Loading...
Search for:
dna
0.005 seconds
Total 173 records
Finding maximum edge bicliques in convex bipartite graphs
, Article Algorithmica ; Volume 64, Issue 2 , October , 2012 , Pages 311-325 ; 01784617 (ISSN) ; Pu, S ; Sack, J. R ; Uno, T ; Zarrabi Zadeh, H ; Sharif University of Technology
Springer
2012
Abstract
A bipartite graph G = (A,B,E) is convex on B if there exists an ordering of the vertices of B such that for any vertex v ? A, vertices adjacent to v are consecutive in B. A complete bipartite subgraph of a graph G is called a biclique of G. Motivated by an application to analyzing DNA microarray data, we study the problem of finding maximum edge bicliques in convex bipartite graphs. Given a bipartite graph G = (A,B,E) which is convex on B, we present a new algorithm that computes a maximum edge biclique of G in O(nlog3 n log log n) time and O(n) space, where n = |A|. This improves the current O(n 2) time bound available for the problem. We also show that for two special subclasses of convex...
What roles do boron substitutions play in structural, tautomeric, base pairing and electronic properties of uracil? NBO & AIM analysis
, Article Journal of Physical Organic Chemistry ; Volume 25, Issue 9 , 2012 , Pages 787-796 ; 08943230 (ISSN) ; Abedin, A ; Shakourian Fard, M ; Fattahi, A ; Sharif University of Technology
Wiley
2012
Abstract
The synthesis of modified versions of deoxyribonucleic acid is an area that is receiving much attention. The replacement of the nitrogen atom on the nucleobases with boron atom has provided insight into deoxyribonucleic acid and ribonucleic acid stability, recognition, and replication at the atomic level. In the present research, we investigated a detailed density functional theory study of the structural, tautomeric, base-pairing ability, bond dissociation energy, and electronic properties of two boron analogues (i.e., boron substitutions at 4-position and 5-position of uracil) of uracil nucleobase. The effects of these modifications on theirs acid-base properties have been considered. Our...
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....
Fabrication of a modified electrode based on Fe3 O4 NPs/MWCNT nanocomposite: Application to simultaneous determination of guanine and adenine in DNA
, Article Bioelectrochemistry ; Volume 86 , 2012 , Pages 78-86 ; 15675394 (ISSN) ; Rastgar, S ; Amini, M. K ; Adeli, M ; Sharif University of Technology
Abstract
Multi-walled carbon nanotubes decorated with Fe 3O 4 nanoparticles (Fe 3O 4NPs/MWCNT) were prepared and used to construct a novel biosensor for the simultaneous detection of adenine and guanine. The direct electro-oxidation of adenine and guanine on the modified electrode were investigated by linear sweep voltammetry. The results indicate a remarkable increase in the oxidation peak currents together with negative shift in the oxidation peak potentials for both adenine and guanine, in comparison to the bare glassy carbon electrode (GCE). The surface morphology and nature of the composite film deposited on GCE were characterized by transmission electron microscopy, atomic force microscopy,...
Toward single-DNA electrochemical biosensing by graphene nanowalls
, Article ACS Nano ; Volume 6, Issue 4 , March , 2012 , Pages 2904-2916 ; 19360851 (ISSN) ; Ghaderi, E ; Rahighi, R ; Sharif University of Technology
2012
Abstract
Graphene oxide nanowalls with extremely sharp edges and preferred vertical orientation were deposited on a graphite electrode by using electrophoretic deposition in an Mg 2+-GO electrolyte. Using differential pulse voltammetry (DPV), reduced graphene nanowalls (RGNWs) were applied for the first time, in developing an ultra-high-resolution electrochemical biosensor for detection of the four bases of DNA (G, A, T, and C) by monitoring the oxidation signals of the individual nucleotide bases. The extremely enhanced electrochemical reactivity of the four free bases of DNA, single-stranded DNA, and double-stranded DNA (dsDNA) at the surface of the RGNW electrode was compared to electrochemical...
