Polymeric Network of Amines, Chemical Modifications, Conformational Analysis of Nanoparticle Interaction, and Orientation of DNA Volume 56- Issue 2

Rajiv Kumar^1,2* and Anil K Aggarwal²

• ¹University of Delhi, India
• ²Department of Chemistry, Shivaji College, University of Delhi, India

Received: April 10, 2024; Published: April 17, 2024

*Corresponding author: Rajiv Kumar, Department of Chemistry, Shivaji College, University of Delhi, New Delhi

DOI: 10.26717/BJSTR.2024.56.008815

Abstract PDF

Nanostructures are used as biomarkers, therapeutics, catalysts, and structural reinforcements. They have a wide range of chemical characteristics. It has a long history and is essential to include specific functionality when using surfactants to embellish. Here, a broad range of surface-active substances, including surface-active chemicals, polymers, standard alkyl modifiers, and biological ligands, are referred to as “surfactants.” This opinion provides a thorough analysis of the covalent and non-covalent interactions of these surfactants with several types of nanomaterials, including layered materials, metals, polymers, and oxides. [1] The degree of surface regularity and defects in the nanoparticle cores and the surfactant shell, as well as surface energy, pH sensitivity, and surface chemistry, are significant factors that contribute to differentiation. The authors discuss a wide range of surface modification sensors, applications in biological recognition and therapeutics, nanomaterials for catalysis, energy storage, and conversion, the dispersion properties of nanoparticles in structural composites and cement, and traditional detergents. [2] Design guidelines for surfactants are presented in order to enhance the functionality of certain nanostructures.

In the field of nanoscale architecture, a notable phenomenon that occurs in topologically preset superstructures is the interaction and orientation of the polymeric network of amines on the surface of colloids. The completion of such techniques requires a general change in manufacturing practices towards biological systems, which is accomplished via physical and chemical stereochemical manipulation. Through the amino groups on their surfaces, the amino groups of a polymeric network of amines assist with nanoparticle surfaces (Figure 1). This interaction event also entails a modification in the protonation state that forms at the end of the functional group (amino or amine) and enhances the length of the sequence of the molecule. Designing, assembling, and using DNA for biological purposes has a lot of potential if we understand how DNA interacts with nanoparticles. [3] There has been an increase in knowledge and use of the processes behind the DNA-nanoparticle interfacial phenomenon. Despite the reporting of some prior reviews, systematic and comprehensive reviews are uncommon. Here, we have summarized the most recent developments in the fundamental theories relating to DNA-nanoparticle interactions and their applications in biosensing in order to gain a better understanding of the processes involved in the interaction between DNA and nanoparticles [4].

Figure 1

Inorganic nanoparticles such as metal nanoparticles, carbon- based compounds, metal oxides, and quantum dots received particular attention. The surface characteristics, interacting processes, kinetics, and spatial control of DNA adsorption for each material were listed and addressed. We also highlighted a few of the most modern biomolecule detection systems based on DNA-NP interactions. Finally, the difficulties and suggested directions for the future were discussed. The comprehensive knowledge of the mechanics behind DNA-nanoparticle interactions provided by this research may provide fresh ideas for creating biosensors with enhanced capabilities. [5] Off-lattice Monte Carlo simulations are used to examine the interfacial characteristics of polymer chains on spherical nanoparticles. Results reveal that as the polymer-nanoparticle interaction strength increases, the number of adsorbed monomers grows while the number of adsorbed polymers drops. The chain length and nanoparticle size have no effect on the interfacial layer thickness. Three unique levels of stacking behaviour are displayed by the interfacial monomers. [6] The polymer-nanoparticle interaction intensity has a significant impact on the mobility of monomers in the topmost layer.

There is never a glassy coating around the nanoparticle because the interfacial monomers are always in motion. Finally, our findings demonstrate that while nanoparticle motion can weaken polymer adsorption, it does not affect the conformational characteristics of adsorbed polymers. Following the aforementioned information, the design of metal-based nanostructure nanoparticles that can act as carriers for cellular transfection has been a prominent objective in bioorganic and medicinal chemistry. [7] Thus, the DNA molecules function as counter ions and block the repellent interactions between positively charged Au/Ag nanoparticles, allowing them to assemble into densely packed superstructures. Enlarged structural and interaction revisions in detail can draw attention to the significance of the colloids/DNA complex. [8] Although these approaches rely on the massive electromagnetic field increase that transpires around metallic nanoparticles, primarily Ag/Au. The conformation of both macromolecules was altered, because of the two polymeric networks of amines adhering to the nanoparticles, which suggests a charge transfer effect on the surface. [9] By using DNA as a template, it is possible to construct nanoparticles with more complex geometries and get insight into the effectiveness of these particles as vectors for delivering genes and drugs [10].

