Charged DNA Research Articles

Mg2+-promoted high-efficiency DNA conjugation on polydopamine surfaces for aptamer-based ochratoxin A detection

BackgroundSurface immobilization of DNA is the foundation of a broad range of applications in biosensing and specific DNA extraction. Polydopamine (PDA) coatings can serve as intermediate layers to immobilize amino- or thiol-labelled molecules, including DNA, onto various materials through Michael addition and/or Schiff base reactions. However, the conjugation efficiency is limited by electrostatic repulsion between negatively charged DNA and PDA. Recently, it has been reported that polyvalent metal ions (such as Mg2+ and Ca2+) can mediate the adsorption of DNA on PDA surfaces. Inspired by this, in this work we aimed to exploit polyvalent metal ions to facilitate the conjugation of DNA on PDA. ResultsMg2+ was used to promote the conjugation of amino-terminated DNA complementary to ochratoxin A (OTA) aptamer (cDNA-NH2) on PDA-coated magnetic nanoparticles (Fe3O4@PDA). After the reaction, the unlinked cDNA-NH2 adsorbed on Fe3O4@PDA mediated by Mg2+ was removed with EDTA. In the presence of 20 mM Mg2+, the amount of covalently linked cDNA-NH2 increased approximately 11-fold compared to that in the absence of Mg2+. The resulting Fe3O4@PDA@cDNA conjugates exhibited superior hybridization capacity towards OTA aptamers, minimal nonspecific adsorption, and excellent chemical stability. The conjugates combined with fluorophore-labelled aptamers were employed for OTA detection, achieving a limit of detection (LOD) of 2.77 ng mL−1. To demonstrate versatility, this conjugation method was extended to Ca2+-promoted conjugation of cDNA-NH2 on Fe3O4@PDA nanoparticles and Mg2+-promoted conjugation of cDNA-NH2 on PDA-coated 96-well plates. SignificanceThe conjugation efficiency of DNA on PDA was significantly improved with the assistance of polyvalent metal ions (Mg2+ and Ca2+), providing a facile and efficient method for DNA immobilization. Due to the substrate-independent adhesion property of PDA, this method demonstrates versatility in DNA surface modification and holds great potential for applications in target extraction, biosensing, and other fields.

Exploring ssDNA translocation through α-hemolysin using coarse-grained steered molecular dynamics.

Protein nanopores have proven to be effective for single-molecule studies, particularly for single-stranded DNA (ssDNA) translocation. Previous experiments demonstrated their ability to distinguish differences in purine and pyrimidine bases and in the orientation of the ssDNA molecule inside nanopores. Unfortunately, the microscopic details of ssDNA translocation over experimental time scales, which are not accessible through all-atom molecular dynamics (MD), have yet to be examined. However, coarse-grained (CG) MD simulations enable systems to be simulated over longer characteristic times closer to experiments than all-atom MD. This paper studies ssDNA translocation through α-hemolysin nanopores exploiting steered MD using the MARTINI CG force field. The impacts of the sequence length, orientation inside the nanopore and DNA charges on translocation dynamics as well as the conformational dynamics of ssDNA during the translocation are explored. Our results highlight the efficacy of CG molecular dynamics in capturing the experimental properties of ssDNA translocation, including a wide distribution in translocation times per base. In particular, the phosphate charges of the DNA molecule are crucial in the translocation dynamics and impact the translocation rate. Additionally, the influence of the ssDNA molecule orientation on the translocation rate is explained by the conformational differences of ssDNA inside the nanopore during its translocation. Our study emphasizes the significance of obtaining sufficient statistics via CG MD, which can elucidate the great variety of translocation processes.

Furan-rich, biobased transfection agents as potential oligomeric candidates for intracellular plasmid DNA delivery.