Effect of cation radical formation on reactivity and acidity enhancement of cytosine nucleobase: Natural bond orbital and atom in molecule analysis
, Article Journal of Theoretical and Computational Chemistry ; Volume 11, Issue 2 , 2012 , Pages 313-327 ; 02196336 (ISSN) ; Javan, M. J ; Fattahi, A ; Hashemi, M. M ; Sharif University of Technology
Abstract
The radical cations of DNA constituents generated by the ionizing radiation initiate an alteration of the bases, which is one of the main types of cytotoxic DNA lesions. These cation radical spices are known for their role in producing nucleic acid strand break. In this study, the gas-phase intrinsic chemical properties of the gaseous radical cations of cytosine and its base pair with guanine were examined by employing density functional theory (B3LYP) with the 6-311++G(d,p) basis set. Structures, geometries, adiabatic ionization energies, adiabatic electron affinities, charge distributions, molecular orbital analysis and proton-transfer process of these molecules were investigated. The...
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) ; 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...
Calculation of melting temperature and transition curve for dickerson DNA dodecamer on the basis of configurational entropy, hydrogen bonding energy, and heat capacity: A molecular dynamics simulation study
, Article Journal of the Iranian Chemical Society ; Volume 8, Issue 3 , 2011 , Pages 708-716 ; 1735207X (ISSN) ; Parsafar, G. A ; Abroshan, H ; Akbarzade, H ; Sharif University of Technology
Abstract
A familiarity with denaturation process is highly significant in understanding the DNA replication, manipulation, and interactions involving DNA double helix stability. We have performed molecular dynamics simulation on B-DNA duplex (CGCGAATTGCGC) at different temperatures. At each temperature, configurational entropy was estimated using the covariance matrix of atom-positional fluctuations. By plotting the configuration entropy versus temperature, we calculated the melting temperature which was found to be 329.7 K. We also calculated the hydrogen bonding energy and heat capacity for the atoms participating in the hydrogen bonding between two strands of DNA. Moreover, their temperature...
Contribution of nonlocal interactions to DNA elasticity
, Article Journal of Chemical Physics ; Volume 134, Issue 12 , 2011 ; 00219606 (ISSN) ; 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
Dose-dependent effects of nanoscale graphene oxide on reproduction capability of mammals
, Article Carbon ; Volume 95 , December , 2015 , Pages 309-317 ; 00086223 (ISSN) ; Ghaderi, E ; Hashemi, E ; Akbari, E ; Sharif University of Technology
Elsevier Ltd
2015
Abstract
In vivo dose-dependent effects of nanoscale graphene oxide (NGO) sheets on reproduction capability of Balb/C mice were investigated. Biodistribution study of the NGO sheets (intravenously injected into male mice at dose of ∼2000 μg/mL or 4 mg/kg of body weight) showed a high graphene uptake in testis. Hence, in vivo effects of the NGO sheets on important characteristics of spermatozoa (including their viability, morphology, kinetics, DNA damage and chromosomal aberration) were evaluated. Significant in vivo effects was found at the injected concentrations ≥200 μg/mL after (e.g., ∼45% reduction in sperm viability and motility at 2000 μg/mL). Observation of remarkable DNA fragmentations and...
Recovery from random samples in a big data set
, Article IEEE Communications Letters ; Volume 19, Issue 11 , September , 2015 , Pages 1929-1932 ; 10897798 (ISSN) ; Gohari, A ; Sharif University of Technology
Institute of Electrical and Electronics Engineers Inc
2015
Abstract
Consider a collection of files, each of which is a sequence of letters. One of these files is randomly chosen and a random subsequence of the file is revealed. This random subsequence can be the result of a random sampling of the file. The goal is to recover the identity of the file, assuming a simple greedy matching algorithm to search the file collection. We study the fundamental limits on the maximum size of the file collection for reliable recovery in terms of the length of the random subsequence. The sequence of each file is assumed to follow a hidden Markov model (HMM), which is a common model for many data structures such as voice or DNA sequences. The connection between this problem...