In this research opinion, the primary goal of the author was to comprehend their chemical and biological efficacy during nucleic acid interactions in cellular transfection. Making high-performance polymer nanocomposites (PNCs) requires a thorough knowledge of the process through which nanoparticles (NPs) fortify polymer matrices. Here, the reinforcing impact of an NP network was specifically investigated using coarse-grained molecular dynamics simulations. According to our findings, NPs self-assembled formed a three-dimensional (3D) network that strengthened the polymer matrix when NP-NP interactions were increased. [11] In contrast to NP-polymer interactions, NP-NP interactions have a very distinct reinforcing mechanism. While the former evenly distributed the stress throughout the NP network, the latter encouraged polymer chains’ orientation in order to transfer the external stress. [12] This research disclosed the chemical mechanism by which the NP network strengthened the polymer matrix and offered directions for creating high-performance PNCs by interfacial modification. This perspective was divided into different sections, with a focus on the biophysical methods used for the synthesis and analysis of polymeric networks of amines and their interactions with metal nanoparticles employed as carriers of medicines and genes.

In the fields of cellular transfection and medicinal chemistry, bottom- up approaches for the synthesis and depiction of various stereochemistry consisting of polymeric networks of amines play a significant role. Examining the adsorption mechanism of diverse polymeric networks of amines on Ag/Au nanoparticles has been done previously using a variety of physiochemical approaches. [13] The structure of artificial polyamine analogs and their conjugates, which serve as perfect vectors, has biological relevance in the transfection process, the development of molecular mechanisms, and therapeutic uses in a variety of biological therapies. [14] Lipopolyamines’ ability to condense DNA was originally noted more than ten years ago. Three years later, it was shown that the DNA/lipid multiplexes have been formed and employed for cellular transfection. [15] When the plasmid interacts with a polymeric network of amines, the plasmid changes structurally from an A-DNA assembly to a B-DNA structure and alters its superhelicity which results in an auxiliary linear form. [16] These molecules conflict with one another due to the high-intermolecular positive charge, which outspreads the molecules and optimizes counter-ion collapse upon interaction with polyanionic DNA because of conformational stabilization.

Nanostructures offer enormous promise for use in many industrial applications, including quantum dot lasers and biomacromolecules sensing technology. [17] One of the most intriguing study areas is the conjugation of biomacromolecules, where noble metal nanoparticles and their interactions have been studied. Most research has been done on Ag/Au nanoparticles concerning biomacromolecules conjugated to chemistry (Figure 2) [18]. These nanoparticles have also undergone additional analysis to comprehend their biochemical efficacy in gene/drug administration. [19] Understanding their fundamental function and determining their binding capacity with the target showed their utmost importance. For example, biosensors for DNA hybridization, for instance, DNA-labeled gold and CdSe nanoparticles with special colorimetric and fluorescent features, have been employed to explore the hidden clues. [20] As well, the gold nanoparticle has drawn a lot of interest. [21]

Figure 2

The utilization of DNA/Au nanoparticles was demonstrated as another alluring method for raising the sensitivity of numerous significant procedures.

For instance, Zhou, et al. [22] and Willner and coworkers [23], had developed a dendritic assembly having nanoparticles, respectively, to intensify the fragile quartz crystal microbalance extra precisely, the thickness-shear mode sensor (TSM) [24] signals in-built in a traditional assembly that can attack hybridization-based HS-ss- OSNs. [25] The electrostatic interfaces among the stimulating DNA/ vector complexes with positive charges and the glycosaminoglycans of the cell membranes that carry negative charges result in an overall, positive charge. These findings have been revealed during in vitro investigations with lipids and polymers that carry a cationic charge. [26] Nowadays, the main goal of the researchers is to discover how to demonstrate other analytical “figures of merit” including selectivity and dynamic range for Ag/Au nanoparticle conjugation in a better way. [27] Using a variety of physiochemical and spectroscopic characterization approaches, most of the researchers examine the significance and newer possibilities that influence the creation of gene-drug delivery systems. In this opinion, the author aims to build following the synthetic procedures that are now in use, with the necessary adjustments made to ensure that linear PA analogs and their conjugates are prepared properly [28].

The investigation of interfacial phenomena and the conformational alterations of PAs that hold various nanoparticles can be conducted successfully using physiochemical characterization techniques that have a wide range of analytical applications and are frequently used in vibrant fields. Despite these developments, general guidelines governing the design of synthetic vectors, as well as their design and synthesis, have not yet been fully realized. [29] The rational modulation of vector designs necessitates a more quantitative examination of the cellular uptake and intracellular processing of these vectors. More theoretically designed mathematical frameworks for PAs will make it easier to evaluate these problematic systems from an assimilated viewpoint. Chemical manipulation in stereochemistry, and conformational analysis of interaction Because of their importance in the pharmaceutical industry, safety, and accessibility in use, the synthetic vector PAs, whether in their free polycationic form or linearly conjugated to other biomacromolecules, transpire naturally and exhibit fascinating biological activities.

