Deoxyribonucleic Acid Binding Research Articles

Experimental and molecular modelling demonstration of effective DNA and protein binding as well as anticancer potential of two mononuclear Cu(II) and Co(II) complexes with isothiocyanate and azide as anionic residues

In the present study, one mononuclear Cu(II) [CuL(SCN)] (1) and one mononuclear Co(II) [CoLN3] (2) complexes, with a Schiff base ligand (HL) formed by condensation of 2-picolylamine and salicylaldehyde, have been successfully developed and structurally characterized. The square planer geometry of both complexes is fulfilled by the coordination of one deprotonated ligand and one ancillary ligand SCN−(1) or N3−(2) to the metal centre. Binding affinities of both complexes with deoxyribonucleic acid (DNA) and human serum albumin (HSA) are investigated using several biophysical and spectroscopic techniques. High values of the macromolecule-complex binding constants and other results confirm the effectiveness of both complexes towards binding with DNA and HSA. The determined values of the thermodynamic parameters support spontaneous interactions of both complexes with HSA, while fluorescence displacement and DNA melting studies establish groove-binding interactions with DNA for both complexes 1 and 2. The molecular modelling study validates the experimental findings. Both complexes are subjected to an MTT test establishing the anticancer property of complex 1 with lower risk to normal cells, confirmed by the IC50 values of the complex for HeLa cancer cells and HEK normal cells. Finally, a nuclear staining analysis reveals that the complexes have caused apoptotic cell death.

Role of Alkali Cations in DNA-Thioflavin T Interaction.

This study investigates the role of alkali cations in modulating the interaction between deoxyribonucleic acid (DNA) and Thioflavin T (ThT) in dilute and condensed phases. The emission characteristics of ThT were analyzed in the presence of double-stranded DNA and G-quadruplex structures with a focus on the effects of four cations: sodium, potassium, calcium, and magnesium. The ThT emission in double-stranded DNA was influenced by direct DNA binding and steric hindrance within the hydration shell of DNA, which was modulated by the presence of alkali cations. Lasing spectroscopy experiments further highlighted ThT sensitivity to the spatial arrangement of water molecules in the DNA hydration shell. Lasing was exclusively observed in the presence of Mg2+ in the G-quadruplex structure, suggesting that the parallel propeller configuration of G4 provides an optimal environment for ThT light amplification. This study highlights the critical role of cations in DNA-dye interactions and reaffirms the significance of ThT in biophysical studies.

Transcription factor ZmDof22 enhances drought tolerance by regulating stomatal movement and antioxidant enzymes activities in maize (Zea mays L.).

The Dof22 gene encoding a deoxyribonucleic acid binding with one finger in maize, which is associated with its drought tolerance. The identification of drought stress regulatory genes is essential for the genetic improvement of maize yield. Deoxyribonucleic acid binding with one finger (Dof), a plant-specific transcription factor family, is involved in signal transduction, morphogenesis, and environmental stress responses. In present study, by weighted correlation network analysis (WGCNA) and gene co-expression network analysis, 15 putative Dof genes were identified from maize that respond to drought and rewatering. A real-time fluorescence quantitative PCR showed that these 15 genes were strongly induced by drought and ABA treatment, and among them ZmDof22 was highly induced by drought and ABA treatment. Its expression level increased by nearly 200 times after drought stress and more than 50 times after ABA treatment. After the normal conditions were restored, the expression levels were nearly 100 times and 40 times of those before treatment, respectively. The Gal4-LexA/UAS system and transcriptional activation analysis indicate that ZmDof22 is a transcriptional activator regulating drought tolerance and recovery ability in maize. Further, overexpressed transgenic and mutant plants of ZmDof22 by CRISPR/Cas9, indicates that the ZmDof22, improves maize drought tolerance by promoting stomatal closure, reduces water loss, and enhances antioxidant enzyme activity by participating in the ABA pathways. Taken together, our findings laid a foundation for further functional studies of the ZmDof gene family and provided insights into the role of the ZmDof22 regulatory network in controlling drought tolerance and recovery ability of maize.