Biobased, DNA delivery vectors have been synthesized with a core motif composed of 2,5-bishydroxymethylfuran (BHMF) readily available from an important biomass feedstock 5-hydroxymethyl furfural (HMF). To generate the product, BHMF was first converted to 2,5-furan bishydroxymethyl diacrylate (2,5-FDA), which was later conjugated with different types of secondary amines. Rich in tertiary nitrogen, these oligomeric FDA-amino esters demonstrated stable electrostatic interactions with negatively charged plasmid DNA in an aqueous environment. We evaluated synthetic routes toward these plasmid DNA-binding amino esters (pFASTs), identified their nanoscale features, and attempted to establish their structure-property relationship in the context of the DNA delivery. Our preliminary studies show that the pFASTs formed stable complexes with the plasmid DNA. Dynamic light scattering indicated that the DNA polyplexes of pFASTs have hydrodynamic diameters within the size range of 100-150 nm with a surface charge (ζ-potential) ranging from -10 to +33 mV, depending on pFAST type. These oligomeric amino esters rich in furan motif were also found to successfully transfect the GFP-expressing plasmid DNA intracellularly. Collectively, this study establishes a new route to produce DNA transfection agents from sustainable resources that can be used for transferring genetic materials for humans, veterinary, and agrochemical purposes.

Compelling DNA intercalation through 'anion-anion' anti-coulombic interactions: boron cluster self-vehicles as promising anticancer agents.

Anticancer drugs inhibit DNA replication by intercalating between DNA base pairs, forming covalent bonds with nucleotide bases, or binding to the DNA groove. To develop safer drugs, novel molecular structures with alternative binding mechanisms are essential. Stable boron hydrides offer a promising alternative for cancer therapy, opening up additional options like boron neutron capture therapy based on 10B and thermal neutron beams or proton boron fusion therapy using 11B and proton beams. These therapies are more efficient when the boron compound is ideally located inside cancer cells, particularly in the nucleus. Current cancer treatments often utilize small, polycyclic, aromatic, planar molecules that intercalate between ds-DNA base pairs, requiring only a spacing of approximately 0.34 nm. In this paper, we demonstrate another type of intercalation. Notably, [3,3'-Fe(1,2-C2B9H11)2]-, ([o-FESAN]-), a compact 3D molecule measuring 1.1 nm × 0.6 nm, can as well intercalate by strong non-bonding interactions preferentially with guanine. Unlike known intercalators, which are positive or neutral, [o-FESAN]- is a negative species and when an [o-FESAN]- molecule approaches the negatively charged DNA phosphate chain an anion-anion interaction consistently anti-electrostatic via Ccluster-H⋯O-P bonds occurs. Then, when more molecules approach, an elongated outstandingly self-assembled structure of [o-FESAN]--[o-FESAN]- forms moving anions towards the interthread region to interact with base pairs and form aggregates of four [o-FESAN]- anions per base pair. These aggregates, in this environment, are generated by Ccluster-H⋯O-C, N-H⋯H-B and Ccluster-H⋯H-B interactions. The ferrabis(dicarbollide) boron-rich small molecules not only effectively penetrate the nucleus but also intercalate with ds-DNA, making them promising for cancer treatment. This amphiphilic anionic molecule, used as a carrier-free drug, can enhance radiotherapy in a multimodal perspective, providing healthcare professionals with improved tools for cancer treatment. This work demonstrates these findings with a plethora of techniques.

Effects of BPQ binding on the nonadiabatic dynamics of excited electrons in poly(dG)-poly(dC) DNA under proton irradiation.

The interaction between DNA and small molecules is important for understanding the mechanisms of DNA-based multifunctional devices and has been extensively studied. However, there are few reports on such interactions in irradiation environments. Here, we investigate the nonadiabatic dynamic behaviors of excited electrons in double-stranded DNA bound to BPQ molecule upon proton irradiation, focusing on the energy deposition and electronic excitation dynamics as protons traverse the DNA along different channels. Our results reveal that the presence of BPQ significantly influences charge migration and DNA damage, with notable differences between CGvdW and CGcovalent adducts. The energy deposition process is highly dependent on charge density, and guanine exhibits higher excitation propensity than cytosine due to its structural characteristics. The BPQ molecule enhances DNA charge migration and promotes damage through secondary electron migration. These findings provide insights into the nonadiabatic dynamics of DNA under ionizing radiation and have implications for designing targeted electrophilic organics to improve radiotherapy efficacy.

