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Nucleoside Structure using Ab-Initio Computational Methods
, M.Sc. Thesis Sharif University of Technology ; Tafazzoli, Mohsen (Supervisor)
Abstract
The spin – spin coupling constants have been calculated by the Gaussian 2009 program in order to study the nucleosides conformation. To study the effect of solvent, the calculations were performed in four solvent including water, DMSO, chloroform and Carbon tetrachloride.
Also, the comparison is done on two computing methods including DFT (B3LYP) and HF using 6-311++g** and 6-311g basis set.One bonding (1JC-H), two bonding (2JN-H, 2JC-H) and three bonging coupling constants (3JC-H) have been calculated for unpaired adenosine, thymidine and uridine molecules.Formation of intra-molecular hydrogen bond and electron pair repulsion, respectively, makes the compounds stable and unstable....
Also, the comparison is done on two computing methods including DFT (B3LYP) and HF using 6-311++g** and 6-311g basis set.One bonding (1JC-H), two bonding (2JN-H, 2JC-H) and three bonging coupling constants (3JC-H) have been calculated for unpaired adenosine, thymidine and uridine molecules.Formation of intra-molecular hydrogen bond and electron pair repulsion, respectively, makes the compounds stable and unstable....
Study of the Affecting Factors on the Stability of G-Quadruplex Structures
, Ph.D. Dissertation Sharif University of Technology ; Tafazzoli, Mohsen (Supervisor)
Abstract
We used spectroscopic techniques to study self-assembled structures based on nucleobases like G-quadruplexes and macrocycles. Also we used DOSY NMR technique to study hydrogen bonding network in alcohol solutions. First part of our results indicate thermodynamic stability and slow kinetic of G-quadruplexes in apolar aromatic solvents like toluene. Also our results show easy monitoring of formation of each K+ or Na+ complex by NMR, due to the low solubility of alkaline metal salts in apolar media and possibility to stop at any given time in order to control G-quadruplex yield. When combined with suitable functional units, these valuable attributes may be used for the noncovalent synthesis of...
Identification of the Set of Single Nucleotide Variants in Genome Responsible for the Differentiation of Expression of Genes
, M.Sc. Thesis Sharif University of Technology ; Rabiee, Hamid Reza (Supervisor) ; Beigi, Hamid (Supervisor)
Abstract
Single nucleotide polymorphs, There are changes caused by a mutation in a nucleotide in the Dena sequence. Mononucleotide polymorphisms are the most common type of genetic variation. Some of these changes have little or no effect on cells, while others cause significant changes in the expression of cell genes that can lead to disease or resistance to certain diseases. Because of the importance of these changes and their effect on cell function, the relationships between these changes are also important. Over the past decade, thousands of single disease-related mononucleotide polymorphisms have been identified in genome-related studies. Studies in this field have shown that the expression of...
Comparative Analysis of Haplotype Assembly Algorithms to Identify and Propose Optimal Methods
, M.Sc. Thesis Sharif University of Technology ; Jahed, Mehran (Supervisor) ; Hossein Khalaj, Babak (Supervisor)
Abstract
Humans, as a diploid species, have two nucleotide sequences of homologous chromosomes in their genomes, where one set is inherited from the mother, and the other comes from the father. The Single Individual Haplotype assembly problem (SIH) refers to the reconstruction of these two distinct nucleotide sequences of a chromosome from the sequencing reads, and it is currently considered one of the most important issues in the field of computational genomics, which plays an essential role in solving various genetic and medical problems.Nowadays direct experimental methods are not welcomed due to their high cost, and labor intensity, and are limited to certain regions of the genome, therefore,...
A tale of two symmetrical tails: Structural and functional characteristics of palindromes in proteins
, Article BMC Bioinformatics ; Volume 9 , 2008 ; 14712105 (ISSN) ; Kargar, M ; Katanforoush, A ; Arab, S ; Sadeghi, M ; Pezeshk, H ; Eslahchi, C ; Marashi, S. A ; Sharif University of Technology
2008
Abstract
Background: It has been previously shown that palindromic sequences are frequently observed in proteins. However, our knowledge about their evolutionary origin and their possible importance is incomplete. Results: In this work, we tried to revisit this relatively neglected phenomenon. Several questions are addressed in this work. (1) It is known that there is a large chance of finding a palindrome in low complexity sequences (i.e. sequences with extreme amino acid usage bias). What is the role of sequence complexity in the evolution of palindromic sequences in proteins? (2) Do palindromes coincide with conserved protein sequences? If yes, what are the functions of these conserved segments?...