Dissecting the effect of ALS mutation S375G on the conformational properties and aggregation dynamics of TDP-43370-375 fragment

The aggregation of transactive response deoxyribonucleic acid (DNA) binding protein of 43 kDa (TDP-43) into ubiquitin-positive inclusions is closely associated with amyotrophic lateral sclerosis (ALS), frontotemporal lobar degeneration, and chronic traumatic encephalopathy. The 370–375 fragment of TDP-43 (370GNNSYS375, TDP-43370-375), the amyloidogenic hexapeptides, can be prone to forming pathogenic amyloid fibrils with the characteristic of steric zippers. Previous experiments reported the ALS-associated mutation, serine 375 substituted by glycine (S375G) is linked to early onset disease and protein aggregation of TDP-43. Based on this, it is necessary to explore the underlying molecular mechanisms. By utilizing all-atom molecular dynamics (MD) simulations of 102 μs in total, we investigated the impact of S375G mutation on the conformational ensembles and oligomerization dynamics of TDP-43370-375 peptides. Our replica exchange MD simulations show that S375G mutation could promote the unstructured conformation formation and induce peptides to form a loose packed oligomer, thus inhibiting the aggregation of TDP-43370-375. Further analyses suggest that S375G mutation displays a reduction effect on the number of total hydrogen bonds and contacts among TDP-43370-375 peptides. Hydrogen bonding and polar interactions among TDP-43370-375 peptides, as well as Y374-Y374 π-π stacking interaction, are attenuated by S375G mutation. Additional microsecond MD simulations demonstrate that S375G mutation could prohibit the conformational conversion to β-structure-rich aggregates and possess an inhibitory effect on the oligomerization dynamics of TDP-43370-375. This study offers for the first time of molecular insights into the S375G mutation affecting the aggregation of TDP-43370-375 at the atomic level, and may open new avenues in the development of future site-specific mutation therapeutics.

Comparative analysis of models in predicting the effects of SNPs on TF-DNA binding using large-scale in vitro and in vivo data.

Non-coding variants associated with complex traits can alter the motifs of transcription factor (TF)-deoxyribonucleic acid binding. Although many computational models have been developed to predict the effects of non-coding variants on TF binding, their predictive power lacks systematic evaluation. Here we have evaluated 14 different models built on position weight matrices (PWMs), support vector machines, ordinary least squares and deep neural networks (DNNs), using large-scale in vitro (i.e. SNP-SELEX) and in vivo (i.e. allele-specific binding, ASB) TF binding data. Our results show that the accuracy of each model in predicting SNP effects in vitro significantly exceeds that achieved in vivo. For in vitro variant impact prediction, kmer/gkm-based machine learning methods (deltaSVM_HT-SELEX, QBiC-Pred) trained on in vitro datasets exhibit the best performance. For in vivo ASB variant prediction, DNN-based multitask models (DeepSEA, Sei, Enformer) trained on the ChIP-seq dataset exhibit relatively superior performance. Among the PWM-based methods, tRap demonstrates better performance in both in vitro and in vivo evaluations. In addition, we find that TF classes such as basic leucine zipper factors could be predicted more accurately, whereas those such as C2H2 zinc finger factors are predicted less accurately, aligning with the evolutionary conservation of these TF classes. We also underscore the significance of non-sequence factors such as cis-regulatory element type, TF expression, interactions and post-translational modifications in influencing the in vivo predictive performance of TFs. Our research provides valuable insights into selecting prioritization methods for non-coding variants and further optimizing such models.

