Showing 6 results for Dna
H Davoodi, S R Hashemi, H F Seow, M Ghorbani,
Volume 3, Issue 2 (10-2009)
Abstract
Abstract Background and objectives: Paraffin-embedded tissues and clinical samples are a valuable resource for molecular genetic studies, but the extraction of high-quality genomic DNA from this tissues is still a problematic issue. In the Present study, the efficiency of two DNA extraction protocols, a commercial kit and a traditional method based on heating and K Proteinase was compared. Material and Methods: Fifty paraffin-embedded blocks of colon cancer tissues (more than 5 years old) were used to compare two methods of DNA extraction. DNA was extracted by traditional method using heat and commercial DNA extraction (Qiagen kit) method. Then the purity and concentration of extracted DNA were measured by Spectrophotometer. Two sequences of TLR4 “The most important receptors in innate immunity” were amplified by polymerase chain reaction. SH-1 ‘188bp’ and SH-2 ‘124bp’ were amplified and then the products were separated on a 2% agarose gel. Results: The results show that the yield of DNA by traditional method (297 mg/ml) is significantly (p<0.01) higher than Commercial kit (176mg/ ml). But traditional method has the lower OD ratio (1.2) Compared to Commercial method. The Amplification of the TLR4 gene sequences is more successful by the traditional method (p<0.01) compared with commercial method. The length of the sequence affects on the results of PCR in that short sequence is amplified more successful compared to the long sequence. Conclusion: The traditional method is more successful in PCR amplification and also simple and cheap. Therefore, we recommend using this method for DNA extraction taken from the paraffin-embedded blocks with more than 5 years old and selecting shorter sequence for better amplification in PCR. Key words: DNA Extraction, paraffin embedded tissue, PCR
Mousazade Moghadam M, Babavalian H, Mirnejad R, Shakeri F,
Volume 6, Issue 1 (4-2012)
Abstract
Abstract
Background and objectives: Genomic DNA extraction of bacterial cells is of processes performed normally in most biological laboratories therefore, various methods have been offered, manually and kit, which may be time consuming and costly. In this paper, genomic DNA extraction of Staphylococcus aureus was investigated using some laundry detergent brands available in Iran to achieve a rapid and cost effective method.
Material and Methods: five-enzyme Taj brand, three-enzyme Saftlan brand ,and Darya and Pak brands without enzyme were used in the concentrations of 10, 20, 40, 80 mg/L. Afterwards, in order to evaluate the efficiency of extracted DNA in downstream processing, PCR test was performed for femA gene in the genome of Staphylococcus aureus.
Results: DNA extraction using different concentrations of the brands show that extracted DNA using 40 mg/L Saftlan and Taj brand powders have the best results according concentration (µg/ml) and purity (A260/A280) parameters. These parameters are 387.5 1.88 (Taj), 254.1 2.80 (Softlan), 396.6 1.95 (Manual) and 423.3 2.2 (Kit), respectively. Afterward, the PCR test results by show that DNA extraction using laundry detergents has no effect on its efficiency in order to be used in downstream processes.
Conclusion: These results indicate that the proper concentrations of laundry detergents can be used to extract genomic DNA with similar efficiency to kit and manual extraction methods.
Key words: Bacterial genome, DNA extraction, laundry powder, PCR, Staphylococcus aureus
H Haghighatfard, Y Yazdani, Y.,
Volume 9, Issue 1 (4-2015)
Abstract
Abstract
Background and Objective: the inhibition of tumor-associated angiogenesis can significantly reduce the tumor proliferation. The basic fibroblast growth factor (bFGF), an important angiogenic factor, is considered as a potential therapeutic target for cancer therapy. The purpose of this study was evaluating, designing and construction of new recombinant DNA molecule in order to have efficient expression of a fusion protein consisting of the bFGF and immunodominant epitopes of Pseudomonas toxin.
Material and Methods: Different types of peptide linker, codon adaptation index (CAI) and adding signal peptide were considered in designing of immunogenic coding sequence. After software evaluation, the recombinant DNA molecule was ordered in the puc57 cloning vector. Then, coding sequence inserted into the multiple cloning site of pET28-a plasmid. Finally, PCR and enzymatic digestion tests were done for evaluation of recombinant expression vector.
Results: Optimization of DNA sequence, codon adaptation index (CAI) increased from 0.69 to 0.83 and GC content decreased from 61 to 54.77. The presence of 1214-bp PCR product and 1029-bp one obtaining from enzymatic digestion confirmed the correction of the cloning process.
Conclusion: According to the previous studies, it is the first work for designing, optimizing and synthesis of recombinant DNA consisting of bFGF and immunodominant epitopes of Pseudomonas toxin.
Keywords: Tumor angiogenesis, immunodominant epitopres of Pseudomonas toxin, Fibroblast growth factor 2, DNA 2 software
Seyedeh Tahereh Haeri, Mohammad Ali Azarbayjani, Maghsoud Peeri,
Volume 14, Issue 4 (7-2020)
Abstract
Background and Objectives: Prolonged exercise can reduce physiological capacities and cause DNA damage by inducing oxidative stress and inflammatory responses. Aerobic exercise reduces the risk of cancer by activating DNA repair enzymes and reducing oxidative stress. The aim of the present study was to investigate effects of eight weeks of aerobic exercise with and without vitamin D supplementation on DNA damage.
