Sharif Digital Repository

A naked-eye (equipment-free), label-free (cost-effective), and RNA extraction-free (to speed up) method for SARS-CoV-2 (as a case study of RNA viruses) detection is developed. Here, the DNA is being used as a template for in situ formation of anisotropic gold nanoparticles (AuNPs) without any chemical modification or DNA labeling. In this study, synthesized AuNPs for the direct detection of N-gene (nucleocapsid phosphoprotein) of SARS-CoV-2 are exploited. To this aim, antisense oligonucleotides (ASOs) with an extra poly guanine tail (G12) were designed. Thus, in the presence of its viral target RNA gene and ASOs@AuNPs-RNA hybridization, there was a red shift in its localized surface plasmon... 

The single stranded DNA can be adsorbed on the negatively charged surface of gold nanoparticles (AuNPs), but the rigid structure of double stranded DNA prevents it from adsorption. Signal of a tagged single stranded DNA will be quenched by the plasmon effect of the AuNP surface after its adsorption. This phenomenon has been used to study the DNA hybridization and interactions of two complementary 21mer oligonucleotides each tagged with a different fluorescent dye in the presence of 13 nm gold nanoparticles. The DNA strands used in this study belong to the genome of HIV. The obtained rank deficient three-way fluorescence data sets were resolved by both PARAFAC and restricted Tucker3 models.... 

Organ-on-chip devices have provided the pharmaceutical and tissue engineering worlds much hope since they arrived and began to grow in sophistication. However, limitations for their applicability were soon realized as they lacked real-time monitoring and sensing capabilities. The users of these devices relied solely on endpoint analysis for the results of their tests, which created a chasm in the understanding of life between the lab the natural world. However, this gap is being bridged with sensors that are integrated into organ-on-chip devices. This review goes in-depth on different sensing methods, giving examples for various research on mechanical, electrical resistance, and bead-based... 

Herein, we present a novel, simple, and ultrasensitive electrochemical DNA (E-DNA) sensor based on hollow carbon spheres (HCS) decorated with polyaniline (PANI). A thiolated 21-mer oligonucleotide, characteristic of HBV DNA, is immobilized via electrodeposited gold nanoparticles on HCS-PANI. Cyclic voltammetry (CV), differential pulse voltammetry (DPV), and electrochemical impedance spectroscopy (EIS) are used to characterize the electrochemical properties of the prepared nanocomposite. Scanning electron microscopy is employed to investigate the morphological texture of the fabricated modifier. An enhanced intrinsic signal of PANI is probed to evaluate the biosensing ability of the prepared... 

In this paper the field-effect transistor DNA biosensor for detecting hepatitis B virus (HBV) based on indium tin oxide nanowires (ITO NWs) in label free approach has been fabricated. Because of ITO nanowires intensive conductance and functional modified surface, the probe immobilization and target hybridization were increased strongly. The high resolution transmission electron microscopy (HRTEM) measurement showed that ITO nanowires were crystalline and less than 50 nm in diameter. The single-stranded hepatitis B virus DNA (SS-DNA) was immobilized as probe on the Au-modified nanowires. The DNA targets were measured in a linear concentration range from 1fM to 10 µM. The detection limit of... 

For the first time, a new platform based on electrochemical growth of Au nanoparticles on aligned multi-walled carbon nanotubes (A-MWCNT) was developed for sensitive lable-free DNA detection of the TP53 gene mutation, one of the most popular genes in cancer research. Electrochemical impedance spectroscopy (EIS) was used to monitor the sequence-specific DNA hybridization events related to TP53 gene. Compared to the bare Ta or MWCNT/Ta electrodes, the synergistic interactions of vertically aligned MWCNT array and gold nanoparticles at modified electrode could improve the density of the probe DNA attachment and resulting the sensitivity of the DNA sensor greatly. Using EIS, over the extended... 