ROS scavenging, DNA binding and NADPH oxidase inhibition potential of N’-Ferrocenylmethyl-N’- phenylpropionohydrazide using cyclic voltammetry and molecular docking

Overactivation of the NOX results in an excess production of ROS, which is linked to oxidative stress and deoxyribonucleic acid (DNA) damage. Free radical formation is a physiological event mainly coming from cellular respiration. Inflammatory diseases, cardiovascular diseases, and cancer are only some illnesses that this could trigger. Therefore, chemicals that can block NADPH oxidase (NOX) are essential in maintaining a healthy level of oxidative stress. However, interacting with DNA can alter its shape and slow replication, protecting cells from death. In this study, cyclic voltammetry (CV) techniques were employed to assess the scavenging activity of N’-Ferrocenylmethyl-N’- phenylpropionohydrazide (NFPP) towards the superoxide anion radical (O2.−). Additionally, the DNA binding modes and binding free energies of NFPP were investigated. To support the experimental results, molecular docking was performed with DNA (PDB ID: 5VY6) and the enzyme NOX1 (PDB ID: 7CFZ). The results were consistent between the two approaches, showing that the chemical investigated had an IC50 lower than that of ascorbic acid (AA) and a spontaneous form of binding with (O2.−) and DNA due to the negative sign of binding energies. Minor groove binding with two conventional hydrogen bonds was the type of interaction with the DNA. The binding energy between NFPP and NADPH exhibited a significant correlation with the experimental findings, indicating a strong affinity and a reduced inhibition concentration compared to ascorbic acid.

The physicochemical and DNA binding studies of ceftazidime pentahydrate and cefotaxime sodium in aqueous medium

Abstract Ceftazidime pentahydrate (CP) and cefotaxime sodium (CS) are semisynthetic cephalosporin antibiotics and are used to treat a variety of diseases worldwide. In order to explore the efficiency of a medicinal compound, it is important to have a deep understanding of its solution and physiochemical behaviour along with its interaction with biological molecules. In this regard, the solution of two drugs i.e., ceftazidime pentahydrate (CP) and cefotaxime sodium (CS) were investigated in detail. The physicochemical properties of drugs solutions and their interaction with deoxyribonucleic acid (DNA) were studied in water under varying experimental parameters. In the present study the physicochemical properties such as density, viscosity, surface tension, and conductance of aqueous solution, having various molar concentrations, of CP and CS were traced out at different temperatures. Five various concentrations (0.05, 0.1, 0.15, 0.2, and 0.3 mol dm−3) of each drug in an aqueous medium were prepared separately, and the physicochemical properties of each solution, were studied individually at temperatures such as 293, 303, 313, 323, and 333 K respectively. Most of these parameters have shown different behaviour with varying concentration of solution and temperature of the medium. In addition, these drugs showed a spontaneous surface-active and association behaviour in aqueous solutions and drug DNA solution. The flow behaviour, surface properties, volumetric behaviour and solute–solvent interaction of this drug were prominently influenced by experimental variables. UV-Visible spectroscopy was also used to study the interaction of these drugs with DNA in aqueous media in detail. Calculated values of binding constants (K b) for all drug–DNA are positive, indicating constructive binding and interactions between the molecules. In addition the binding efficiency of ceftazidime pentahydrate was found more than that of cefotaxime sodium. The interaction of drug–DNA was not only affected by the nature of the drug but also by the drug-to-DNA ratio and nature of the medium used.

Design of Azomethine based Metalloorganic Complexes and their Binding Interactions with Nucleic Acid and Protein

Mononuclear nickel, copper, and zinc complexes based on salen type (ONNO) donor acting as a tetradentate ligand obtained by the condensation of 4-methyl-o-phenylenediamine and 5-fluoro salicylaldehyde in 1:2 ratios. The compounds are characterized using UV-visible, FT-IR, 1H, 13C-NMR, HR-MS, Elemental (CHN) analyses ESR spectral techniques, and single crystal X-ray diffraction studies (SC-XRD). The binding interactions of the metal complexes with deoxyribonucleic acid (DNA) and bovine serum albumin (BSA) are monitored using UV absorption titration and tryptophan emission quenching techniques, respectively. The complexes possess strong binding propensities with DNA and prefer groove binding, as indicated by the hyperchromic effect. The complexes quench the intrinsic fluorescence of BSA with increasing amounts of the complex concentration in a dose-dependent manner. The gel electrophoresis was carried out against pBR322 to analyze the cleaving ability of the complexes. The results of the NBO (natural bond orbitals) analysis performed in combination with the Time-dependent Density Functional Theory (TD-DFT) calculations provided a good explanation of their electronic and structural characteristics. Further, the predictions of molecular docking studies support the experimental observations. The Gel electrophoresis study reveals the cleaving ability of the complexes by their interactions with DNA. In addition, the cell viability of the complexes is assessed based on MTT assay and the results indicate that they have a good antiproliferative activity only on liver cancer cell-line HepG-2 and does not show cytotoxic effect on normal vero cell lines with 90% viability.