Extreme bendability of DNA double helix due to bending asymmetry
, Article Journal of Chemical Physics ; Volume 143, Issue 10 , 2015 ; 00219606 (ISSN) ; 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...
Carbon nanotubes part I: Preparation of a novel and versatile drug-delivery vehicle
, Article Expert Opinion on Drug Delivery ; Volume 12, Issue 7 , 2015 , Pages 1071-1087 ; 17425247 (ISSN) ; Solati, N ; Amiri, M ; Mirshekari, H ; Mohamed, E ; Taheri, M ; Hashemkhani, M ; Saeidi, A ; Estiar, M. A ; Kiani, P ; Ghasemi, A ; Basri, S. M. M ; Aref, A. R ; Hamblin, M. R ; Sharif University of Technology
Informa Healthcare
2015
Abstract
Introduction: It is 23 years since carbon allotrope known as carbon nanotubes (CNT) was discovered by Iijima, who described them as "rolled graphite sheets inserted into each other". Since then, CNTs have been studied in nanoelectronic devices. However, CNTs also possess the versatility to act as drug- and gene-delivery vehicles.Areas covered: This review covers the synthesis, purification and functionalization of CNTs. Arc discharge, laser ablation and chemical vapor deposition are the principle synthesis methods. Non-covalent functionalization relies on attachment of biomolecules by coating the CNT with surfactants, synthetic polymers and biopolymers. Covalent functionalization often...
Carbon nanotubes part II: A remarkable carrier for drug and gene delivery
, Article Expert Opinion on Drug Delivery ; Volume 12, Issue 7 , 2015 , Pages 1089-1105 ; 17425247 (ISSN) ; Solati, N ; Ghasemi, A ; Estiar, M. A ; Hashemkhani, M ; Kiani, P ; Mohamed, E ; Saeidi, A ; Taheri, M ; Avci, P ; Aref, A. R ; Amiri, M ; Baniasadi, F ; Hamblin, M. R ; Sharif University of Technology
Informa Healthcare
2015
Abstract
Introduction: Carbon nanotubes (CNT) have recently been studied as novel and versatile drug and gene delivery vehicles. When CNT are suitably functionalized, they can interact with various cell types and are taken up by endocytosis.Areas covered: Anti-cancer drugs cisplatin and doxorubicin have been delivered by CNT, as well as methotrexate, taxol and gemcitabine. The delivery of the antifungal compound amphotericin B and the oral administration of erythropoietin have both been assisted using CNT. Frequently, targeting moieties such as folic acid, epidermal growth factor or various antibodies are attached to the CNT-drug nanovehicle. Different kinds of functionalization (e.g., polycations)...
Molecular dynamics simulation of supercoiled DNA rings
, Article Macromolecules ; Volume 48, Issue 1 , December , 2015 , Pages 164-172 ; 00249297 (ISSN) ; Schiessel, H ; Ejtehadi, M. R ; Sharif University of Technology
American Chemical Society
2015
Abstract
DNA supercoiling is a widespread phenomenon in biology. Here we introduce a coarse-grained DNA model and study supercoiled DNA rings via a rigid body molecular dynamics simulation. Our model allows us to investigate these structures in more detail than previously. The simulations are performed on rings of one to six kilobase pairs length and are compared to available experimental data and former simulation studies. The current study provides new additional information about some of the geometrical parameters of the supercoiled DNA rings. It also shows how enforcing a supercoiled DNA ring to two-dimensional space changes its geometrical parameters. Finally, our molecular dynamics method...