Dna-Rna hybrid (R-loop): From a unified picture of the mammalian telomere to the genome-wide profile
, Article Cells ; Volume 10, Issue 6 , 2021 ; 20734409 (ISSN) ; Sharifi Zarchi, A ; Kianmehr, L ; Sharif University of Technology
MDPI
2021
Abstract
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...
Design and fabrication of an electrochemical aptasensor using Au nanoparticles/carbon nanoparticles/cellulose nanofibers nanocomposite for rapid and sensitive detection of Staphylococcus aureus
, Article Bioelectrochemistry ; Volume 123 , 2018 , Pages 70-76 ; 15675394 (ISSN) ; Shahrokhian, S ; Sharif University of Technology
Elsevier B.V
2018
Abstract
Since that pathogenic bacteria are major threats to human health, this paper describes the fabrication of an effective and durable sensing platform based on gold nanoparticles/carbon nanoparticles/cellulose nanofibers nanocomposite (AuNPs/CNPs/CNFs) at the surface of glassy carbon electrode for sensitive and selective detection of Staphylococcus aureus (S. aureus). The AuNPs/CNPs/CNFs nanocomposite with the high surface area, excellent conductivity, and good biocompatibility was used for self-assembled of the thiolated specific S. aureus aptamer as a sensing element. The surface morphology of AuNPs/CNPs/CNFs nanocomposite was characterized with field emission scanning electron microscopy...
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...
Meta-aligner: long-read alignment based on genome statistics
, Article BMC Bioinformatics ; Volume 18, Issue 1 , 2017 ; 14712105 (ISSN) ; Aliyari, A ; Ahmadian Moghadam, A ; Edrisi, M. A ; Motahari, S. A ; Khalaj, B. H ; Sharif University of Technology
Abstract
Background: Current development of sequencing technologies is towards generating longer and noisier reads. Evidently, accurate alignment of these reads play an important role in any downstream analysis. Similarly, reducing the overall cost of sequencing is related to the time consumption of the aligner. The tradeoff between accuracy and speed is the main challenge in designing long read aligners. Results: We propose Meta-aligner which aligns long and very long reads to the reference genome very efficiently and accurately. Meta-aligner incorporates available short/long aligners as subcomponents and uses statistics from the reference genome to increase the performance. Meta-aligner estimates...
Small RNA sequencing reveals dlk1-dio3 locus-embedded microRNAs as major drivers of ground-state pluripotency
, Article Stem Cell Reports ; Volume 9, Issue 6 , 2017 , Pages 2081-2096 ; 22136711 (ISSN) ; Sharifi Zarchi, A ; Ahmadi, A ; Mollamohammadi, S ; Stubenvoll, A ; Günther, S ; Hosseini Salekdeh, G ; Asgari, S ; Braun, T ; Baharvand, H ; Sharif University of Technology
Abstract
Ground-state pluripotency is a cell state in which pluripotency is established and maintained through efficient repression of endogenous differentiation pathways. Self-renewal and pluripotency of embryonic stem cells (ESCs) are influenced by ESC-associated microRNAs (miRNAs). Here, we provide a comprehensive assessment of the “miRNome” of ESCs cultured under conditions favoring ground-state pluripotency. We found that ground-state ESCs express a distinct set of miRNAs compared with ESCs grown in serum. Interestingly, most “ground-state miRNAs” are encoded by an imprinted region on chromosome 12 within the Dlk1-Dio3 locus. Functional analysis revealed that ground-state miRNAs embedded in the...
