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nucleic-acid
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Synthesis of Cationic Mesoporous Silica Nanoparticles as a Carrier for the Deliveryof Nucleic Acids
, M.Sc. Thesis Sharif University of Technology ; Vosoughi, Manouchehr (Supervisor) ; Arpanaei, Ayyoob (Supervisor) ; Javadi, Hamid Reza (Co-Advisor)
Abstract
Mesoporous silica nanoparticles (MSNP) have attracted lots of attentions because of their particular characteristics. Physical characteristics such as structure, morphology, porosity, and size of these nanoparticles have strong impact on their function and it can be conceived a wide range of applications for them by manipulating these characteristics. In this research, monodispersed MSNPs with a controllable size in the range of 50-130 nm and pore size in the range of 4-24 nm were synthesized and positively functionalized in order to develop a carrier for the delivery of nucleic acids (siRNA and pDNA). The MSNPs were synthesized by the template removing method.In this method, sodium...
You are what you eat: Sequence analysis reveals how plant microRNAs may regulate the human genome
, Article Computers in Biology and Medicine ; Volume 106 , 2019 , Pages 106-113 ; 00104825 (ISSN) ; Hasani Bidgoli, M ; Motahari, S. A ; Sedaghat, N ; Modarressi, M. H ; Sharif University of Technology
Elsevier Ltd
2019
Abstract
Background: Nutrigenomic has revolutionized our understanding of nutrition. As plants make up a noticeable part of our diet, in the present study we chose microRNAs of edible plants and investigated if they can perfectly match human genes, indicating potential regulatory functionalities. Methods: miRNAs were obtained using the PNRD database. Edible plants were separated and microRNAs in common in at least four of them entered our analysis. Using vmatchPattern, these 64 miRNAs went through four steps of refinement to improve target prediction: Alignment with the whole genome (2581 results), filtered for those in gene regions (1371 results), filtered for exon regions (66 results) and finally...
The field effect transistor DNA biosensor based on ITO nanowires in label-free hepatitis B virus detecting compatible with CMOS technology
, Article Biosensors and Bioelectronics ; Volume 105 , 15 May , 2018 , Pages 58-64 ; 09565663 (ISSN) ; Sharif University of Technology
Elsevier Ltd
2018
Abstract
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...
Superparamagnetic iron oxide nanoparticles with rigid cross-linked polyethylene glycol fumarate coating for application in imaging and drug delivery
, Article Journal of Physical Chemistry C ; Volume 113, Issue 19 , 2009 , Pages 8124-8131 ; 19327447 (ISSN) ; Simchi, A ; Imani, M ; Hafeli, U. O ; Sharif University of Technology
2009
Abstract
Superparamagnetic iron oxide nanoparticles with proper surface coatings are increasingly being evaluated for clinical applications such as hyperthermia, drug delivery, magnetic resonance imaging, transfection, and cell/protein separation. To enhance the applicability of magnetic nanoparticles, two main problems must be overcome. First, as the drug coats the particle surface, a significant portion of it is quickly released upon injection (burst effect). Therefore, only small amounts of the drug reach the specific site after, for example, magnetic drug targeting. Second, once the surface-derivatized nanoparticles are inside the cells, the coating is likely digested, leaving the bare particles...
Solving MEC model of haplotype reconstruction using information fusion, single greedy and parallel clustering approaches
, Article 6th IEEE/ACS International Conference on Computer Systems and Applications, AICCSA 2008, Doha, 31 March 2008 through 4 April 2008 ; 2008 , Pages 15-19 ; 9781424419685 (ISBN) ; Moeinzadeh, M. H ; Sharifian-R, S ; Najafi-A, A ; Ramezani, A ; Habibi, J ; Mohammadzadeh, J ; Sharif University of Technology
2008
Abstract
Haplotype information has become increasingly important in analyzing fine-scale molecular genetics data, Due to the mutated form in human genome; SNPs (Single Nucleotide Polymorphism) are responsible for some genetic diseases. As a consequence, obtaining all SNPs from human populations is one of the primary goals of studies in human genomics. In this paper, a data fusion method based on multiple parallel classifiers for reconstruction of haplotypes from a given sample Single Nucleotide Polymorphism (SNP) is proposed. First, we design a single greedy algorithm for solving haplotype reconstructions. [2] is used as an efficient approach to be combined with first classification method. The...