Synthesis, structure elucidation, SC-XRD/DFT, molecular modelling simulations and DNA binding studies of 3,5-diphenyl-4,5-dihydro-1H-pyrazole chalcones

Deoxyribonucleic acid (DNA) acts as the most important intracellular target for various drugs. Exploring the DNA binding interactions of small bioactive molecules offers a structural guideline for designing new drugs with higher clinical efficacy and enhanced selectivity. This study presents the facile synthesis of pyrazoline-derived compounds (4a)-(4f) by reacting substituted chalcones with hydrazine hydrate using formic acid. The structure elucidation of substituted pyrazoline compounds was carried out using 1H-NMR, FT-IR and elemental analyses. While the crystal structures of two compounds (4a) and (4b) have been resolved by single-crystal X-ray diffraction (SC-XRD) analysis. Hirshfeld surface analysis also endorsed their greater molecular stability. Computational calculations at DFT/B3LYP/6-311++G(d,p) were executed to compare the structural properties (bond angle and bond length) and explore reactivity descriptors, frontier molecular orbitals (FMO), Mulliken atomic charges (MAC), molecular electrostatic potential (MEP) and electronic properties. All the compounds were evaluated for DNA binding interactions by UV-Vis spectrophotometric analysis. The results revealed that compounds (4a)-(4f) bind to DNA via non-covalent binding mode having binding constant values ranging from 1.22 × 103 to 6.81 × 104 M−1. The negative values of Gibbs free energy also proved the interaction of studied compounds with DNA as a spontaneous process. The findings of molecular docking simulations depicted that these studied compounds showed significant binding interactions with DNA and these results were consistent with experimental findings. Compound (4b) was concluded as the most potent compound of the series with the highest binding constant (4.95 × 104) and strongest binding affinity (-8.48 kcal/mol). Communicated by Ramaswamy H. Sarma

Targeting Progranulin as an Immuno-Neurology Therapeutic Approach

Immuno-neurology is an emerging therapeutic strategy for dementia and neurodegeneration designed to address immune surveillance failure in the brain. Microglia, as central nervous system (CNS)-resident myeloid cells, routinely perform surveillance of the brain and support neuronal function. Loss-of-function (LOF) mutations causing decreased levels of progranulin (PGRN), an immune regulatory protein, lead to dysfunctional microglia and are associated with multiple neurodegenerative diseases, including frontotemporal dementia caused by the progranulin gene (GRN) mutation (FTD-GRN), Alzheimer’s disease (AD), Parkinson’s disease (PD), limbic-predominant age-related transactivation response deoxyribonucleic acid binding protein 43 (TDP-43) encephalopathy (LATE), and amyotrophic lateral sclerosis (ALS). Immuno-neurology targets immune checkpoint-like proteins, offering the potential to convert aging and dysfunctional microglia into disease-fighting cells that counteract multiple disease pathologies, clear misfolded proteins and debris, promote myelin and synapse repair, optimize neuronal function, support astrocytes and oligodendrocytes, and maintain brain vasculature. Several clinical trials are underway to elevate PGRN levels as one strategy to modulate the function of microglia and counteract neurodegenerative changes associated with various disease states. If successful, these and other immuno-neurology drugs have the potential to revolutionize the treatment of neurodegenerative disorders by harnessing the brain’s immune system and shifting it from an inflammatory/pathological state to an enhanced physiological/homeostatic state.