Optimized condition for pei-based transient transfection of lifeact-gfp/nls-mcherry expressing plasmid used as cell barcode for syncytia live cell imaging

The transfection efficiency positively affects the successful plasmid DNA transfer into cells, with the highlight on the amount of plasmid DNA and its ratio to the transfection reagent. Polyethyleneimine (PEI) is a cost-effective transfection reagent that facilitates DNA transfer by forming positively charged DNA complexes. It allows DNA to interact with negatively charged cell surfaces and enter the cells by endocytosis. In this study, we optimized the condition for transient transfection of life act-GFP/NLS-mCherry-expressing plasmid in BHK-21 and 293T cells using PEI. This plasmid is helpful as a biosensor of the cytoskeleton and nucleus that enables live imaging observation using a fluorescence microscope, for instance, in the observation of syncytium. Here, we optimized two independent variables: the amount of DNA (0.5 and 1 µg) and the ratio of DNA-PEI (1:3 and 1:4). GFP and mCherry expressions were observed at 24, 48, and 72 h post-transfection. As a result, transfection efficiency achieved by using PEI in 293T cells is higher than in BHK-21 cells, which are ~90% and ~50%, respectively. Moreover, amongst four different transfection conditions, in both cell lines, 1 µg of plasmid DNA with a 1:3 DNA-PEI ratio yields the most efficiency with the least amount of toxicity. We used this condition for the syncytia observation in 293T cells as a model of the cell-to-cell transmission of SARS-CoV-2. Syncytia formation was successfully observed by detecting the giant cells expressing GFP/mCherry with multiple nuclei.

An electrochemical biosensor to assay Trop-2 of breast cancer cells fabricated by methylene blue-assisted assembly of DNA nanoparticles

Human trophoblast surface cell antigen 2 (Trop-2) on the tumor cell membrane can not only serve as the target for chemotherapy drugs, but also as a biomarker for typing and prognosis of breast cancer; however, assay of Trop-2 is seriously hampered due to the limitations of available tool. Herein, we have designed and fabricated an electrochemical biosensor for the assay of Trop-2 based on methylene blue (MB)-assisted assembly of DNA nanocomposite particles (DNPs). Specially, the recognition between Trop-2 and its aptamer may activate the primer exchange reaction (PER) on an electrode surface to produce long single-strand DNA (ssDNA) which can be self-assembled into DNPs by electrostatic interaction between negative charged DNA and positive charged and electro-active MB molecules which can also be used to give electrochemical signal. By using this electrochemical biosensor, ultrasensitive detection of tumor cells with high Trop-2 expressions can be conducted, with the limit of detection (LOD) of 1 cell/mL. Moreover, this biosensor can be further used for accurately profiling Trop-2 expression of tumor cells in mouse tissues, suggesting its great potential in the precise definition of breast cancer.

Combing of picogram level DNA equivalent to genomic DNA present in single human cell by self propelled droplet motion over a stable gradient surface