Solving haplotype reconstruction problem in MEC model with hybrid information fusion
, Article EMS 2008, European Modelling Symposium, 2nd UKSim European Symposium on Computer Modelling and Simulation, Liverpool, 8 September 2008 through 10 September 2008 ; 2008 , Pages 214-218 ; 9780769533254 (ISBN) ; Moeinzadeh, M. H ; Habibi, J ; Sharifian-R, S ; Rasooli-V, A ; Najafi-A, A ; Sharif University of Technology
2008
Abstract
Single Nucleotide Polymorphisms (SNPs), a single DNA base varying from one individual to another, are believed to be the most frequent form responsible for genetic differences. Genotype is the conflated information of a pair of haplotypes on homologous chromosomes. Although haplotypes have more information for disease associating than individual SNPs and genotype, it is substantially more difficult to determine haplotypes through experiments. Hence, computational methods which can reduce the cost of determining haplotypes become attractive alternatives. MEC, as a standard model for haplotype reconstruction, is fed by fragments as input to infer the best pair of haplotypes with minimum error...
Single-centered hydrogen-bonded enhanced acidity (SHEA) acids: a new class of Bronsted acids
, Article Journal of the American Chemical Society ; Volume 131, Issue 46 , 2009 , Pages 16984-16988 ; 00027863 (ISSN) ; Fattahi, A ; Lis, L ; Kass, S. R ; Sharif University of Technology
2009
Abstract
Hydrogen bonds are the dominant motif for organizing the three-dimensional structures of biomolecules such as carbohydrates, nucleic acids, and proteins, and serve as templates for proton transfer reactions. Computations, gas-phase acidity measurements, and pKa determinations in dimethyl sulfoxide on a series of polyols indicate that multiple hydrogen bonds to a single charged center lead to greatly enhanced acidities. A new class of Brønsted acids, consequently, is proposed. © 2009 American Chemical Society
Simulation of DNA electrophoresis through microstructures
, Article Electrophoresis ; Volume 28, Issue 3 , 2007 , Pages 301-308 ; 01730835 (ISSN) ; Sarbolouki, M. N ; Rouhani, S ; Sharif University of Technology
2007
Abstract
The dependence of the mobility of DNA molecules through an hexagonal array of micropillars on their length and the applied electric field was investigated and it was found that mobility is a nonmonotonic function of their length. Results also revealed that the size dependence of the DNA mobility depends on the applied electric field and there is a crossover around E ≈ 25 V/cm for the mobility of λ-DNA and T4-DNA. These observations are explained in terms of the diffusion process inside the structure affected by the solvent and are modeled using the Langevin and its corresponding Fokker-Planck equations. The phenomenon is generalized under three regimes in a phase diagram relating the...
Self-assembly of tryptophan-capped gold nanoparticles onto DNA network template
, Article Journal of Dispersion Science and Technology ; Volume 30, Issue 2 , 2009 , Pages 254-258 ; 01932691 (ISSN) ; Vosoughi, M ; Alemsadeh, I ; Sharif University of Technology
2009
Abstract
In this study, a simple route to the formation of DNA-gold complex has been reported, using immobilized DNA as a template. The nanoporous gold films have been prepared by the electrostatic self assembly of gold nanoparticles capped with tryptophan. Tryptophan would improve surface properties of gold nanoparticles for strongly attaching to DNA. Fourier transform infrared spectroscopy confirmed that gold nanoparticles have been capped by tryptophan. Also measured zeta potential shows that there are positive charges on the surface of gold nanoparticles. Investigations by atomic force microscopy substantially confirm that tryptophan-capped gold nanoparticles can be bonded to DNA template...
Rigid-body molecular dynamics of DNA inside a nucleosome
, Article European Physical Journal E ; Volume 36, Issue 3 , March , 2013 ; 12928941 (ISSN) ; Berdy Besya, A ; Ejtehadi, M. R ; Schiessel, H ; Sharif University of Technology
2013
Abstract
The majority of eukaryotic DNA, about three quarter, is wrapped around histone proteins forming so-called nucleosomes. To study nucleosomal DNA we introduce a coarse-grained molecular dynamics model based on sequence-dependent harmonic rigid base pair step parameters of DNA and nucleosomal binding sites. Mixed parametrization based on all-atom molecular dynamics and crystallographic data of protein-DNA structures is used for the base pair step parameters. The binding site parameters are adjusted by experimental B-factor values of the nucleosome crystal structure. The model is then used to determine the energy cost for placing a twist defect into the nucleosomal DNA which allows us to use...