N’-Ferrocenylmethyl-N’-phenylbenzohydrazide as a potential DNA binding compound: a combined experimental and computational study

Due to increased lipophilicity, stability, and decreased cytotoxicity in biological systems, ferrocene derivatives are promising building blocks for therapeutic agents. This manuscript reports the binding of N’-ferrocenylmethyl-N’-phenylbenzohydrazide (FhD) with deoxyribonucleic acid (DNA) studied by absorption spectroscopy and cyclic voltammetry. Binding constants and binding free energies for the FhD-DNA complex were measured using these two methods as 5100 M−1, 6109 M−1 and −21.2 kJ/mol, −21.6 kJ/mol, respectively. DFT calculations were also performed and revealed important physical characteristics of the FhD compound. Subsequently, the system was explored by computational molecular docking, confirming a non-covalent mode of binding via minor groove with a binding energy of −25.5 kJ/mol. Furthermore, molecular dynamics of the docked complex of FhD with DNA were carried out for 100 ns followed by MM-GBSA to have a deep understanding of the complex’s dynamic behavior in physiological systems, and to determine the Gibbs free energy which was −14.31 Kcal/mol over a 100 ns window. The results show important antitumor potential of FhD due to its spontaneous non-covalent interaction with DNA and the efficient binding stability of the FhD-DNA complex in a physiological system.

DeepSATA: A Deep Learning-Based Sequence Analyzer Incorporating the Transcription Factor Binding Affinity to Dissect the Effects of Non-Coding Genetic Variants.

Utilizing large-scale epigenomics data, deep learning tools can predict the regulatory activity of genomic sequences, annotate non-coding genetic variants, and uncover mechanisms behind complex traits. However, these tools primarily rely on human or mouse data for training, limiting their performance when applied to other species. Furthermore, the limited exploration of many species, particularly in the case of livestock, has led to a scarcity of comprehensive and high-quality epigenetic data, posing challenges in developing reliable deep learning models for decoding their non-coding genomes. The cross-species prediction of the regulatory genome can be achieved by leveraging publicly available data from extensively studied organisms and making use of the conserved DNA binding preferences of transcription factors within the same tissue. In this study, we introduced DeepSATA, a novel deep learning-based sequence analyzer that incorporates the transcription factor binding affinity for the cross-species prediction of chromatin accessibility. By applying DeepSATA to analyze the genomes of pigs, chickens, cattle, humans, and mice, we demonstrated its ability to improve the prediction accuracy of chromatin accessibility and achieve reliable cross-species predictions in animals. Additionally, we showcased its effectiveness in analyzing pig genetic variants associated with economic traits and in increasing the accuracy of genomic predictions. Overall, our study presents a valuable tool to explore the epigenomic landscape of various species and pinpoint regulatory deoxyribonucleic acid (DNA) variants associated with complex traits.

Experimental and theoretical approaches to interactions between DNA and purine metabolism products

Deoxyribonucleic acid (DNA) is a significant target for small organic and inorganic drug molecules. Understanding the DNA interaction mechanism of these molecules is vital for new drug designs. In this work, interactions between xanthine (XT), theophylline (TP), and theobromine (TB) with calf-thymus double-strained DNA (dsDNA) were monitored via an experimental and theoretical approach. Experimentally, cyclic voltammetry (CV) and differential pulse voltammetry (DPV) techniques were used on the surface of the NiO/MWCNT/NNaM/PGE electrochemical platform in vitro. Kinetic parameters, including diffusion coefficients, surface concentrations, and standard heterogeneous rate constants, were measured in the absence and presence of DNA using scan rate studies. In the presence of DNA, kinetic parameters were observed to be reduced significantly. Thermodynamic parameters, such as DNA binding constants and standard free Gibbs energies, were calculated for each molecule using the CV and DPV techniques. Both techniques suggested a binding affinity order of XT > TB > TP. Theoretically, density functional theory was applied for geometry optimization, natural bond orbital analyses, and molecular orbital energies of XT, TP, and TB. Experimental and theoretical binding affinities confirm each other. The most energetically stable ligand-DNA complexes expressed that XT, TP, and TB interact with dsDNA via minor groove binding mode, using mostly hydrogen bonds.

