Modares Journal of Biotechnology

Abstract Abstract:

Aptamers are single-stranded sequences of RNA, DNA, or highly specific proteins that tend to bind to a wide range of target molecules. Aptamers are widely used in various fields, especially medicine and diagnostics, and are similar in their application to antibodies. There are many benefits to using aptamer instead of antibodies, such as low cost, longer life, increased tissue permeability, and more. There are several methods for producing aptamer that in silico methods can shorten and simplify the steps of aptamer production. With aptamer modeling, a set of in silico methods such as modeling, docking, and molecular dynamics can be used to screen for the best aptamer sequence. In this article, a review of the types of aptamers, their structure and design methods in silico is briefly stated.

Keywords: Aptamer, DNA, RNA, Protein, insilico



Keywords: Aptamer, DNA, RNA, Protein, insilico

Abstract The high quality and quantity of extracted DNA is necessary for a variety of molecular biology studies. Low yields and poor quality of genomic DNA extracted from petal due to high levels of secondary metabolites. Carotenoids, anthocyanins, phenolic acids and flavonoids are the most effective secondary metabolites in petals, which are considered as contaminating compounds and could lead to interfere with DNA during extraction and purification. Considering that the basis of the most molecular research in genetic engineering and genomics is high-quality of DNA, therefore, it seems that finding an efficient method for reducing adverse effects of these contaminating compounds for the exteraction is essential. In this regard, iron-magnetic nanoparticles have been used to improve the exteraction of high yields and quality of DNA from rose petals in the present work. In the following, to compare the efficiency of DNA extraction, modified CTAB (Cetyl Trimethyl Ammonium Bromide) and rapid detection methods were used. The results showed that petal’s extracted DNA quantification and qualification by iron-magnetic nanoparticles procedure was much more reliable than two other methods. Inaddition, this method could extract optimal amount of DNA with the lowest amounts of samples within few minutes. Due to high qualification and quantification of DNA purification by iron-magnetic nanoparticles, the present procedure could be recommended as an efficient protocol for rose petal DNA extraction.

Abstract Aims: Targeting DNA lies at the heart of anti-cancer therapies. Hence, DNA-binding drugs and their interaction with DNA have recently drawn the attention of researchers. Since DNA minor groove binders (MGBs) act as potent anti-tumor agents, there is a need to have detailed insights on how they interact with DNA. The mechanism of action of the majority of MGBs is not well studied at the molecular level.
Materials and Methods: Herein, molecular docking and dynamics simulations were performed, using AutoDock Vina and NAMD softwares, respectively, to evaluate the binding of A derivatives (Tallimustine, PNU 151807, and ) to , and to compare their interaction energy and binding patterns.
Findings: All three drugs were stably bound throughout the simulation, causing only minor modifications to the structure of DNA. Results of interaction energy analyses together with LigPlot outcomes showed that A/T residues are responsible for making the majority of non-bonding interactions in the case of all three drugs, showing a good agreement with previously reported findings on MGBs.
Conclusion: A/T residues are responsible for making the majority of non-bonding interactions in the case of all three drugs, showing a good agreement with previously reported findings on MGBs. Furthermore, our studies have shown that to the other members of the Distamycin A family, makes stronger interactions with , making it a better candidate for cancer therapy goals.

Abstract Aims: Compelling approach in molecular self-assembly has caused an appropriate bottom-up approach to build and design the systems and patterns with specific performance and capabilities. The aim of the current study was the design and fabrication of self-assembled super nanonetworks of carbon nanotube by self-complementary DNA and its spectroscopic study.
Materials and Methods: In the present experimental study, the sticky oligonucleotide sequence, connected to the amine groups at one end, was connected to the carboxyl groups at the beginning and end of the carbon nanotubes with covalent bond. Then, oligonucleotide connected these systems as interconnected networks. After the preparation of these nanonetworks, their biophysical properties were studied through ultraviolet–visible spectroscopy (UV-vis) and polarimetry and circular dichroism (CD) spectroscopy.
Findings: UV-vis specific absorption peak increased and DNA sequences specific peak in CD spectra appeared with DNA sequences bind to carbon nanotubes.
Conclusion: After adding the connecting sequences to the constructive units, carbon nanotubes come in the form of a complex network. The formation of network nanostructures made of carbon nanotubes by the base pair of paired oligonucleotide sequences is clearly visible in UV-vis spectra.