DNA combing is a powerful technique for studying replication profile, fork-directionality and fork velocity. At present, there is requirement of a methodology to comb DNA present in a single human cell for studying replication dynamics at early embryonic stage. In our study, a surface having dual characteristics i.e., affinity towards negatively charged single DNA molecules and a hydrophobic gradient for self propelled droplet motion of combing solution was developed. The surface was made by coating of TCOS (trichloro-octylsilane) by vapor diffusion on APTES (Aminopropyl-triethoxysilane) coated glass slides. A gradient surface having high deposition efficiency (DE) was developed on which 5 picogram DNA equivalent to genomic DNA present in one single human cell can be combed. The gradient surface was thermostable in nature having the ability to sustain boiling temperature for two hours and sustain anisotropy in 70 % ethanol for 80 h. Applicability for multiple runs was enhanced such that the surface can be used for 13–14 times. Factors associated with gradient surface are unidirectional movement of combing solution droplet over the gradient surface for combing straight DNA molecules and a longer gradient surface of more than 1 cm such that long size DNA molecules can be combed. Ellipsometry and contact angle hysteresis confirmed the presence of hydrophobic gradient. XPS (X-ray photoelectron spectroscopy) and FTIR (Fourier Transform Infrared Spectroscopy) confirmed the presence of characteristic affinity towards negatively charged DNA molecules on the gradient surface. Combing solution was optimized for increasing deposition efficiency and for increasing the applicability of gradient surface for multiple runs. High temperature of combing solution was found to increase Deposition Efficiency. Combing solution was also optimized for combing single DNA molecules over the gradient surface. Single DNA molecules were combed by reducing pH and lowering concentration of triton-X in the combing solution. Dye: bp ratio was optimized for high fluorescent intensity and low surface background.

Integrating multiple probes for simplifying signal-on photoelectrochemical biosensing of microRNA with ultrasensitivity and wide detection range based on biofunctionalized porous ferroferric oxide and hypotoxic quaternary semiconductor

A facile and signal-on photoelectrochemical (PEC) biosensing strategy was designed based on hypotoxic Cu2ZnSnS4 NPs nanoparticles (NPs) and biofunctionalized Fe3O4 NPs that integrated recognition units with signal elements, without the need for immobilization of probes on the electrode. Cu2ZnSnS4 NPs were used as the PEC substrate to produce intensive and stable photocurrent. The porous magnetic Fe3O4 NPs displayed favorable loading capacity for CdS QDs and easy biofunctionalization by negatively charged capture DNA (cDNA). cDNA sealed the pore of Fe3O4 NPs, avoiding the escape of CdS QDs as a PEC sensitizer. After hybridizing with target microRNA (miRNA), cDNA split away off Fe3O4 NPs whose porous channel might open and release sealed CdS QDs (signal element), resulting in a dramatical enhancement of PEC response. Herein, miRNA hardly contacted with CdS QDs, effectively avoiding harm to the target miRNA. This proposed strategy simplified procedures of assembly and made the biorecognition process sufficient for promoting a stationary quantity of probes, which was expected to obtain satisfactory performance for bioassay. Using miRNA-155 as a model analyte and combining with duplex-specific nuclease (DSN)-assisted amplification, a simplified and signal-on PEC biosensing platform for miRNA-155 with wonderful performance was proposed. DSN-assisted amplification further promoted PEC signal increment, leading to ulteriorly improving sensitivity (detection limit of 0.17 fM) and linear range (6.5 orders of magnitude) for miRNA-155 assay. Moreover, the developed PEC biosensing platform exhibited satisfactory stability, excellent specificity, and favorable accuracy for miRNA-155, which would have a promising prospect for monitoring miRNA expression in tumor cells.

Tailoring high-energy self-powered sensing system by Walker-mediated CRISPR/Cas12a cascade signal amplification and hybridization chain reaction for ultrasensitive microRNA detection

MicroRNAs (miRNAs) are important cancer-associated biomarkers for early detection. However, accurately measuring miRNAs is challenging due to their low abundance and high homogeneity in human serum. CRISPR technology can greatly improve the specificity and sensitivity of detection in biosensor construction. In this study, we develop a remarkably responsive self-powered biosensing platform for detecting microRNA-21 (miRNA-21) using hybridization chain reaction (HCR) and CRISPR/Cas12a amplification cascade mediated by 3D DNA walkers. Carbon-coated molybdenum disulfide nanotubes with a large surface area and excellent conductivity are fabricated on flexible carbon paper as the anode and cathode for biological fuel cell construction. Glucose oxidase is loaded onto the anode surface, while serving as the biological cathode, it initiated HCR, generating abundant double-stranded DNA. The negatively charged DNA backbone captures electron acceptors [Ru(NH3)6]3+ through electrostatic adsorption, resulting in a significant open circuit voltage (EOCV) signal. Through CRISPR/Cas12a amplification cascade mediated by 3D DNA walkers, a smaller EOCV is produced, enabling sensitive target detection. The method exhibits a detection range spanning from 0.0001 to 10,000 pM and capable of detecting as low as 19.0 aM (S/N = 3). This highly selective and sensitive method provides an effective approach for accurately detecting tumor markers in clinical applications.