Global status and research trends of cuprotosis research: A bibliometrics study via CiteSpace.

Cuproptosis, a novel copper ion-dependent cell death type being regulated in cells, has raised concerns but lacks scientific analysis. Therefore, this study aimed to analyze the global status and emerging trends in cuprotosis research using bibliometric methods. Publications related to cuprotosis were systematically retrieved from the Web of Science Core Collection and then screened according to the inclusion criteria. Next, CiteSpace and Microsoft Excel 2021 were used to measure and visualize annual publications, categories, journals, countries, institutions, authors, co-cited references, and keywords to identify future global status and trends. A total of 2776 publications on cuprotosis were included, and the overall trend in the number of publications exhibited a rapid increase over the years. Biochemistry and Molecular Biology is the most common category, whereas the Journal of Inorganic Biochemistry is the most active. The United States is the country that produces the most articles, and University of Melbourne in Australia is the core institution involved in this field. Furthermore, Chan Pak of Stanford University is the most prolific author. Oxidative stress and antioxidant, the toxicity of copper in vitro, anticancer mechanism, and brain injury in neurological diseases are hot topics. The research frontiers are copper complexes, anticancer activity, DeoxyriboNucleic Acid binding, inflammation, and nanoparticles. This study provides the current status and trends in cuprotosis research. It may help researchers to identify hot topics and get ideas for future research directions in this field, focusing on copper complexes, anticancer activity, DeoxyriboNucleic Acid binding, inflammation, and nanoparticles.

Structural, spectral and biological studies of (E)-2-((2-(benzo[d]thiazol-2-yl)hydrazineylidene)methyl)-4,6-dibromophenol (HL) and its metal complexes of Mn(II), Cu(II), Co(II), Ni(II), and Zn(II)

In this article there are five mononuclear complexes were discovered, 1. [Mn(II)(2-BHMBP)2], 2. [Cu(II)(2-BHMBP)2], 3. [Co(II)(2-BHMBP)2], 4. [Ni(II)(2-BHMBP)2] and 5. [Zn(II)(2-BHMBP)2] utilising a Imine base ligand, HL C14H9Br2N3OS (E)-2-((2-(benzo[d]thiazol-2-yl)hydrazineylidene)methyl)-4,6-dibromophenol were prepared and structurally characterised by the FT-IR spectra (vibrational spectroscopy), Proton NMR (1H NMR) spectroscopy, Carbon NMR (13C NMR) spectroscopy, ESI- Mass, SEM, EDX, powder XRD, TGA and ESR/EPR strategies. The complexes preliminary Deoxyribonucleic acid (DNA) binding activity was investigated by electronic absorption, fluorescence and viscosity spectroscopy in the presence of Calf thymus-DNA (CT-DNA). Using the agarose gel electrophoresis method in the presence of H2O2, DNA photo cleavage studies were performed on all metal complexes. The MTT assay was utilized to assess the cytotoxicity of all the compounds against two human cancer cell lines: HeLa and MCF-7. The compounds along with ligand have been screened for antifungal activity against fungal species Candida albicans and it is found that all Complexes are more potent than free ligand.