Two new methods for DNA splice site prediction based on neuro-fuzzy network and clustering
, Article Neural Computing and Applications ; Volume 23, Issue SUPPL1 , 2013 , Pages 407-414 ; 09410643 (ISSN) ; Manzuri Shalmani, M. T ; Khaki Sedigh, A ; Kia, M ; Sharif University of Technology
2013
Abstract
Nowadays, genetic disorders, like cancer and birth defects, are a great threat to human life. Since the first noticing of these types of diseases, many efforts have been made and researches performed in order to recognize them and find a cure for them. These disorders affect genes and they appear as abnormal traits in a genetic organism. In order to recognize abnormal genes, we need to predict splice sites in a DNA signal; then, we can process the genetic codes between two continuous splice sites and analyze the trait that it represents. In addition to abnormal genes and their consequent disorders, we can also identify other normal human traits like physical and mental features. So the...
F.C.A: designing a fuzzy clustering algorithm for haplotype assembly
, Article IEEE International Conference on Fuzzy Systems, 20 August 2009 through 24 August 2009 ; 2009 , Pages 1741-1744 ; 10987584 (ISSN) ; 9781424435975 (ISBN) ; Asgarian, E ; Noori, M. M ; Sadeghi, M ; Sharifian R., S ; Sharif University of Technology
Abstract
Reconstructing haplotype in MEC (Minimum Error Correction) model is an important clustering problem which focuses on inferring two haplotypes from SNP fragments (Single Nucleotide Polymorphism) containing gaps and errors. Mutated form of human genome is responsible for genetic diseases which mostly occur in SNP sites. In this paper, a fuzzy clustering approach is performed for haplotype reconstruction or haplotype assembly from a given sample Single Nucleotide Polymorphism (SNP). In the best previous approach based on reconstruction rate (Wang 2007[2]), all SNP-fragments are considered with equal values. In our proposed method the value of the fragments are based on the degree of membership...
Mechanical differences between ATP and ADP actin states: A molecular dynamics study
, Article Journal of Theoretical Biology ; Volume 448 , 2018 , Pages 94-103 ; 00225193 (ISSN) ; Shamloo, A ; Sharif University of Technology
Academic Press
2018
Abstract
This paper aims to give a comprehensive atomistic modeling of the nanomechanical behavior of actin monomer. Actin is a ubiquitous and essential component of cytoskeleton which forms many different cellular structures. Despite for several years great effort has been devoted to the investigation of mechanical properties of the actin filament, studies on the nanomechanical behavior of actin monomer are still lacking. These scales are, however, important for a complete understanding of the role of actin as an important component in the cytoskeleton structure. Based on the accuracy of atomistic modeling methods such as molecular dynamics simulations, steered molecular dynamics method is performed...
OmpF, a nucleotide-sensing nanoprobe, computational evaluation of single channel activities
, Article Physica A: Statistical Mechanics and its Applications ; Volume 457 , 2016 , Pages 215-224 ; 03784371 (ISSN) ; Mobasheri, H ; Nikouee, A ; Ejtehadi, M. R ; Sharif University of Technology
Elsevier B.V
2016
Abstract
The results of highthroughput practical single channel experiments should be formulated and validated by signal analysis approaches to increase the recognition precision of translocating molecules. For this purpose, the activities of the single nano-pore forming protein, OmpF, in the presence of nucleotides were recorded in real time by the voltage clamp technique and used as a means for nucleotide recognition. The results were analyzed based on the permutation entropy of current Time Series (TS), fractality, autocorrelation, structure function, spectral density, and peak fraction to recognize each nucleotide, based on its signature effect on the conductance, gating frequency and voltage...
Elastic properties of actin assemblies in different states of nucleotide binding
, Article Cellular and Molecular Bioengineering ; Volume 5, Issue 1 , 2012 , Pages 1-13 ; 18655025 (ISSN) ; Kazemi, M. T ; Sharif University of Technology
Abstract
In this paper, the elastic properties of monomeric actin (G-actin) and the trimer nucleus (G-actin trimer) in different states of nucleotide binding are estimated using steered molecular dynamic (SMD) simulations. Three nucleotide binding states are considered: ADP- and ATP-bound actin and nucleotide-free actin assemblies. Our results show that nucleotide binding and the corresponding changes in structure have significant effects on the mechanical behaviors of actin assemblies. Simulations reveal that the deformation behavior of G-actin monomers is generally elastic up to engineering strains of 16 and 40% in the tension and shear tests, respectively. In addition, the G-actin trimers react...
