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    CANCERSIGN: a user-friendly and robust tool for identification and classification of mutational signatures and patterns in cancer genomes

    , Article Scientific Reports ; Volume 10, Issue 1 , 2020 Bayati, M ; Rabiee, H. R ; Mehrbod, M ; Vafaee, F ; Ebrahimi, D ; Forrest, A. R. R ; Alinejad Rokny, H ; Sharif University of Technology
    Nature Research  2020
    Abstract
    Analysis of cancer mutational signatures have been instrumental in identification of responsible endogenous and exogenous molecular processes in cancer. The quantitative approach used to deconvolute mutational signatures is becoming an integral part of cancer research. Therefore, development of a stand-alone tool with a user-friendly interface for analysis of cancer mutational signatures is necessary. In this manuscript we introduce CANCERSIGN, which enables users to identify 3-mer and 5-mer mutational signatures within whole genome, whole exome or pooled samples. Additionally, this tool enables users to perform clustering on tumor samples based on the proportion of mutational signatures in... 

    Asymmetric elastic rod model for DNA

    , Article Physical Review E - Statistical, Nonlinear, and Soft Matter Physics ; Volume 80, Issue 1 , 2009 ; 15393755 (ISSN) Eslami Mossallam, B ; Ejtehadi, M. R ; Sharif University of Technology
    2009
    Abstract
    In this paper we consider the anharmonic corrections to the anisotropic elastic rod model for DNA. Our model accounts for the difference between the bending energies of positive and negative rolls, which comes from the asymmetric structure of the DNA molecule. We will show that the model can explain the high flexibility of DNA at small length scales, as well as kink formation at high deformation limit. © 2009 The American Physical Society  

    Synthesis of Cationic Mesoporous Silica Nanoparticles as a Carrier for the Deliveryof Nucleic Acids

    , M.Sc. Thesis Sharif University of Technology Kermanshah, Leyla (Author) ; 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... 

    Contribution of nonlocal interactions to DNA elasticity

    , Article Journal of Chemical Physics ; Volume 134, Issue 12 , 2011 ; 00219606 (ISSN) Eslami Mossallam, B ; Ejtehadi, M. R ; Sharif University of Technology
    2011
    Abstract
    A nonlocal harmonic elastic rod model is proposed to describe the elastic behavior of short DNA molecules. We show that the nonlocal interactions contribute to effective bending energy of the molecule and affect its apparent persistence length. It is also shown that the anomalous behavior which has been observed in all-atom molecular dynamic simulations [A. K. Mazur, Biophys. J. 134, 4507 (2006)] can be a consequence of both nonlocal interactions between DNA base pairs and the intrinsic curvature of DNA  

    Colourimetric-based method for the diagnosis of spinal muscular atrophy using gold nanoprobes

    , Article IET Nanobiotechnology ; Volume 9, Issue 1 , Feb , 2015 , Pages 5-10 ; 17518741 (ISSN) Ahmadpour Yazdi, H ; Hormozi Nezhad, M. R ; Abadi, A. R ; Sanati, M. H ; Kazemi, B ; Sharif University of Technology
    Institution of Engineering and Technology  2015
    Abstract
    Although numerous molecular methods for spinal muscular atrophy (SMA) detection have been exploited, most of hem are laborious, time consuming and costly. Recently, gold nanoparticles (AuNPs) have attracted attention in the field of colourimetric bioanalysis, because AuNP aggregation can be tracked with the naked eye as well as ultraviolet-visible (UV-vis) peak analysis. Here, based on a non-cross linking platform, a colourimetric-based method was used to evaluate the capability of thiolated oligo-AuNPs (Au nanoprobes) to distinguish between normal individuals, carriers and those with SMA. In this platform, removal of the repulsive force of the Au nanoprobes using high salt concentration... 

    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) Tian, Z ; 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  

    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) Naghdloo, A ; 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... 

    Simulation of DNA electrophoresis through microstructures

    , Article Electrophoresis ; Volume 28, Issue 3 , 2007 , Pages 301-308 ; 01730835 (ISSN) Maleki Jirsaraei, N ; 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... 

    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) Kashani, B ; 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... 

    Histidine-enhanced gene delivery systems: The state of the art

    , Article Journal of Gene Medicine ; Volume 24, Issue 5 , 2022 ; 1099498X (ISSN) Hooshmand, S. E ; 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,... 

    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) Shariati, M ; 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... 

    DFT study of the interaction of cytidine and 2′-deoxycytidine with Li+, Na+, and K+: effects of metal cationization on sugar puckering and stability of the N-glycosidic bond

    , Article Carbohydrate Research ; Volume 344, Issue 6 , 2009 , Pages 771-778 ; 00086215 (ISSN) Aliakbar Tehrani, Z ; Fattahi, A. R ; Pourjavadi, A ; Sharif University of Technology
    2009
    Abstract
    Density functional theory (DFT) calculations were performed at the B3LYP level with a 6-311++G(d,p) basis set to systematically explore the geometrical multiplicity and binding strength for complexes formed by Li+, Na+, and K+ with cytidine and 2′-deoxycytidine. All computational studies indicate that the metal ion affinity (MIA) decreases from Li+ to Na+ and K+ for cytosine nucleosides. For example, for cytidine the affinity for the above metal ions are 79.5, 55.2, and 41.8 and for 2′-deoxycytidine, 82.8, 57.4, and 42.2 kcal/mol, respectively. It is also interesting to mention that linear correlations between calculated MIA values and the atomic numbers (Z) of the above metal ions were... 

