plasmonic resonant shift. The AuNP size, surface chemistry, and concentration are characterized to maximize the LSPR effect. A 31 nm redshift is achieved when the AuNMs are saturated by the AuNPs. This giant redshift also increases the full width of the spectrum and is explained by the 3D finite-difference time-domain (FDTD) calculation. In addition, this LSPR substrate is packaged in a microfluidic cell and integrated with a CRISPR-Cas13a RNA detection assay for the detection of the SARS-CoV-2 RNA targets. Once activated by the target, the AuNPs are cleaved from linker probes and randomly deposited on the AuNM substrate, demonstrating a large redshift. The novel LSPR chip using AuNP as an indicator is simple, specific, isothermal, and label-free; and thus, provides a new opportunity to achieve the next generation multiplexing and sensitive molecular diagnostic system.

Computational tools for aptamer identification and optimization

Aptamers are single-stranded DNA or RNA oligonucleotides that can selectively bind to a specific target. They are generally obtained by SELEX, but the procedure is challenging and time-consuming. Moreover, the identified aptamers tend to be insufficient in stability, specificity, and affinity. Thus, only a handful of aptamers have entered the practical use stage. Recently, computational approaches have demonstrated a significant capacity to assist in the discovery of high-performance aptamers. This review discusses the advances achieved in several aspects of computational tools in this field, as well as the new progress in machine learning and deep learning, which are used in aptamer identification and optimization. To illustrate these computationally aided processes, aptamer selections against SARS-CoV-2 are discussed in detail as a case study. We hope that this review will aid and motivate researchers to develop and utilize more computational techniques to discover ideal aptamers effectively. Copyright © 2022 Elsevier B.V.

Development of colloidal Gold nanoparticle based lateral-flow assay for rapid detection of SARS-CoV-2 showing enhanced sensitivity and specificity

To stop the spread of COVID-19 in this outbreak, diagnostic testing is essential. Quick diagnostic tests must be employed in this pandemic, which is brought on by the severe acute respiratory syndrome (SARS)-CoV-2 virus, to successfully treat and manage COVID-19. There are several problems with the present RT-PCR system that the lateral flow assay (LFA), a kind of clinically sensitive diagnostic test, may be able to fix, especially in low-and middle-income nations. Gold nanoparticle-(AuNP-LFA) is a practical method for detecting COVID-19 in basic hospitals and laboratories, particularly in emergency situations where many samples must be quickly examined. Safe, accurate, and non-toxic diagnostic tests must be employed during the pandemic, to successfully treat and manage COVID-19. Recombinant SARS-CoV-2 nucleocapsid monoclonal antibody was employed to detect COVID-19 antigens in the presence of patients to establish a fast LFA for COVID-19. Synthesis of colloidal gold particles and antibody colloidal gold conjugates was evaluated by using UV/Vis spectroscopy. A capture line made of anti-SARS-CoV-2 antibody was coated on nitrocellulose membrane. To create the control line, goat anti-mouse IgG monoclonal antibody was coated. On a polystyrene backing board, the immunochromatographic strip was constructed in the ideal order. Using ELISA as the standard procedure, the strips' sensitivity and specificity were assessed. The results' stability and repeatability were evaluated over a 9-month period. Colloidal gold nanoparticle-based LFAs created in this study can be employed for quicker and more accurate detection of SARS-CoV-2. © 2023 Singh, et al.

Detection of COVID-19 DNA using Förster Resonance Energy Transfer between upconversion and gold nanoparticles

FRET is ascribed to the spectral overlapping of upconversion luminescence and the absorption of AuNPs. This experiment enables early-stage coronavirus detection. The results show a sensitivity of 100 fM for the detection of COVID-19 DNA. © 2022 The Author(s)

Detection of COVID-19 DNA using Förster Resonance Energy Transfer between upconversion and gold nanoparticles

FRET is ascribed to the spectral overlapping of upconversion luminescence and the absorption of AuNPs. This experiment enables early-stage coronavirus detection. The results show a sensitivity of 100 fM for the detection of COVID-19 DNA. © 2022 The Author(s)