A quantum mechanical approach towards the calculation of transition probabilities between DNA codons
, Article BioSystems ; Volume 184 , 2019 ; 03032647 (ISSN) ; Shafiee, A ; Sharif University of Technology
Elsevier Ireland Ltd
2019
Abstract
The role of quantum tunneling in altering the structure of nucleotides to each other and causing a mutational event in DNA has been a topic of debate for years. Here, we introduce a new quantum mechanical approach for analyzing a typical point-mutation in DNA strands. Assuming each codon as a base state, a superposition of codon states could provide a physical description for a set of codons encoding the same amino acid and there are transition amplitudes between them. We choose the amino acids Phe and Ile as our understudy bio-systems which are encoded by two and three codons, respectively. We treat them as large quantum systems and use double- and triple-well potential models to study the...
Application of single-nucleotide polymorphisms in the diagnosis of autism spectrum disorders: a preliminary study with artificial neural networks
, Article Journal of Molecular Neuroscience ; Volume 68, Issue 4 , 2019 , Pages 515-521 ; 08958696 (ISSN) ; Taheri, M ; Omrani, M. D ; Daaee, A ; Mohammad Rahimi, H ; Kazazi, H ; Sharif University of Technology
Springer New York LLC
2019
Abstract
Autism spectrum disorder (ASD) includes different neurodevelopmental disorders characterized by deficits in social communication, and restricted, repetitive patterns of behavior, interests or activities. Based on the importance of early diagnosis for effective therapeutic intervention, several strategies have been employed for detection of the disorder. The artificial neural network (ANN) as a type of machine learning method is a common strategy. In the current study, we extracted genomic data for 487 ASD patients and 455 healthy individuals. All individuals were genotyped in certain single-nucleotide polymorphisms within retinoic acid-related orphan receptor alpha (RORA), gamma-aminobutyric...
Application of artificial neural network for prediction of risk of multiple sclerosis based on single nucleotide polymorphism genotypes
, Article Journal of Molecular Neuroscience ; Volume 70, Issue 7 , 2020 , Pages 1081-1087 ; Taheri, M ; Omrani, M. D ; Daaee, A ; Mohammad Rahimi, H ; Sharif University of Technology
Humana Press Inc
2020
Abstract
The artificial neural network (ANN) is a sort of machine learning method which has been used in determination of risk of human disorders. In the current investigation, we have created an ANN and trained it based on the genetic data of 401 multiple sclerosis (MS) patients and 390 healthy subjects. Single nucleotide polymorphisms (SNPs) within ANRIL (rs1333045, rs1333048, rs4977574 and rs10757278), EVI5 (rs6680578, rs10735781 and rs11810217), ACE (rs4359 and rs1799752), MALAT1 (rs619586 and rs3200401), GAS5 (rs2067079 and rs6790), H19 (rs2839698 and rs217727), NINJ2 (rs11833579 and rs3809263), GRM7 (rs6782011 and rs779867), VLA4 (rs1143676), CBLB (rs12487066) and VEGFA (rs3025039 and...
Dependency of codon usage on protein sequence patterns: A statistical study
, Article Theoretical Biology and Medical Modelling ; Vol. 11, issue. 1 , 2014 ; ISSN: 17424682 ; Goliaei, B ; Alishahi, K ; Sadeghi, M ; Sharif University of Technology
Abstract
Background: Codon degeneracy and codon usage by organisms is an interesting and challenging problem. Researchers demonstrated the relation between codon usage and various functions or properties of genes and proteins, such as gene regulation, translation rate, translation efficiency, mRNA stability, splicing, and protein domains. Researchers usually represent segments of proteins responsible for specific functions or structures in a family of proteins as sequence patterns or motifs. We asked the question if organisms use the same codons in pattern segments as compared to the rest of the sequence. Methods. We used the likelihood ratio test, Pearson's chi-squared test, and mutual information...
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...