Sharif Digital Repository

Equilibrium constants for formation of a cobalt(II) complex with the bidentate ligand dopamine have been studied with spectrophotometric methods in water + ethanol cosolvent systems at 15, 25, and 35 (±0.1)∈°C and an ionic strength of 0.2 mol·dm-3. The ionic strength was maintained using sodium chloride and a phosphate buffer. The stability constants of the complex and the resulting Gibbs energy changes are obtained. The results are discussed in terms of the effect of solvent on protonation and complexation. © Springer Science+Business Media, LLC 2007  

Current techniques in sequencing a genome allow a service provider (e.g. a sequencing company) to have full access to the genome information, and thus the privacy of individuals regarding their lifetime secret is violated. In this paper, we introduce the problem of private DNA sequencing, where the goal is to keep the DNA sequence private to the sequencer. We propose an architecture, where the task of reading fragments of DNA and the task of DNA assembly are separated, the former is done at the sequencer(s), and the later is completed at a local trusted data collector. To satisfy the privacy constraint at the sequencer and reconstruction condition at the data collector, we create an... 

By considering the detailed structure of DNA in the base pair level, two possible definitions of the persistence length are compared. One definition is related to the orientation of the terminal base pairs, and the other is based on the vectors which connect two adjacent base pairs at each end of the molecule. It is shown that although these definitions approach each other for long DNA molecules, they are dramatically different on short length scales. We show analytically that the difference mostly comes from the shear flexibility of the molecule and can be used to measure the shear modulus of DNA  

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... 

DNA sequencing has faced a huge demand since it was first introduced as a service to the public. This service is often offloaded to the sequencing companies who will have access to full knowledge of individuals' sequences, a major violation of privacy. To address this challenge, we propose a solution, which is based on separating the process of reading the fragments of sequences, which is done at a sequencing machine, and assembling the reads, which is done at a trusted local data collector. To confuse the sequencer, in a pooled sequencing scenario, in which multiple sequences are going to be sequenced simultaneously, for each target individual, we add fragments of one non-target individual,... 

Etheno-damaged DNA adducts such as 3,N4- ethenocytosine, N 2,3-ethenoguanine, and 1,N2-ethenoguanine are associated with carcinogenesis and cell death. These inevitable damages are counteracted by glycosylase enzymes, which cleave damaged nucleobases from DNA. Escherichia coli alkyl purine DNA glycosylase is the enzyme responsible for excising damaged etheno adducts from DNA in humans. In an effort to understand the intrinsic properties of these molecules, we examined gasphase acidity values and proton affinities (PA) of multiple sites of these molecules as well as equilibrium tautomerization and base pairing properties by quantum mechanical calculations. We also used calculations to compare... 

The authors describe an impedimetric method for the quantitation of the DNA of the human papilloma virus (HPV) type 16. A glassy carbon electrode (GCE) was modified with gold nanosheets and is shown to be superior to a common gold disk electrode. A single-stranded 25mer oligonucleotide (ssDNA) acting as the probe DNA was immobilized via its thiolated 5′ end on both electrodes. After hybridization with target (analyte) DNA, electrochemical impedance spectra were acquired in the presence of hexacyanoferrate as a redox marker. The sensor can distinguish between complementary, non-complementary and single base pair mismatches of HPV ssDNA. At a 1 mM hexacyanoferrate concentration, the biosensors... 

In this study, optical technology is considered as SA issues' solution with the potential ability to increase the speed, overcome memory-limitation, reduce power consumption, and increase output accuracy. So we examine the effect of bio-data encoding and the creation of input images on the pattern-recognition error-rate at the output of optical Vander-lugt correlator. Moreover, we present a genetic algorithm-based coding approach, named as GAC, to minimize output noises of cross-correlating data. As a case study, we adopt the proposed coding approach within a correlation-based optical architecture for counting k-mers in a DNA string. As verified by the simulations on Salmonella whole-genome,... 

In this study, optical technology is considered as SA issues' solution with the potential ability to increase the speed, overcome memory-limitation, reduce power consumption, and increase output accuracy. So we examine the effect of bio-data encoding and the creation of input images on the pattern-recognition error-rate at the output of optical Vander-lugt correlator. Moreover, we present a genetic algorithm-based coding approach, named as GAC, to minimize output noises of cross-correlating data. As a case study, we adopt the proposed coding approach within a correlation-based optical architecture for counting k-mers in a DNA string. As verified by the simulations on Salmonella whole-genome,... 