Evaluation of the size effect of hydrophobic ring substitution on 9-O position of berberine on DNA binding

The interaction of deoxyribonucleic acid (DNA) with medicinally significant small molecules has long piqued the interest of researchers because its applications are directly related to the discovery of new classes of drugs. Keeping this in mind, here we report berberine derivatives and their interaction with calf thymus DNA (CT-DNA). In this report we discussed on the structural perspectives and thermodynamic characteristics of the interaction of four 9-O-substituted berberines (BRDR1 to BRDR4) with CT-DNA. The binding affinity of BRDR–DNA complexes increased with increasing the cycloalkane ring size of the substitution except BRDR2. The binding constant value obtained from UV–Visible spectral analysis was 1.12 × 106 for BRDR1, 0.37 × 106 for BRDR2, 1.72 × 106 for BRDR3 and 3.20 × 106 for BRDR4. Ferrocyanide quenching experiments revealed unequivocally that the analogues except BRDR2 had a partly intercalative binding to DNA. From the ITC experiment it was found that the bindings of BRDR1, BRDR3 and BRDR4 to DNA was favoured by negative enthalpy and positive entropy while BRDR2 was driven by positive enthalpy and positive entropy. In all cases the hydrophobic interaction plays a crucial role. Thus, the complete multispectroscopic and thermodynamic binding studies may be useful for new drug design and development.Communicated by Ramaswamy H. Sarma

Analysis of the Mechanism of T Lymphocytes Promoting Immune Platelet Transfusion Refractoriness by Gene Chip Technique

The main objective of this study is to analyze the expression levels of messenger ribonucleic acid and long non-coding ribonucleic acid in patients with platelet transfusion refractoriness and reveal the mechanism of T lymphocytes in immune platelet transfusion refractoriness. The Agilent expression profile chip was used to detect the expression levels; gene ontology and Kyoto encyclopedia of genes and genomes enrichment analysis were performed on the differential genes to determine their main biological functions. Unsupervised hierarchical clustering was used to process differential genes and the differential genes among samples were represented in a heat map. The differentially expressed messenger ribonucleic acids and long non-coding ribonucleic acids in different groups were found as 720 and 1719 in normal control group vs. platelet transfusion effective group; 4254 and 12491 in normal control group vs. platelet transfusion ineffective group and 1806 and 6216 in platelet transfusion effective group vs. platelet transfusion ineffective group. Gene ontology and Kyoto encyclopedia of genes and genomes enrichment analysis were performed on differentially expressed genes, and the results were annotated to be related to T cells. The co-expression of the target gene Ras-related protein 1A and long non-coding transactive response deoxyribonucleic acid binding protein 2 was determined through the national center for biotechnology information database and the interaction between micro ribonucleic acid-4739 and Ras-related protein 1A was predicted using the starBase and TargetScan databases. T lymphocytes play an important role in immune platelet transfusion refractoriness and long non-coding transactive response deoxyribonucleic acid binding protein 2 may affect the differentiation of T lymphocytes and promote the occurrence of immune platelet transfusion refractoriness through micro ribonucleic acid-4739 targeting Rasrelated protein 1A gene regulation.

Mechanism of interactions of dsDNA binding with quercetin and its two novel sulfonate derivatives using multispectroscopic, voltammetric, and molecular docking studies

Flavonoids have an important place in chemistry and pharmacology. Several flavonoids, especially Quercetin, have the potential to form molecular complexes with nucleic acid structure and have recently attracted attention due to their prospective clinical and pharmacological uses. DNA is the main target for a wide variety of therapeutic agents. Therefore, there is great interest in studies of binding small molecules with DNA. The interaction of small molecules with DNA provides a structural guide in rational drug design and the synthesis of new and improved drugs with enhanced selective activity and higher clinical efficacy. Even if newly synthesized candidate drug molecules with small molecular weight are capable of indirectly interacting with DNA, the mechanisms that accomplish this need to be clearly known. In this study, the mechanism of fish sperm double strain deoxyribonucleic acid (dsDNA) binding with Quercetin (QCR) and its two novel sulfonate derivatives (quercetin mesylate (QMS) and quercetin tosylate-A (QTS-A)) were researched. For investigating the interaction between the molecules and dsDNA was studied by analytical (spectrophotometric, viscosimetric, and electrochemical) methods. The interaction of dsDNA and two quercetin sulfonate derivatives were compared with the interaction of the QCR standard after all experimental studies. Moreover, the DNA binding constants Kb were determined using each method. The Kb constants calculated for QCR, QMS, and QTS-A are in harmony for all techniques. The results showed that QCR binds to dsDNA via intercalation mode, while QMS and QTS-A bind through minor groove binding mode. In addition to experimental studies, theoretical studies were conducted at room temperature under physiological conditions (pH 7.4). Molecular docking calculations and molecular dynamics (MD) simulations have been found to be compatible with experimental studies.