An impedimetric human papilloma virus (HPV) DNA biosensor based on gold nanotubes (AuNTs) in label free detection was materialized. The AuNTs decorated nanoporous polycarbonate (AuNTs-PC) template as biosensor electrode was fabricated by electrodeposition method. The single strand DNA (ss-DNA) probe was covalently immobilized onto the AuNTs-PC electrode. The hybridization of target sequences with the ss-DNA probe was observed by the electrochemical impedance spectroscopy (EIS). The biosensor showed high selectivity and could differentiate between the complementary, mismatch and non-complementary DNA sequences. The EIS measurements were matched to Randle's equivalent circuit. The... 

A simple platform based on a hairpin oligonucleotide switch and multi-walled carbon nanotubes (MWCNTs) for the ultrasensitive detection of specific DNA sequences has been developed. In this approach, the π-stacking interaction of single-strand DNA-MWCNT was employed to construct an electrochemical DNA biosensor. Changes to the surface conductivity, based on the MWCNT replacement, were monitored by using the electrochemical species [Fe(CN)6]3-/4- as a redox probe. Morphological and voltammetric characterizations of the electrode surface were performed using atomic force microscopy (AFM), energy dispersive spectroscopy (EDS), cyclic voltammetry (CV), differential pulse voltammetry (DPV) and... 

An impedimetric human papilloma virus (HPV) DNA biosensor based on gold nanotubes (AuNTs) in label free detection was materialized. The AuNTs decorated nanoporous polycarbonate (AuNTs-PC) template as biosensor electrode was fabricated by electrodeposition method. The single strand DNA (ss-DNA) probe was covalently immobilized onto the AuNTs-PC electrode. The hybridization of target sequences with the ss-DNA probe was observed by the electrochemical impedance spectroscopy (EIS). The biosensor showed high selectivity and could differentiate between the complementary, mismatch and non-complementary DNA sequences. The EIS measurements were matched to Randle's equivalent circuit. The... 

The highly sensitive impedimetric biosensor in label free approach for hepatitis B virus DNA (HPV DNA) detection based on tellurium doped ZnO nanowires was fabricated. The NWs were grown by hybrid thin film oxidation in the physical vapor deposition (PVD) mechanism. The morphology characterization of the synthesized NWs was performed by field emission scanning electron microscopy (FESEM) and the images demonstrated that the diameter and the length of the materialized NWs were around 50 nm and several micrometers, respectively. The high-resolution transmission electron microscopy (HRTEM) image indicated that the fabricated NWs were crystalline and their phase characterization was validated by... 

Breast cancer is the most prevalent type of cancer in women; hence, many researches have been focused on developing effective treatment protocols. In this study, a novel nanocarrier was fabricated for gene and photothermal combination cancer therapy by conjugating histone methyltransferase complex subunit SET1 (hSET1) on reduced polydopamine coated graphene oxide nanosheets (rGO-PDA). The rGO-PDA nanocarriers provide higher near-infrared absorption and further integrating with hSET1 antisense as an anticancer gene that down-regulates the amount of hSET1 overexpressed and suppresses the proliferation of cancer cells. The nanoplatform was prepared by polymerizing of dopamine, a mussel adhesive... 

Graphene oxide nanowalls with extremely sharp edges and preferred vertical orientation were deposited on a graphite electrode by using electrophoretic deposition in an Mg 2+-GO electrolyte. Using differential pulse voltammetry (DPV), reduced graphene nanowalls (RGNWs) were applied for the first time, in developing an ultra-high-resolution electrochemical biosensor for detection of the four bases of DNA (G, A, T, and C) by monitoring the oxidation signals of the individual nucleotide bases. The extremely enhanced electrochemical reactivity of the four free bases of DNA, single-stranded DNA, and double-stranded DNA (dsDNA) at the surface of the RGNW electrode was compared to electrochemical... 

Local three-stranded DNA/RNA hybrid regions of genomes (R-loops) have been detected either by binding of a monoclonal antibody (DRIP assay) or by enzymatic recognition by RNaseH. Such a structure has been postulated for mouse and human telomeres, clearly suggested by the identification of the complementary RNA Telomeric repeat-containing RNA “TERRA”. However, the tremendous disparity in the information obtained with antibody-based technology drove us to investigate a new strategy. Based on the observation that DNA/RNA hybrids in a triplex complex genome co-purify with the double-stranded chromosomal DNA fraction, we developed a direct preparative approach from total protein-free cellular...