dorsa pascal system, inc.

Publications

Biosensors and Bioelectronics, 2025

ViPER: A visual bipolar electrochemical biosensor based on isothermal addition of a universal tag for detection of SARS-CoV-2

PUBLICATION DATE: February 2025

JOURNAL: Biosensors and Bioelectronics

AUTHORS: Seyedeh Malahat Shadman, Reyhaneh Tavakoli-Koopaei, Masoud A. Mehrgardi, Fatemeh Javadi-Zarnaghi

ABSTRACT:

Emergence of recent pandemics/endemics e.g. COVID-19 and Dengue fever, demonstrated the necessity of development of strategies for swift adaptation of present biosensor for detection of the new emerging pathogens. However, development of a biosensor for a new target is time- and labor-consuming. In this study, we aimed to integrate the primer exchange reaction (PER), an isothermal technique that extends an initiator DNA with a user-defined single-stranded DNA tail, with bipolar electrochemistry. This integration led to the development of a universal biosensor, termed ViPER. We demonstrated the utility of the developed system to detect severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) genomic RNA as a model. The genomic RNA was reverse transcribed to a short cDNA and was tailed with a universal tag, consequently, the tagged cDNA was applied to an electrochemiluminescence integrated bipolar electrochemical biosensor (BPE-ECL). ECL signals were recorded using a digital camera and analyzed by ImageJ. The platform demonstrated a linear response over a wide dynamic range of 10−7-10−17 M for the target nucleic acid with a detection limit of 2.31 × 10−17 M for synthetic targets. The biosensor could also successfully discriminate between biological RNA samples from infected and non-infected individuals. This study introduces the potential of DNA-based visual biosensors for detecting single-stranded RNAs in low-equipped environments, and it holds promises for further development of an ultrasensitive method for various human RNA-based viral pathogens. Moreover, we can design a platform with a predetermined DNA probe sequence for a vast variety of different targets, simply by changing the PER input.

DOI: https://doi.org/10.1016/j.bios.2025.117199

Infection 2023

LAMPPrimerBank, a manually curated database of experimentally validated loop-mediated isothermal amplification primers for detection of respiratory pathogens

PUBLICATION DATE: October 2023

JOURNAL: Infection

AUTHORS: Fatemeh Arabi-Jeshvaghani, Fatemeh Javadi-Zarnaghi, Hannah Franziska Löchel, Roman Martin & Dominik Heider

ABSTRACT:

Purpose and methods

The emergence of coronavirus disease 2019 (COVID-19) has once again affirmed the significant threat of respiratory infections to global public health and the utmost importance of prompt diagnosis in managing and mitigating any pandemic. The nucleic acid amplification test (NAAT) is the primary detection method for most pathogens. Loop‐mediated isothermal amplification (LAMP) is a rapid, simple, sensitive, and specific epitome of isothermal NAAT performed using a set of four to six primers. Primer design is a fundamental step in LAMP assays, with several complexities and experimental screening requirements. To address this challenge, an online database is presented here. Its workflow comprises three steps: literature aggregation, data curation, and database and website implementation.

Results

LAMPPrimerBank (https://lampprimerbank.mathematik.uni-marburg.de) is a manually curated database dedicated to experimentally validated LAMP primers, their peculiarities of assays, and accompanying literature, with a primary emphasis on respiratory pathogens. LAMPPrimerBank, with its user-friendly web interface and an open application programming interface, enables the accelerated and facile exploration, comparison, and exportation of LAMP primer sequences and their respective information from the massively scattered literature. LAMPPrimerBank currently comprises LAMP primers for diagnosing viral, bacterial, and fungal respiratory pathogens. Additionally, to address the challenge of false-positive results generated by nonspecific amplifications, LAMPPrimerBank computationally predicted and visualized the sizes of LAMP products for recorded primer sets in the database.

Conclusion

LAMPPrimerBank, as a pioneering database in the rapidly expanding field of isothermal NAAT, endeavors to confront the two challenges of the LAMP: primer design and discrimination of false-positive results.