Ratiometric fluorescent nanoprobes for visual detection: Design principles and recent advances - A review
, Article Analytica Chimica Acta ; Volume 1079 , 2019 , Pages 30-58 ; 00032670 (ISSN) ; Ghasemi, F ; Abbasi Moayed, S ; Shahrajabian, M ; Fahimi Kashani, N ; Jafarinejad, S ; Farahmand Nejad, M. A ; Hormozi Nezhad, M. R ; Sharif University of Technology
Elsevier B.V
2019
Abstract
Signal generation techniques for visual detection of analytes have received a great deal of attention in various sensing fields. These approaches are considered to be advantageous when instrumentation cannot be employed, such as for on-site assays, point-of-care tests, and he althcare diagnostics in resource-constrained areas. Amongst various visual detection approaches explored for non-invasive quantitative measurements, ratiometric fluorescence sensing has received particular attention as a potential method to overcome the limitations of intensity-based probes. This technique relies on changes in the intensity of two or more emission bands (induced by an analyte), resulting in an effective...
Point-of-use rapid detection of sars-cov-2: Nanotechnology-enabled solutions for the covid-19 pandemic
, Article International Journal of Molecular Sciences ; Volume 21, Issue 14 , 2020 , Pages 1-23 ; Bagherzadeh, M ; Ghasemi, A ; Zare, H ; Ahmadi, S ; Fatahi, Y ; Dinarvand, R ; Rabiee, M ; Ramakrishna, S ; Shokouhimehr, M ; Varma, R. S ; Sharif University of Technology
MDPI AG
2020
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) caused the COVID-19 pandemic that has been spreading around the world since December 2019. More than 10 million affected cases and more than half a million deaths have been reported so far, while no vaccine is yet available as a treatment. Considering the global healthcare urgency, several techniques, including whole genome sequencing and computed tomography imaging have been employed for diagnosing infected people. Considerable efforts are also directed at detecting and preventing different modes of community transmission. Among them is the rapid detection of virus presence on different surfaces with which people may come in...
Numerical simulation of mixing and heat transfer in an integrated centrifugal microfluidic system for nested-PCR amplification and gene detection
, Article Sensors and Actuators, B: Chemical ; Volume 283 , 2019 , Pages 831-841 ; 09254005 (ISSN) ; Ghazimirsaeed, E ; Shamloo, A ; Sharif University of Technology
Elsevier B.V
2019
Abstract
Nucleic acid amplification via polymerase chain reaction (PCR) is one of the essential and powerful methods used in a myriad of bio-assays in clinical laboratories. Application of microfluidic devices in biologically-related processes like PCR can result in the usage of less volume of reactant samples and reduce the processing time. By implementing PCR systems on centrifugal microfluidic platforms, automation and portability can be easily achieved. Although several methods have been developed, most of them are still dealing with challenges of the required high processing time. This study presents the numerical simulation of a fully automated PCR system with the goal of enhancing the mixing...
Multiway investigation of interaction between fluorescence labeled DNA strands and unmodified gold nanoparticles
, Article Analytical Chemistry ; Volume 84, Issue 15 , July , 2012 , Pages 6603-6610 ; 00032700 (ISSN) ; Kompany Zareh, M ; Hormozi Nezhad, M. R ; Sharif University of Technology
ACS
2012
Abstract
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....
Mining DNA sequences based on spatially coded technique using spatial light modulator
, Article IWCIT 2016 - Iran Workshop on Communication and Information Theory, 3 May 2016 through 4 May 2016 ; 2016 ; 9781509019229 (ISBN) ; Abdollahramezani, S ; Bahrani, S ; Chizari, A ; Jamali, M. V ; Khorramshahi, P ; Tashakori, A ; Shahsavari, S ; Salehi, J. A ; Sharif University of Technology
Institute of Electrical and Electronics Engineers Inc
2016
Abstract
In this paper, we present an optical computing method for string data alignment applicable to genome information analysis. By applying moire technique to spatial encoding patterns of deoxyribonucleic acid (DNA) sequences, association information of the genome and the expressed phenotypes could more effectively be extracted. Such moire fringes reveal occurrence of matching, deletion and insertion between DNA sequences providing useful visualized information for prediction of gene function and classification of species. Furthermore, by applying a cylindrical lens, a new technique is proposed to map two-dimensional (2D) association information to a one-dimensional (1D) column of pixels, where...
Laboratory detection methods for the human coronaviruses
, Article European Journal of Clinical Microbiology and Infectious Diseases ; Volume 40, Issue 2 , 2021 , Pages 225-246 ; 09349723 (ISSN) ; Dowlatshahi, S ; Abdekhodaie, M. J ; Sharif University of Technology
Springer Science and Business Media Deutschland GmbH
2021
Abstract
Coronaviruses are a group of envelop viruses which lead to diseases in birds and mammals as well as human. Seven coronaviruses have been discovered in humans that can cause mild to lethal respiratory tract infections. HCoV-229E, HCoV-OC43, HCoV-NL63, and HCoV-HKU1 are the low-risk members of this family and the reason for some common colds. Besides, SARS-CoV, MERS-CoV, and newly identified SARS-CoV-2, which is also known as 2019-nCoV, are the more dangerous viruses. Due to the rapid spread of this novel coronavirus and its related disease, COVID-19, a reliable, simple, fast, and low-cost detection method is necessary for patient diagnosis and tracking worldwide. Human coronaviruses detection...