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.... 

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... 

DNA polymerase η (polη) is of significant value for designing new families of anticancer drugs. This protein takes a role in many stages of the cell cycle, including DNA replication, translesion DNA synthesis, and the repairing process of DNA. According to many studies, a high level of expression of polη in most cases has been associated with low rates of patients' survival, regardless of considering the stage of tumor cells. Thus, the design of new drugs with fewer side effects to inhibit polη in cancerous cells has attracted attention in recent years. This project aims to design and explore the alternative inhibitors for polη, which are based on carbohydrates and amino acids. In terms of... 

In this work, an electrochemical DNA biosensor, based on a dual signal amplified strategy by employing a polyaniline film and gold nanoparticles as a sensor platform and enzyme-linked as a label, for sensitive detection is presented. Firstly, polyaniline film and gold nanoparticles were progressively grown on graphite screen-printed electrode surface via electropolymerization and electrochemical deposition, respectively. The sensor was characterized by scanning electron microscopy (SEM), cyclic voltammetry and impedance measurements. The polyaniline-gold nanocomposite modified electrodes were firstly modified with a mixed monolayer of a 17-mer thiol-tethered DNA probe and a spacer thiol,... 

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... 

Using analytical approach and Monte Carlo (MC) simulations, we study the elastic behavior of the intrinsically twisted elastic ribbons with bending anisotropy, such as double-stranded DNA (dsDNA), in two-dimensional (2D) confinement. We show that, due to the bending anisotropy, the persistence length of dsDNA in 2D conformations is always greater than three-dimensional (3D) conformations. This result is in consistence with the measured values for DNA persistence length in 2D and 3D in equal biological conditions. We also show that in two dimensions, an anisotropic, intrinsically twisted polymer exhibits an implicit twist-bend coupling, which leads to the transient curvature increasing with a... 

The primary challenge of spectroscopic techniques in selective detection and characterization of tautomeric structures of DNA and RNA bases, and moreover, the accurate interpretation and explanation of the experimental results are the main motives of theoretical studies. Surface-enhanced Raman spectroscopy (SERS) can be a powerful approach to distinguish cytosine in the presence of its tautomers. For this respect, herein, the theoretical simulation of the SERS spectra of cytosine and its three most stable tautomers adsorbed on silver clusters is carried out. The calculations of SERS spectra is based on the excited-state energy gradient approximation as a well-established approach that gives... 

Single cell gel electrophoresis was used to observe the effect of bifenthrin and chlorpyrifos on Labeo rohita. The present work was planned to study the genotoxic effect of pesticide mixture on the major indian carp, L. rohita at sub-lethal concentration 33% LC50. First of all, 96-hr LC50 was determined for L. rohita, then fish was given sub-lethal environment for 70 days. Erythrocytes from blood were taken after each fortnight for the assessment of time dependent DNA damage (% damage), aggregate tail length of comets and genomic destruction. There was increase in damage up to 56 days and after that a slight decrease was observed in next fourteen days. After statistical analysis, it was... 

In the past decade, assays that profile different aspects of the epigenome have grown exponentially in number and variation. However, standard guidelines for researchers to choose between available tools depending on their needs are lacking. Here, we introduce a comprehensive collection of the most commonly used bulk and single-cell epigenomic assays and compare and contrast their strengths and weaknesses. We summarize some of the most important technical and experimental parameters that should be considered for making an appropriate decision when designing epigenomic experiments. © Copyright © 2021 Mehrmohamadi, Sepehri, Nazer and Norouzi  

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  

An impedimetric human papilloma virus (HPV) DNA biosensor based on gold nanotubes (AuNTs) in label free detection was materialized. The AuNTs decorated nanoporous polycarbonate (AuNTs-PC) template as biosensor electrode was fabricated by electrodeposition method. The single strand DNA (ss-DNA) probe was covalently immobilized onto the AuNTs-PC electrode. The hybridization of target sequences with the ss-DNA probe was observed by the electrochemical impedance spectroscopy (EIS). The biosensor showed high selectivity and could differentiate between the complementary, mismatch and non-complementary DNA sequences. The EIS measurements were matched to Randle's equivalent circuit. The...