DOI: 10.1007/s15010-023-02100-0

Scientific reports 2023

Analysis of critical protein-protein interactions of SARS-CoV-2 capping and proofreading molecular machineries towards designing dual target inhibitory peptides

PUBLICATION DATE: January 2023

JOURNAL: Scientific Reports

AUTHORS: Fatemeh Arabi-Jeshvaghani, Fatemeh Javadi-Zarnaghi, Mohamad Reza Ganjalikhany

ABSTRACT:

In recent years, the emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), as the cause of the coronavirus disease (COVID-19) global pandemic, and its variants, especially those with higher transmissibility and substantial immune evasion, have highlighted the imperative for developing novel therapeutics as sustainable solutions other than vaccination to combat coronaviruses (CoVs). Beside receptor recognition and virus entry, members of the SARS-CoV-2 replication/transcription complex are promising targets for designing antivirals. Here, the interacting residues that mediate protein-protein interactions (PPIs) of nsp10 with nsp16 and nsp14 were comprehensively analyzed, and the key residues' interaction maps, interaction energies, structural networks, and dynamics were investigated. Nsp10 stimulates both nsp14's exoribonuclease (ExoN) and nsp16's 2'O-methyltransferase (2'O-MTase). Nsp14 ExoN is an RNA proofreading enzyme that supports replication fidelity. Nsp16 2'O-MTase is responsible for the completion of RNA capping to ensure efficient replication and translation and escape from the host cell's innate immune system. The results of the PPIs analysis proposed crucial information with implications for designing SARS-CoV-2 antiviral drugs. Based on the predicted shared protein-protein interfaces of the nsp16-nsp10 and nsp14-nsp10 interactions, a set of dual-target peptide inhibitors was designed. The designed peptides were evaluated by molecular docking, peptide-protein interaction analysis, and free energy calculations, and then further optimized by in silico saturation mutagenesis. Based on the predicted evolutionary conservation of the interacted target residues among CoVs, the designed peptides have the potential to be developed as dual target pan-coronavirus inhibitors.

DOI: 10.1038/s41598-022-26778-8

Nucleic Acids Research 2022

DNAzymeBuilder, a web application for in situ generation of RNA/DNA-cleaving deoxyribozymes

PUBLICATION DATE: April 2022

JOURNAL: Nucleic Acids Research

AUTHORS: Razieh Mohammadi-Arani, Fatemeh Javadi-Zarnaghi, Pietro Boccaletto, Janusz M. Bujnicki and Almudena Ponce-Salvatierra.

ABSTRACT:

Nucleic acid cleaving DNAzymes are versatile and robust catalysts that outcompete ribozymes and protein enzymes in terms of chemical stability, affordability and ease to synthesize. In spite of their attractiveness, the choice of which DNAzyme should be used to cleave a given substrate is far from obvious, and requires expert knowledge as well as in-depth literature scrutiny. DNAzymeBuilder enables fast and automatic assembly of DNAzymes for the first time, superseding the manual design of DNAzymes. DNAzymeBuilder relies on an internal database with information on RNA and DNA cleaving DNAzymes, including the reaction conditions under which they best operate, their kinetic parameters, the type of cleavage reaction that is catalyzed, the specific sequence that is recognized by the DNAzyme, the cleavage site within this sequence, and special design features that might be necessary for optimal activity of the DNAzyme. Based on this information and the input sequence provided by the user, DNAzymeBuilder provides a list of DNAzymes to carry out the cleavage reaction and detailed information for each of them, including the expected yield, reaction products and optimal reaction conditions. DNAzymeBuilder is a resource to help researchers introduce DNAzymes in their day-to-day research, and is publicly available at https://iimcb.genesilico.pl/DNAzymeBuilder.

DOI: 10.1093/nar/gkac269

Sensors And Actuators B: Chemical 2022

Unified-amplifier based primer exchange reaction (UniAmPER) enabled detection of SARS-CoV-2 from clinical samples

PUBLICATION DATE: January 2022

JOURNAL: Sensors And Actuators B: Chemical

AUTHORS: Reyhaneh Tavakoli-Koopaei, Fatemeh Javadi-Zarnaghi, Hossein Mirhendi

ABSTRACT:

Primer exchange reaction (PER) is an emergent method for non-templated synthesis of single stranded DNA molecules. PER has been shown to be effective in cell imaging systems and for detection of macromolecules. A particular application of PER is to detect a specific target nucleic acid. To this endeavor, two coupled DNA hairpins, a detector and an amplifier, play in accordance to extend a target nucleic acid with a concatemer DNA sequence. Here we introduced unified-amplifier based primer exchange reaction (UniAmPER) that beneficially extends the target by a unified-amplifier. The unified-amplifier operates as both detector and amplifier hairpins. The extension resulted in synthesis of concatemer G-rich sequences. The G-rich sequences were expected to form G-quadruplex (GQ) structures. Presence of the GQ structures were investigated by peroxidase activity of GQs in presence of hemin, H2°2 and 3,3',5,5'-Tetramethylbenzidine (TMB) as well as by fluorescence signal generation upon intercalation of thioflavin T (ThT). The presented unified-amplifier in this study facilitates application of PER systems for development of colorimetric or fluorogenic biosensors. As a proof of principle, the method has been applied for detection of reversely transcribed cDNAs from clinical SARS-CoV-2 samples.