Histidine-enhanced gene delivery systems: The state of the art
, Article Journal of Gene Medicine ; Volume 24, Issue 5 , 2022 ; 1099498X (ISSN) ; Jahanpeimay Sabet, M ; Hasanzadeh, A ; Kamrani Mousavi, S. M ; Haeri Moghaddam, N ; Hooshmand, S. A ; Rabiee, N ; Liu, Y ; Hamblin, M. R ; Karimi, M ; Sharif University of Technology
John Wiley and Sons Inc
2022
Abstract
Gene therapy has emerged as a promising tool for treating different intractable diseases, particularly cancer or even viral diseases such as COVID-19 (coronavirus disease 2019). In this context, various non-viral gene carriers are being explored to transfer DNA or RNA sequences into target cells. Here, we review the applications of the naturally occurring amino acid histidine in the delivery of nucleic acids into cells. The biocompatibility of histidine-enhanced gene delivery systems has encouraged their wider use in gene therapy. Histidine-based gene carriers can involve the modification of peptides, dendrimers, lipids or nanocomposites. Several linear polymers, such as polyethylenimine,...
Green chemistry and coronavirus
, Article Sustainable Chemistry and Pharmacy ; Volume 21 , 2021 ; 23525541 (ISSN) ; Rabiee, N ; Fatahi, Y ; Hooshmand, S. E ; Bagherzadeh, M ; Rabiee, M ; Jajarmi, V ; Dinarvand, R ; Habibzadeh, S ; Saeb, M. R ; Varma, R. S ; Shokouhimehr, M ; Hamblin, M. R ; Sharif University of Technology
Elsevier B.V
2021
Abstract
The novel coronavirus pandemic has rapidly spread around the world since December 2019. Various techniques have been applied in identification of SARS-CoV-2 or COVID-19 infection including computed tomography imaging, whole genome sequencing, and molecular methods such as reverse transcription polymerase chain reaction (RT-PCR). This review article discusses the diagnostic methods currently being deployed for the SARS-CoV-2 identification including optical biosensors and point-of-care diagnostics that are on the horizon. These innovative technologies may provide a more accurate, sensitive and rapid diagnosis of SARS-CoV-2 to manage the present novel coronavirus outbreak, and could be...
Green chemistry and coronavirus
, Article Sustainable Chemistry and Pharmacy ; Volume 21 , 2021 ; 23525541 (ISSN) ; Rabiee, N ; Fatahi, Y ; Hooshmand, S. E ; Bagherzadeh, M ; Rabiee, M ; Jajarmi, V ; Dinarvand, R ; Habibzadeh, S ; Saeb, M. R ; Varma, R.S ; Shokouhimehr, M ; Hamblin, M. R ; Sharif University of Technology
Elsevier B.V
2021
Abstract
The novel coronavirus pandemic has rapidly spread around the world since December 2019. Various techniques have been applied in identification of SARS-CoV-2 or COVID-19 infection including computed tomography imaging, whole genome sequencing, and molecular methods such as reverse transcription polymerase chain reaction (RT-PCR). This review article discusses the diagnostic methods currently being deployed for the SARS-CoV-2 identification including optical biosensors and point-of-care diagnostics that are on the horizon. These innovative technologies may provide a more accurate, sensitive and rapid diagnosis of SARS-CoV-2 to manage the present novel coronavirus outbreak, and could be...
Fabrication of metal nanowires based on self assembly of tryptophan-capped gold nanoparticle onto DNA network template
, Article International Journal of Nanotechnology ; Volume 6, Issue 10-11 , 2009 , Pages 1041-1049 ; 14757435 (ISSN) ; Vossoughi, M ; Alemzadeh, I ; Sharif University of Technology
2009
Abstract
In this study, synthesis of conductive metal nanowires by using aligned and immobilised DNA strand on solid substrate is reported. The nanoporous gold film was prepared by electrostatic self assembly of gold nanoparticles capped with tryptophan. Tryptophan would improve surface properties of gold nanoparticles for strongly attaching to DNA. Fourier transform infrared (FTIR) spectroscopy confirmed that gold nanoparticles have been capped by tryptophan. Also measured zeta potential shows that there are positive charges on the surface of gold nanoparticles. Investigations by AFM observati on substantially confirm that tryptophan-capped gold nanoparticles can be bonded to DNA template...