Methods: Forty-eight adult male rats were randomly divided into six groups: control (C), H2O2 (H), H2O2 and vitamin D (HD), H2O2 and exercise (HE), H2O2,, vitamin D and exercise (HDE), and dimethyl sulfoxide. Cancer was stimulated through intraperitoneal injection of H2O2 (2 mmol/kg). Animals in groups HE and HDE ran on treadmill for eight weeks. Concentration of 8-hydroxy-2'-deoxyguanosine (8-OHdG) and O6-methylguanine DNA methyltransferase (MGMT) was measured by enzyme-linked immunosorbent assay. Statistical analysis of data was carried out using SPSS 22 at significance level of 0.05.
Results: Vitamin D supplementation significantly lowered the level of 8-OHdG expression compared to the control group (P=0.0001). The 8-OHdG expression in the exercise group was slightly lower than control group (P=0.063). Combination of exercise and vitamin D supplementation had no significant effect on expression of 8-OHdG (P=0.281). Both exercise and vitamin D supplementation significantly increased MGMT expression compared to the control group (P=0.0001 and P=0.040). However, combination of exercise and vitamin D supplementation had no significant effect on MGMT expression (P=0.326).
Conclusion: The results showed that aerobic exercise and vitamin D supplementation can have protective effects against DNA damage, possibly by increasing antioxidant capacity and DNA repair.
Rajneesh Prajapat, Suman Jain,
Volume 16, Issue 6 (11-2022)
Abstract
Background and objectives: The outbreak of coronavirus disease 2019 (COVID-19) has become a global health emergency. The severe acute respiratory syndrome coronavirus 2 (SARS‑CoV‑2) NSP13 helicase plays an important role in SARS-CoV-2 replication and could serve as a target for the development of antivirals. The objective of the study was to perform homology modeling and docking analysis of SARS-CoV-2 NSP13 helicase as a drug target.
Methods: The structure and function of SARS-CoV-2 NSP13 helicase were predicted by in-silico modeling studies. The SWISS-MODEL structure assessment tool was used for homology modeling and visual analysis of the crystal structure of the protein. The validation for structure models was performed using PROCHECK. Model quality was estimated based on the QMEAN and ProSA. The MCULE-1-Click docking and InterEvDock-2.0 server were used for protein-ligand docking.
Results: The SARS-CoV-2 NSP13 helicase model corresponded to probability confirmation with 90.9% residue of the core section, which highlights the accuracy of the predicted model. ProSA Z-score of -9.17 indicated the good quality of the model. Inhibitor N-(3-(carbamoylamino) phenyl) acetamide exhibited effective binding affinity against the NSP13 helicase. The docking results revealed that Lys-146, Leu-147, Ile-151, Tyr-185, Lys-195, Tyr-224, Val-226, Leu-227, Ser-229 residues exhibit good binding interactions with inhibitor ligand N-(3-(carbamoyl amino) phenyl) acetamide.
Conclusion: Hence, the proposed inhibitor could potently inhibit SARS-CoV-2 NSP13 helicase, which is thought to play key roles during viral replication. The results of this study indicate that N-(3-(carbamoylamino) phenyl) acetamide could be a valuable lead molecule with great potential for SARS-CoV-2 NSP13 helicase inhibition.
Parisa Hasanein, Fahime Javadi Hedaiat Abad, Musa Bohlooli, Mostafa Khajeh, Sedigheh Esmaielzadeh Bahabadi, Neda Poormolaei,
Volume 19, Issue 1 (4-2025)
Abstract
Introduction: DNA Glycation damages DNA by inducing breaks of strands, mutations, and finally changes in gene expression, which is assumed as a main factor in pathogenesis of diabetes and its complications. Therefore, antiglycation agents have been focused recently for preventing and alleviating diabetes complications. According to the reported antidiabetic effects of Tamarix aphylla (T. aphylla) leaves extract, this study was aimed to determine the effect of T. aphylla on glucose-mediated DNA glycation for the first time.
Methods: DNA incubated with glucose for 4 weeks and the inhibitory or fascilitatory effects of T. aphylla on DNA structural changes were studied by various techniques. These techniques were included UV–Vis, fluorescence spectroscopy, circular dichroism (CD) and agarose gel electrophoresis.
Results: The findings of UV–Vis and fluorescence spectroscopy showed that T. aphylla decreased the DNA-AGE (advanced glycation end products) formation. Based on the CD and agarose gel electrophoresis results, the structural changes of glycated DNA was decreased in the presence of T. aphylla.
Conclusion: Thus T. aphylla has beneficial effects against DNA glycation and could be a promising agent for ameliorate the adverse effects of glycation in the presence of glucose and conditions of raised blood glucose after confirming in further studies.