Functionalizing Gold Nanostars with Ninhydrin as Vehicle Molecule for Biomedical Applications

In recent years, there has been an explosion in Gold NanoParticle (GNP) research, with a rapid increase in publications in diverse fields, including imaging, bioengineering, and molecular biology. GNPs exhibit unique physicochemical properties, including surface plasmon resonance (SPR) and bind amine and thiol groups, allowing surface modification and use in biomedical applications. Nanoparticle functionalization is the subject of intense research, with rapid progress being made towards developing biocompatible, multi-functional particles. In the present study, the photochemical method has been done to functionalize various-shaped GNPs like nanostars by the molecules like ninhydrin. Ninhydrin is bactericidal, virucidal, fungicidal, antigen-antibody reactive, and used in fingerprint technology in forensics. The GNPs functionalized with ninhydrin efficiently will bind to the amino acids on the target protein, which is of eminent importance during the pandemic, especially where long-term treatments of COVID-19 bring many side effects of the drugs. The photochemical method is adopted as it provides low thermal load, selective reactivity, selective activation, and controlled radiation in time, space, and energy. © 2022, Avestia Publishing. All rights reserved.

Novel RT-PCR Using Sugar Chain-Immobilized Gold-Nanoparticles Correlates Patients' Symptoms: The Follow-Up Study of COVID-19 Hospitalized Patients.

Background: The transmissible capacity and toxicity of SARS-CoV-2 variants are continually changing. We report here the follow-up study of hospitalized COVID-19 patients from 2020 to 2022. It is known that the PCR diagnosis for hospitalized patients sometimes causes confusion because of the incompatibility between their diagnosis and symptoms. We applied our sugar chain-immobilized gold-nanoparticles for the extraction and partial purification of RNA from specimens for quantitative RT-PCR assay and evaluated whether the results correlate with patients' symptoms. Methods and Results: Saliva specimens were taken from hospitalized patients with mild or moderate symptoms every early morning. At the time of RT-PCR diagnosis, two methods for the extraction and partial purification of RNA from the specimen were performed: a commonly used Boom (Qiagen) method and our original sugar chain-immobilized gold nanoparticle (SGNP) method. For symptoms, body temperature and oxygen saturation (SpO2) of patients were monitored every 4 h. Conclusions: It was clear that patients infected with the Delta variant needed more time to recover than those with the Omicron variant, and that the SGNP method showed more realistic correlation with the symptoms of patients compared with the common Qiagen method.

Optical reflectometric measurement of SARS-CoV-2 (COVID-19) RNA based on cationic cysteamine-capped gold nanoparticles.

The coronavirus disease (COVID-19) caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) emerged as a major public health outbreak in late 2019 and was proclaimed a global pandemic in March 2020. A reflectometric-based RNA biosensor was developed by using cysteamine-stabilized gold nanoparticles (cysAuNPs) as the colorimetric probe for bioassay of COVID-19 RNA (SARS-CoV-2 RNA) sequence. The cysAuNPs aggregated in the presence of DNA probes via cationic and anionic electrostatic attraction between the positively charged cysteamine ligands and the negatively charged sugar-phosphate backbone of DNA, whilst in the presence of target RNAs, the specific recognition between DNA probes and targets depleted the electrostatic interaction between the DNA probes and cysAuNPs signal probe, leading to dispersed particles. This has rendered a remarkable shifting in the surface plasmon resonance (SPR) on the basis of visual color change of the RNA biosensor from red to purplish hue at the wavelength of 765 nm. Optical evaluation of SARS-CoV-2 RNA by means on reflectance transduction of the RNA biosensor based on cysAuNPs optical sensing probes demonstrated rapid response time of 30 min with high sensitivity, good linearity and high reproducibility across a COVID-19 RNA concentration range of 25 nM to 200 nM, and limit of detection (LOD) at 0.12 nM. qPCR amplification of SARS-CoV-2 viral RNA showed good agreement with the proposed RNA biosensor by using spiked RNA samples of the oropharyngeal swab from COVID-19 patients. Therefore, this assay is useful for rapid and early diagnosis of COVID-19 disease including asymptomatic carriers with low viral load even in the presence of co-infection with other viruses that manifest similar respiratory symptoms.