DOI: 10.1016/J.SNB.2022.131409

Analytical Methods 2020

Performance of a template enhanced hybridization process in biological media for the detection of a breast cancer biomarker

JOURNAL: Analytical Methods

AUTHORS: Tavakoli-Koopaei, R., Javadi-Zarnaghi, F., Aghahosseini, M., Tavassoli, M., Rasaee, M.J.

ABSTRACT:

Single stranded nucleic acids, for e.g., exosomal microRNAs, have been utilized widely for the analysis of the pathological status of individuals in recent years. Template enhanced hybridization process (TeHyP) is a promising strategy for the detection and quantification of such nucleic acid biomarkers. In the TeHyP strategy, two separate DNA strands only assemble for their performance when the target template is present. A TeHyP strategy may be combined with a split G-quadruplex peroxidase mimic to be a colorimetric assay of single stranded nucleic acids. In this study, a special case of such TeHyP was designed and investigated for its detection performance for a microRNA that was reported as a biomarker for triple negative breast cancer. The performance of the colorimetric assay was analyzed comprehensively in the presence of biological media, for e.g., blood, urine, plasma, serum, and saliva. The impact of biological media on the peroxidase mimic activity of the TeHyP system in the presence of the target or its mutants has been quantitatively investigated here.

DOI: 10.1039/C9AY02517K

Strategies for characterization of nucleic acids, 2017

Strategies for characterization of nucleic acids, book chapter in “Enzymatic nucleic acids”

PUBLICATION DATE: June 2017

Book chapter in Advances in Biochemical Engineering/Biotechnology

AUTHORS: Javadi-Zarnaghi, F., Höbartner, C.

Part of the Advances in Biochemical Engineering/Biotechnology book series (ABE,volume 170)

DOI: 10.1007/ 10_2016_59

Scientific Reports 2020

Glycated albumin precipitation using aptamer conjugated magnetic nanoparticles

PUBLICATION DATE: July 2020

JOURNAL: Scientific Reports

AUTHORS: Fayazi, R., Habibi‑Rezaei, M., Heiat M., Javadi‑Zarnaghi, F.,Taheri, R.A.

ABSTRACT:

To develop a strategy for the elimination of prefibrillar amyloid aggregates, a three-step non-modified DNA aptamer conjugation on silica-coated magnetic nanoparticles was carried out to achieve aptamer conjugated on MNP (Ap-SiMNP). Prefibrillar amyloid aggregates are generated under a diabetic condition which are prominently participated in developing diabetic complications. The binding properties of candidate DNA aptamer against serum albumin prefibrillar amyloid aggregates (AA20) were verified using electrophoretic mobility shift assay (EMSA) and surface plasmon resonance spectroscopy (SPR) analysis. The chloro-functionalized silica-coated MNPs were synthesized then a nano-targeting structure as aptamer conjugated on MNP (Ap-SiMNP) was constructed. Finally, Ap-SiMNP was verified for specific binding efficiency and AA20 removal using an external magnetic field. The candidate aptamer showed a high binding capacity at EMSA and SPR analysis (KD = 3.4 × 10─9 M) and successfully used to construct Ap-SiMNP. Here, we show a proof of concept for an efficient bio-scavenger as Ap-SiMNP to provide a promising opportunity to consider as a possible strategy to overcome some diabetic complications through specific binding/removal of toxic AA20 species.

DOI: 10.1038/S41598-020-67469-6

Journal of Applied Microbiology 2021

Novel luminescent affiprobes for molecular detection of Staphylococcus aureus using flow cytometry

PUBLICATION DATE: February 2021

JOURNAL: Journal of Applied Microbiology

AUTHORS: Shakeran, Z., Javadi-Zarnaghi, F., Emamzadeh, R.

ABSTRACT:

Diagnosis of Staphylococcus aureus is important in various diseases from hospital‐acquired infections to foodborne diseases. This work reports two new luminescent affiprobes for specific detection of S. aureus.