Protamine folds DNA into flowers and loop stacks

DNA in sperm undergoes an extreme compaction to almost crystalline packing levels. To produce this dense packing, DNA is dramatically reorganized in minutes by protamine proteins. Protamines are positively charged proteins that coat negatively charged DNA and fold it into a series of toroids. The exact mechanism for forming these ∼50-kbp toroids is unknown. Our goal is to study toroid formation by starting at the “bottom” with folding of short lengths of DNA that form loops and working “up” to more folded structures that occur on longer length scales. We previously measured folding of 200–300 bp of DNA into a loop. Here, we look at folding of intermediate DNA lengths (L = 639–3003 bp) that are 2–10 loops long. We observe two folded structures besides loops that we hypothesize are early intermediates in the toroid formation pathway. At low protamine concentrations (∼0.2 μM), we see that the DNA folds into flowers (structures with multiple loops that are positioned so they look like the petals of a flower). Folding at these concentrations condenses the DNA to 25% of its original length, takes seconds, and is made up of many small bending steps. At higher protamine concentrations (≥2 μM), we observe a second folded structure—the loop stack—where loops are stacked vertically one on top of another. These results lead us to propose a two-step process for folding at this length scale: 1) protamine binds to DNA, bending it into loops and flowers, and 2) flowers collapse into loop stacks. These results highlight how protamine uses a bind-and-bend mechanism to rapidly fold DNA, which may be why protamine can fold the entire sperm genome in minutes.

Quantification of Global Histone Post Translational Modifications Using Intranuclear Flow Cytometry in Isolated Mouse Brain Microglia.

Gene expression control occurs partially by modifications in chromatin structure, including the addition and removal of posttranslational modifications to histone tails. Histone post-translational modifications (HPTMs) can either facilitate gene expression or repression. For example, acetylation of histone tail lysine residues neutralizes the positive charge and reduces interactions between the tail and negatively charged DNA. The decrease in histone tail-DNA interactions results in increased accessibility of the underlying DNA, allowing for increased transcription factor access. The acetylation mark also serves as a recognition site for bromodomain-containing transcriptional activators, together resulting in enhanced gene expression. Histone marks can be dynamically regulated during cell differentiation and in response to different cellular environments and stimuli. While next-generation sequencing approaches have begun to characterize genomic locations for individual histone modifications, only one modification can be examined concurrently. Given that there are hundreds of different HPTMs, we have developed a high throughput, quantitative measure of global HPTMs that can be used to screen histone modifications prior to conducting more extensive genome sequencing approaches. This protocol describes a flow cytometry-based method to detect global HPTMs and can be conducted using cells in culture or isolated cells from in vivo tissues. We present example data from isolated mouse brain microglia to demonstrate the sensitivity of the assay to detect global shifts in HPTMs in response to a bacteria-derived immune stimulus (lipopolysaccharide). This protocol allows for the rapid and quantitative assessment of HPTMs and can be applied to any transcriptional or epigenetic regulator that can be detected by an antibody.