Predicting Binding Free Energies for DPS Protein-DNA Complexes and Crystals Using Molecular Dynamics

The interaction between deoxyribonucleic acid (DNA) and deoxyribonucleic acid-binding protein from starved cells (DPS) in bacterial cells leads to intracellular crystallization of the genetic material of bacteria, which contributes to the survival of bacteria under stress factors, including antibacterial agents. Molecular modeling can help explain the molecular mechanisms of DNA binding to this protein. In this paper, we report a supercomputer simulation of the molecular dynamics of several types DNA-DPS complexes and crystals ranging from DPS+DNA dimer to DNA in periodic crystal channels of Escherichia coli DPS protein using a coarse-grained Martini force field. By modeling DNA of 24 base pairs, comparable in size to the diameter of the DPS protein, we use the slow-growth thermodynamic integration method to find binding protein-DNA free energy and discuss the contribution of ions and the length of trajectories sufficient for this type of simulations. The results obtained are important for further research in the field of simulation of biological DNA-protein crystals and the study of the molecular mechanisms of DNA interaction with the DPS protein.

Using clinically derived human tissue to 3-dimensionally bioprint personalized testicular tubules for in vitro culturing: first report

To study the feasibility and spermatogenic potential of 3-dimensional (3D) bioprinting personalized human testicular cells derived from a patient with nonobstructive azoospermia (NOA). A human testicular biopsy from a single donor with NOA was dissociated into single cells, expanded invitro, and 3D bioprinted into tubular structures akin to the seminiferous tubule using AGC-10 bioink and an RX1 bioprinter with a CENTRA coaxial microfluidic printhead from Aspect Biosystems. Three-dimensional organoid cultures were used as a nonbioprinted invitro control. Academic medical center. A 31-year-old man with NOA with testis biopsy demonstrating Sertoli cell-only syndrome. Three-dimensional bioprinting and invitro culturing of patient-derived testis cells. Cellular viability after printing was determined, along with the expression of phenotypic and spermatogenic functional genetic markers after 12 days of invitro culture. Testicular cultures were expandable invitro and generated sufficiently large numbers for 3D bioprinting at 35 million cells per mL of bioink. Viability 24 hours after printing was determined to be 93.4% ± 2.4%. Immunofluorescence staining for the phenotype markers SRY-Box transcription factor 9, insulin-like 3, actin alpha 2 smooth muscle, and synaptonemal complex protein 3 after 12 days was positive, confirming the presence of Sertoli, Leydig, peritubular myoid, and meiotic germ cells. Reverse transcription qualitative polymerase chain reaction analysis showed that after 12 days in spermatogenic media, the bioprints substantially up-regulated spermatogenic gene expression on par with nonbioprinted controls and showed a particularly significant improvement in genes involved in spermatogonial stem cell maintenance: inhibitor of deoxyribonucleic acid binding 4 by 365-fold; fibroblast growth factor 3 by 94,152-fold; stem cell growth factor receptor KIT by twofold; stimulated by retinoic acid 8 by 125-fold; deleted in azoospermia-like by 114-fold; synaptonemal complex protein 3 by sevenfold; zona pellucida binding protein by twofold; transition protein 1 by 2,908-fold; and protamine 2 by 11-fold. This study demonstrates for the first time the feasibility of 3D bioprinting adult human testicular cells. We show that the bioprinting process is compatible with high testicular cell viability and without loss of the main somatic phenotypes within the testis tissue. We demonstrate an increase in germ cell markers in the 3D bioprinted tubules after 12 days of invitro culture. This platform may carry future potential for disease modeling and regenerative opportunities in a personalized medicine framework.