LAMPPrimerBank, a manually curated database of experimentally validated loop-mediated isothermal amplification primers for detection of respiratory pathogens
JOURNAL: Infection
AUTHORS: Fatemeh Arabi-Jeshvaghani, Fatemeh Javadi-Zarnaghi, Hannah Franziska Löchel, Roman Martin & Dominik Heider
ABSTRACT:
DOI: 10.1007/s15010-023-02100-0
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
AUTHORS: Fatemeh Arabi-Jeshvaghani, Fatemeh Javadi-Zarnaghi, Mohamad Reza Ganjalikhany
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
DNAzymeBuilder, a web application for in situ generation of RNA/DNA-cleaving deoxyribozymes
PUBLICATION DATE: April 2022
AUTHORS: Razieh Mohammadi-Arani, Fatemeh Javadi-Zarnaghi, Pietro Boccaletto, Janusz M. Bujnicki and Almudena Ponce-Salvatierra.
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
Unified-amplifier based primer exchange reaction (UniAmPER) enabled detection of SARS-CoV-2 from clinical samples
PUBLICATION DATE: January 2022
AUTHORS: Reyhaneh Tavakoli-Koopaei, Fatemeh Javadi-Zarnaghi, Hossein Mirhendi
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
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.
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
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.
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
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.
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.
DOI: 10.1111/JAM.14799