    Comparison of gas phase intrinsic properties of cytosine and thymine nucleobases with their O-alkyl adducts: Different hydrogen bonding preferences for thymine versus O-alkyl thymine

    , Article Journal of Molecular Modeling ; Volume 19, Issue 8 , 2013 , Pages 2993-3005 ; 16102940 (ISSN) Aliakbar Tehrani, Z ; Fattahi, A ; Sharif University of Technology
    2013
    Abstract
    In recent years, there has been increasing interest in damaged DNA and RNA nucleobases. These damaged nucleobases can cause DNA mutation, resulting in various diseases such as cancer. Alkylating agents are mutagenic and carcinogenic in a variety of prokaryotic and eukaryotic organisms. The present study employs density functional theory (DFT/B3LYP) with the 6-311++G(d,p) basis set to investigate the effect of chemical damage in O-alkyl pyrimidines such as O4-methylthymine, O2-methylcytosine and O 2-methylthymine. We compared the intrinsic properties, such as proton affinities, gas phase acidities, equilibrium tautomerization and nucleobase pair's hydrogen bonding properties, of these... 

    Rigid-body molecular dynamics of DNA inside a nucleosome

    , Article European Physical Journal E ; Volume 36, Issue 3 , March , 2013 ; 12928941 (ISSN) Fathizadeh, A ; 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... 

    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) Akhlaghi, Y ; 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.... 

    Denaturation of Drew-Dickerson DNA in a high salt concentration medium: Molecular dynamics simulations

    , Article Journal of Computational Chemistry ; Volume 32, Issue 16 , September , 2011 , Pages 3354-3361 ; 01928651 (ISSN) Izanloo, C ; Parsafar, G. A ; Abroshan, H ; Akbarzadeh, H ; Sharif University of Technology
    2011
    Abstract
    We have performed molecular dynamics simulation on B-DNA duplex (CGCGAATTGCGC) at different temperatures. The DNA was immerged in a salt-water medium with 1 M NaCl concentration to investigate salt effect on the denaturation process. At each temperature, configurational entropy is estimated using the covariance matrix of atom-positional fluctuations, from which the melting temperature (T m) was found to be 349 K. The calculated configuration entropy for different bases shows that the melting process involves more peeling (including fraying from the ends) conformations, and therefore the untwisting of the duplex and peeling states form the transition state of the denaturation process. There... 

    Extreme bendability of DNA double helix due to bending asymmetry

    , Article Journal of Chemical Physics ; Volume 143, Issue 10 , 2015 ; 00219606 (ISSN) Salari, H ; Eslami Mossallam, B ; Naderi, S ; Ejtehadi, M. R ; Sharif University of Technology
    American Institute of Physics Inc  2015
    Abstract
    Experimental data of the DNA cyclization (J-factor) at short length scales exceed the theoretical expectation based on the wormlike chain (WLC) model by several orders of magnitude. Here, we propose that asymmetric bending rigidity of the double helix in the groove direction can be responsible for extreme bendability of DNA at short length scales and it also facilitates DNA loop formation at these lengths. To account for the bending asymmetry, we consider the asymmetric elastic rod (AER) model which has been introduced and parametrized in an earlier study [B. Eslami-Mossallam and M. R. Ejtehadi, Phys. Rev. E 80, 011919 (2009)]. Exploiting a coarse grained representation of the DNA molecule... 

    Development of a nanocellulose composite based voltammetric sensor for vitamin B9 analysis

    , Article Current Nanoscience ; Volume 12, Issue 4 , 2016 , Pages 493-499 ; 15734137 (ISSN) Ghalkhani, M ; Shahrokhian, S ; Sharif University of Technology
    Bentham Science Publishers B.V 
    Abstract
    As a B group vitamins, vitamin B9 is a Water-soluble vitamin which is produced by plants and microorganisms (bacteria and yeasts). Vitamin B9 plays an important role in the production of proteins and nucleic acids in body and also is one of the substances that prevents the development of neural tube defects in the fetus. Methods: Electrochemical behavior of vitamin B9 was studied using a potentiostat/galvanostat SAMA 500, electroanalyzer system, I. R. Iran. A three-electrode system was used, including a glassy carbon working electrode (d = 2.0 mm, purchased from Azar Electrode Co., Urmia, I.R. Iran), an Ag/AgCl (saturated KCl) reference electrode and a Pt wire auxiliary electrode.... 

    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) Fazelian, M ; 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... 

    Cytotoxicity and cell cycle effects of bare and poly(vinyl alcohol)-coated iron oxide nanoparticles in mouse fibroblasts

    , Article Advanced Engineering Materials ; Volume 11, Issue 12 , 2009 , Pages B243-B250 ; 14381656 (ISSN) Mahmoudi, M ; Simchi, A ; Vali, H ; Imani, M ; Shokrgozar, M. A ; Azadmanesh, K ; Azari, F ; Sharif University of Technology
    Abstract
    Super-paramagnetic iron oxide nanoparticles (SPIONs) are recognized as powerful biocompatible materials for use in various biomedical applications, such as drug delivery, magnetic-resonance imaging, cell/protein separation, hyperthermia and transfection. This study investigates the impact of high concentrations of SPIONs on cytotoxicity and cell-cycle effects. The interactions of surfacesaturated (via interactions with cell medium) bare SPIONs and those coated with poly(vinyl alcohol) (PVA) with adhesive mouse fibroblast cells (L929) are investigated using an MTT assay. The two SPION formulations are synthesized using a co-precipitation method. The bare and coated magnetic nanoparticles with...