Extraction of DNA from trace forensic samples with a modified lysis buffer and chitosan coated magnetic beads

The trace amounts of human tissue cells or body fluids left at the crime scene are often mixed with inhibitors such as rust, pigments, and humic acid. The extraction of the DNA from the trace cells is crucial for the investigation of cases. Usually, specially designed magnetic nanoparticles were chosen by the case investigators to enrich and elute DNA, which was then used for polymerase chain reaction (PCR) and short tandem repeat (STR) analysis. The traditional approach often had the following problems, such as low DNA enrichment efficiency, possible DNA breakage, and complex operations. Here, the 1%(w/v) of chitosan (75% deacetylation degree) was used to modify the 50 nm magnetic nanoparticles to gain the Chitosan@Beads, which theoretically carried positively charged in the pH = 5 of lysis buffer so as to adsorb negatively charged DNA through electrostatic interactions. The XPS and FT-IR results demonstrated that chitosan was successfully attached to the surface of magnetic nanoparticles. A set of simulated samples, containing 20 mg/μL of humic acid, pigments, iron ions (Fe2+, Fe3+), and the coexistence of the above three substances, were prepared to simulate the case scene. Human bronchial epithelial cells were mixed with the 200 μL of the above simulated samples for DNA extraction. 400 μL of lysis buffer, 20 μL of proteinase K (10 mg/mL) and 20 μL of Chitosan@Beads solution (20 mg/mL) was used for cell disruption and DNA enrichment. The extraction sensitivity of Chitosan@Beads was confirmed to be 10 cells, superior to commercial reagent kits. The Chitosan@Beads@DNA can directly use for “In-situ PCR” with elution-free operations. The STR loci rate of DNA extracted by Chitosan@Beads was around 97.9%, higher than the commercial kit (66.7%). In short, we foresee here developed novel Chitosan@Beads and modified lysis buffer could provide a new model for the DNA extraction of forensic trace evidence.

Sulfonium-cation-containing aggregation-induced emission block copolymers: self-assembly, multicolor emission, and detection for DNA polyplexes

Amphiphilic aggregation-induced emission (AIE) polymers have emerged as highly attractive materials that exhibit the synergistic effect of functional polymeric self-assemblies with AIE luminogens. In this study, we design and synthesize block copolymers containing sulfonium cations and a hydrophobic tetraphenylethene (TPE) unit. These copolymers exhibit distinct self-assembly behaviors with AIE, polyplex formation with DNA, and tunable color emissions. Amphiphilic block copolymer PMTEAMe+Cl--b-PATPE, consisting of 4-(1,2,2-triphenylvinyl)phenyl acrylate (ATPE) and cationized 2-(methylthio)ethyl acrylate (MTEAMe+Cl-), was synthesized via reversible addition–fragmentation chain transfer polymerization, followed by cationization. Self-assembled structures containing TPE-aggregated cores and cationic PMTEAMe+Cl- shells and their emission behaviors were investigated. By introducing charged fluorescent dyes (Rose Bengal and Rhodamine B) into aqueous solutions of amphiphilic PMTEAMe+Cl--b-PATPE, we observed a shift in the emission color from blue to orange/red, which was attributed to the electrostatic interactions and fluorescence resonance energy transfer between the dyes and the copolymers. The emission color and intensity were also governed by polyplex formation between the negatively charged DNA and the positively charged sulfonium segments in the shell, depending on the charged states of the dyes. This system provides a method for efficient visual detection of DNA polyplex formation using multicolor fluorescent coding.