The effect of energy spectrum change on DNA damage in and out of field in 10-MV clinical photon beams
, Article Medical and Biological Engineering and Computing ; Volume 53, Issue 1 , January , 2015 , Pages 67-75 ; 01400118 (ISSN) ; Xiao, Y ; Sohrabpour, M ; Studenski, M. T ; Sharif University of Technology
Springer Verlag
2015
Abstract
The aim of this study was to quantify the DNA damage induced in a clinical megavoltage photon beam at various depths in and out of the field. MCNPX was used to simulate 10 × 10 and 20 × 20 cm2 10-MV photon beams from a clinical linear accelerator. Photon and electron spectra were collected in a water phantom at depths of 2.5, 12.5 and 22.5 cm on the central axis and at off-axis points out to 10 cm. These spectra were used as an input to a validated microdosimetric Monte Carlo code, MCDS, to calculate the RBE of induced DSB in DNA at points in and out of the primary radiation field at three depths. There was an observable difference in the energy spectra for photons and electrons for points...
Investigating optimum procedures needed to maintain a model satellite's CG stable about design point, under subsystem configuration changes
, Article ASME 2010 10th Biennial Conference on Engineering Systems Design and Analysis, ESDA2010, 12 July 2010 through 14 July 2010, Istanbul ; Volume 4 , 2010 , Pages 585-588 ; 9780791849187 (ISBN) ; Abedian, A ; Teimouri, H ; Sharif University of Technology
2010
Abstract
During design, microsatellites are subject to different changes like the changes in weight, location and dimension of parts and elements of subsystems and the payload. These changes should be accumulated by the structure subsystem in a way that some key structural parameters like the center of gravity (CG) and inertia moments remain unchanged. This subject is also important regarding the design of a modular structure of a satellite. In the present study it is tried to accommodate any changes in weight and location of any part(s) and element(s) of a microsatellite by optimum (minimum) rearrangement of other parts on their plane of rest in order to keep the CG and inertia moments unchanged....
A Thesis Submitted in Partial Fulfillment of the Requirement for the Degree of Master of Science in Electrical Engineering
, M.Sc. Thesis Sharif University of Technology ; Jahed, Mehran (Supervisor) ; Motahhari, Abolfazl (Co-Advisor)
Abstract
Dnase I Hypersensitive Sites (DHSs) are known as comprehensive markers of DNA regulatory elements. The main function of regulatory elements is repressing or enhancing transcription of genes. Hence, the recruitment of the data is prevalent in many studies of genome. One of the applications of this data is to utilize it to predict active regulatory regions (Transcription Factor Binding Sites).There are different means to do this, divided in three major groups: first, the methods only use the number of DNase-seq reads that surround a candidate binding site. While robust, these methods do not reflect the shape of the signal. A second strategy uses a variety of approaches to model and identify...
Evaluation of Base Calling Methods in Next Generation Sequencing
, M.Sc. Thesis Sharif University of Technology ; Hossein Khalaj, Babak (Supervisor) ; Motahhari, Abolfazl (Supervisor)
Abstract
In the mid twentieth century by discovering the existence of genetic strands and understanding their role in diseases and phenotypes of species, research initiated to decipher their content. Sequencing of the first human genome at early twenty-first century paved the way to study and even cure complex human deseases having genetic origin. Next Generation Sequencing (NGS) Technologies have significantly reduced the expenses and the timing complexity of DNA Sequencing and this has an improving trend. In this thesis, we evaluate Base Calling methods, a critical step in analyzing next generation sequencing information and deals with massive sequencing data. Base Calling tries to optimally detect...
Production and Purification of Recombinant Amylin Peptide and Investigating the Effects of Synthetic and Natural Products on Amyloid Fibril Formation
, M.Sc. Thesis Sharif University of Technology ; KAalhor, Hamid Reza (Supervisor) ; Matloubi Moghaddam, Firouz (Co-Advisor)
Abstract
What determines the function of a protein, after its synthesis by the ribosome, is its unique three dimensional structure. The unique structure of protein is achieved through process of folding which is detrimental to protein function. Although this unique structure is stable in a variety of situations, the protein may undergo conformational change, due to slight changes in physiological conditions, affecting the protein structure and function. In certain conditions, the conformational change brings about misfolding of the protein leading to protein aggregation. The protein aggregation can also result in amyloid formation in which a soluble protein is converted to fibrils with specific...