Integrating Single Domain Antibodies into Field-Deployable Rapid Assays.

Single domain antibodies (sdAb) are the recombinant variable heavy domains derived from camelid heavy-chain antibodies. While they have binding affinities equivalent to conventional antibodies, sdAb are only one-tenth the size and possess numerous advantages such as excellent thermal stability with the ability to refold following denaturation, and inexpensive production in Escherichia coli or yeast. However, their small size does have drawbacks, one being that they can lose activity upon attachment or adsorption to surfaces, or may fail to adsorb efficiently, as they are highly soluble. This can make the transition from using conventional antibodies to sdAb nontrivial for assay development. Specifically, it is often necessary to re-optimize the protocols and tailor the recombinant sdAb through protein engineering to function efficiently in handheld assays, which currently are utilized for point of care testing and field applications. This work focuses on optimizing the integration of sdAb into rapid vertical flow assays. To achieve this goal, we engineered sdAb-based constructs and developed general protocols for the attachment of the sdAb to both gold nanoparticles and a support membrane. We achieved a limit of detection of 0.11 µg/mL for toxins staphylococcal enterotoxin B and ricin, both potential biothreat agents. Additionally, we demonstrated the ability to detect the nucleocapsid protein of SARS-CoV-2, a common target of antigen tests for COVID-19.

Integration of Power-Free and Self-Contained Microfluidic Chip with Fiber Optic Particle Plasmon Resonance Aptasensor for Rapid Detection of SARS-CoV-2 Nucleocapsid Protein.

The global pandemic of COVID-19 has created an unrivalled need for sensitive and rapid point-of-care testing (POCT) methods for the detection of infectious viruses. For the novel coronavirus SARS-CoV-2, the nucleocapsid protein (N-protein) is one of the most abundant structural proteins of the virus and it serves as a useful diagnostic marker for detection. Herein, we report a fiber optic particle plasmon resonance (FOPPR) biosensor which employed a single-stranded DNA (ssDNA) aptamer as the recognition element to detect the SARS-CoV-2 N-protein in 15 min with a limit of detection (LOD) of 2.8 nM, meeting the acceptable LOD of 106 copies/mL set by the WHO target product profile. The sensor chip is a microfluidic chip based on the balance between the gravitational potential and the capillary force to control fluid loading, thus enabling the power-free auto-flowing function. It also has a risk-free self-contained design to avoid the risk of the virus leaking into the environment. These findings demonstrate the potential for designing a low-cost and robust POCT device towards rapid antigen detection for early screening of SARS-CoV-2 and its related mutants.

Printed Capacitive Immunoassay for Detecting SARS-CoV-2 Viral Particles

The key to fight against a global pandemic such as COVID-19 is to have low-cost, reliable and fast response diagnostic tools. Electronic biosensors are preferred because of their ease of integration into current centralized health care networks and integration with modern point-of-care testing (POCT) devices. Printed electronic sensors provide a sensitive and reliable diagnostic platform to aid in controlling transmissible diseases. In this work, we demonstrate a fully printed capacitive biosensor. The sensor uses coplanar electrodes, coupled with capture antibodies immobilized on microporous Polyvinylidene-fluoride (PVDF) film to detect the SARS-CoV-2 spike protein in spiked buffer solutions. Antibody immobilization on PVDF surface is confirmed with confocal fluorescent imaging microscopy. Gold nanoparticle (GNP) tagged detection antibodies are also introduced to provide increased sensitivity. The gold nanoparticles provide a reflectance layer which leads to increased capacitance. This increased capacitance can be measured directly and has demonstrated the ability to screen for spiked samples with statistical significance. This fully printed capacitive immunoassay has the potential to be used as a transmissible disease screening and vaccine efficacy assessment tool for resource-limited areas. IEEE