DETERMINING THE ROLE OF GALECTIN1/HOXA5 INTERACTION AND REGULATION IN GLIOBLASTOMA DEVELOPMENT

Abstract LGALS1 is directly transcribed by STAT3, which promotes glioblastoma tumorigenesis via its interaction with HOXA5. However, the underling molecular mechanism of this interaction remains uninvestigated. In this study, we predicted the interacting mode between galectin1 and HOXA5 using a protein-protein docking method. Our analysis suggests that the interaction between Galectin1 monomer and the homeobox domain of HOXA5 impedes the interaction between the homeobox domain of HOXA5 and DNA. In contrast, the interaction of Galectin1 homodimer and the N-terminal region of HOXA5 facilitates or stabilizes the homeobox domain of HOXA5 to bind DNA. Based on this predicted binding mode, we hypothesized that HOXA5 transcriptional activity is regulated by phosphorylated HOXA5, which may impact the interaction by attenuating the binding of HOXA5 to negatively charged DNA. To validate this model, we generated a mutant Galectin1 that cannot form dimers by substituting Cys at position 2 with Ser and Val at position 5 with Asp. We also generated functional domain deletion mutants of HOXA5 to confirm the interaction of the N- terminal region of HOXA5 with Galectin1, according to the prediction on functional domains in HOXA5 by Pfam. Using wild type (dimer) and mutant (monomer) recombinant galectin1 proteins and deletion-mutant proteins of HOXA5, we are conducting a binding assay to validate this model. Next, we employed knock-in lines to explore the role of HOXA5 phosphorylation in tumorigenesis using a glioblastoma mouse model. The proposed models will help uncover the underlying regulatory mechanisms of HOXA5/Galectin1 on BTSC self-renewal and glioblastoma tumorigenesis.

Stimuli-responsive aggregation-induced emission of molecular probes by electrostatic and hydrophobic interactions: Effect of organic solvent content and application for probing of alkaline phosphatase activity

We suggest that aggregation-induced emission (AIE) molecular probes with single charged/reactive group can exist in the formation of nanostructures but not monomers at extremely low organic solvent content. The nanoaggregates show good dispersivity and emit week emission. Stimuli-responsive assembly of nanoaggregates by electrostatic interactions can turn on the fluorescence, facilitating the design of biosensors with single-charged molecular probes as the AIE fluorogens. To prove the concept, tetraphenylethene-substituted pyridinium salt (TPE-Py) was used as the AIE fluorogen for probing of alkaline phosphatase (ALP) activity with pyrophosphate ion (PPi) as the enzyme substrate. The dynamic light scattering and transmission electron microscope experiments demonstrated that TPE-Py probes existed in aqueous solution at nanometer size and morphology. Stimuli such as the negatively charged PPi, citrate, ATP, ADP, NADP and DNA could trigger the aggregation of the positively charged TPE-Py nanoparticles, thus enhancing the fluorescence via AIE effect. ALP-enzymatic hydrolysis of PPi into two phosphate ions (Pi) limited the aggregation of TPE-Py nanoparticles. The strategy was used for the assay of ALP with a low detection limit (1 U/L) and wide linear range (1–200 U/L). We also investigated the effect of organic solvent content on the AIE process and found that high concentration of organic solvent can prevent the hydrophobic interaction between AIE molecules but show no essential influence on the electrostatic interaction-mediated assembly. The work should be evaluable for understanding AIE phenomenon and developing novel, simple and sensitive biosensors using a molecular probe with single charged/reactive group as the signal reporter.

Electrochemical aptamer biosensor for DNA detection based on label-free aptamers

Electrochemical aptasensor has been broadly advanced for nucleic acid detection. However, it is a long-term goal to design an aptasensor with high specificity, flexibility, and simplicity. In this work, we develop a strategy of triblock DNA probe, which consists of two DNA probes at both ends and ployA fragments in the middle as probe-polyA-probe. PolyA fragment has high affinity to the surface of gold electrode, so it can be assembled on the electrode surface via polyA instead of traditional Au-S bonds. When the target DNA is simultaneously hybridized with the two capture probes, the hybridization stability can be improved due to the strong base stacking effect. [Ru(NH3)6]3+, as signal probe, can be electrostatically adsorbed on the negatively charged DNA skeleton. A wide linear range (10 pM-10 μM) is obtained with a detection limit of 2.9 pM. Our electrochemical aptasensor has good repeatability, stability, and specificity. More importantly, the electrochemical sensor can successfully detect DNA in human serum samples, which proves its practical value and extensive applicability in complex environment.

Thermoreversible Gels Based on Chitosan Copolymers as "Intelligent" Drug Delivery System with Prolonged Action for Intramuscular Injection.

Thermosensitive gels based on copolymers (PEG-chitosan, chitosan-polyethylenimine, chitosan-arginine and glycol-chitosan-spermine) are presented as promising polycations for the formation of DNA polyplexes and the potential for the development of drugs with prolonged release (up to 30 days). Being in liquid form at room temperature, such compounds can be injected into muscle tissue with rapid gel formation at human body temperature. An intramuscular depot is formed with a therapeutic agent that provides a gradual release of the drug, such as an antibacterial or cytostatic. The physico-chemical parameters of the formation of polyplexes between polycationic polymers of various compositions and molecular architecture and DNA were studied via FTIR, UV-vis and fluorescence spectroscopy using the dyes rhodamine 6G (R6G) and acridine orange (AO). The competitive displacement of AO from AO-DNA complexes showed that, with a ratio of N/P = 1, most of the DNA is bound to a polycation. During the formation of polyplexes, the DNA charge is neutralized by a polycation, which is reflected in electrophoretic immobility. The cationic polymers described in this work at a concentration of 1-4% are capable of forming gels, and the thermoreversible property is most characteristic of pegylated chitosan. BSA, as a model anionic molecule, is released by half in 5 days from the Chit5-PEG5 gel; full release is achieved in 18-20 days. At the same time, in 5 days, the gel is destroyed up to 30%, and in 20 days, by 90% (release of chitosan particles). For the first time, flow cytometry was used to study DNA polyplexes, which showed the existence of fluorescent particles in a much larger number in combination with free DNA. Thus, functional stimulus-sensitive polymers are potentially applicable for the creation of prolonged therapeutic formulations for gene delivery systems, which were obtained. The revealed regularities appear to be a platform for the design of polyplexes with controllable stability, in particular, fulfilling the requirements imposed for gene delivery vehicles.

Molecular Mechanism of Ligand Binding to the Minor Groove of DNA

Although DNA–ligand binding is pervasive in biology, little is known about molecular-level binding mechanisms. Using all-atom, explicit-solvent molecular dynamics simulations in conjunction with weighted ensemble (WE)-enhanced sampling, an ensemble of 2562 binding trajectories of Hoechst 33258 (H33258) to d(CGC AAA TTT GCG) was generated from which the binding mechanism was extracted. In particular, the electrostatic interaction between the positively charged H33258 and the negatively charged DNA backbone drives the formation of initial H33258–DNA contacts. After this initial contact, a hinge-like intermediate state is formed in which one end of H33258 inserts into the minor groove of DNA. Following hinge state formation is a concerted motion whereby the second end of H33258 swings into the minor groove and the spine of hydration along the minor groove causing dehydration. This study illustrates how WE-enhanced simulations of biomolecular ligation processes can offer novel mechanistic insights by generating ensembles of binding events.

Silver Nanomaterials Applied in the Field of Diagnosis and Treatment

Nanomaterials have great application prospect in biological medicine due to their strong permeability, repair and regeneration. In particular, nano silver has excellent antibacterial ability and no toxic effect, which makes it widely used. The specific content of this paper introduces a method of using silver nanoparticles to generate silver ions, and then make it react with hydrogen peroxide, through the colorimetric device to react with different color changes corresponding to different concentrations, through this biosensor to determine the concentration of such as cholesterol lactic acid and other substances.And when detecting miRNA,AuNPs were further modified by complementing the DNA (cDNA) of target mirnas. AgNPs could not be attracted to negatively charged DNA due to electrostatic repulsion by immobilized modified gold nanoparticles on the electrode surface. After analyzing the peak of silver stripping, miRNA can be accurately detected.Furthermore, chitosan coated silver nanoparticles were designed, and polyethylene glycol was used as a stabilizer. Finally, its good blood compatibility and antibacterial ability, as well as its cytotoxicity to cervical cancer cells were demonstrated by characterization.Finally, the accumulation and changes of reactive oxygen species (ROS) and reactive nitrogen (RNS) induced by silver nano are introduced, and it is confirmed by measurement that they are important factors in apoptosis of human pancreatic ductal adenocarcinoma.