However, a profile of their potential benefits and drawbacks has emerged, including a description of their efficiency in some viral systems. Pour cette raison, several methods for determining their structural analysis should be used, and a greater comprehension of their mechanism of action is required to prepare a wide range of synthetic PAs analogues and conjugates. [30] Therefore, the current medical science requires modeling as a necessity that depends on the biological systems of potential gene delivery vehicles. We need to create novel polymeric networks of amines for nucleic acid delivery systems, considering all these developments in science, particularly in the field of gene-related biomacromolecules. Only these carrier systems (Figure 3) can offer the nanoparticles adequate support and keep them from aggregating. Thus, in this view, the author explores the growth of such delivery methods, which may have greater benefits. Additionally, the author emphasizes mostly simple, modifiable synthetic procedures that enable the effective manufacture of linear PA analogs and conjugates for a given purpose. The phenomenon of adsorption and conformational changes occurring on the surface of nanoparticles/ biomacromolecules is being explored. Thus, the 3D conformation of biomolecules is essential for biological features to explore the route of action and efficiency of these discussed networks. Henceforth, the aiming scheme addresses the following points:

Figure 3

A. Design, Synthesis, and Characterization of Polyamines

How will it play a major and appealing function in developing suitable gene delivery vectors as drug carriers for treating diseases? By taking this into account, the various stereochemistry of polymeric networks of amines that alter the contact and orientation capabilities of these cation/colloid complexes is proposed. This is the primary objective of this opinion. These methodologies either entail selective functionalization of the amino functionalities, the use of appropriate- guarding assemblies or acylating mediators, or protocols for fragment creation. Branched hexamines (Ia-b) [31], derivatives of polyamine (III and IVa-f) [32], and tris(2-aminoethyl)amine (IIa-b), as well as other PA analogs with their derivatives, can be studied, the elucidation and analysis of their performance can be further studied (Figure 4). To further investigate synthetic PA analogues and conjugates in the quest to produce PA-based molecules with potential pharmacological or technical applications and gene delivery vehicles, it is essential to better understand their structure and mode of action. [33] These methods will likely be widely applied soon to hasten the process of identifying the strongest synthetic PA analogs and conjugates and to make it easier to develop PA-based drugs or molecules with agrochemical or technical interest.

Figure 4

Because of this, researchers will try to have a detailed description of the structural variety as well as their synthetic analogues and the biological importance of these compounds. [34] With the effects of these factors in mind, this discussion also focuses on the physical and chemical characteristics of PAs. With the help of fragment-synthesis- related methods and selective alterations of PA’s functional groups, the PA skeleton is put together to the necessary length for nanoparticles and DNA.

On the number of differently functionalized nitrogen atoms.

1. By using relatively simple amino building blocks.

2. By using conjugates that can perform either by selecting the amino features of PAs or the assembly of the PA skeleton. Based on the above important characteristics, the author explores the importance of the polyamine network for gene-drug delivery. B. In structure–activity relationship studies of biologically active molecules bearing PAs, how does the chain also try to give an understanding of their mode of action and the development of potent analogs with important medicinal applications? The author can build the necessary and effective vector for gene/drug delivery, as well as their more practical handling, thanks to the systematic synthesis of metallic nanoparticles embedded in a polymeric network coupled to a colloidal core particle. The key goal of this study was to create such inventive drug delivery methods.

a. Preparation of gold nanoparticles [35]: Citrate solutions By creating aqueous stock solutions of the requisite percent HAu- Cl4.3H2O and required percent sodium citrate, reduced gold nanoparticles have been created. The sodium citrate solution will be added in the necessary amount after the HAuCl4.3H2O solution has been heated to a boil while being stirred. Before making wine red, the reaction mixture underwent a sequence of color changes. After the last color change, the boiling went on for another 30 minutes. The gold nanoparticle solution will be diluted to the necessary volume using DI water after cooling to room temperature. Most gold solutions’ isolated, almost spherical particles have varied sizes before salt or analysis are added.

b. Preparation of silver nanoparticles [36]: When the hydrated solution of AgNO3 is heated to its boiling point, the necessary concentration of trisodium citrate solution is added. The combination is then heated to the proper reaction temperature. This creates silver colloids. All of the solutions have been prepared using triple-distilled water. The average diameter of the silver colloids is a defining characteristic.

C. Since the release and integration of DNA by the cell depend on the polymeric network of PAs/DNA complexes adhering to a negative surface, the analysis of structural alterations caused by this adsorption is also essential in determining the efficacy of the vector. The key goal to be identified, according to the author, is to characterize the gene delivery vector to examine conformational changes that occurred because of PA adsorption on the surface of a metal. Another objective is to investigate its interaction with DNA. Because of the protonation state and how it will affect the chemical and physical features of the ethylene functional groups in the skeleton of the polymer and their function in the creation of bonds with the metal, PAs will experience significant conformational changes. [37] The charge transfer that resulted from this contact between the surface and the PA accounts for the resonance phenomenon seen with various spectral techniques. [38] How are scientists able to use various biophysical characterization techniques to show that structural alterations are obvious at various molecular levels? On the one hand, it appears that after interacting with PAs, the DNA takes on a more linear form.

The current study has assessed target definition for vaginal cuff SBRT with comparative analysis of CT and MRI. Stereotactic irradiation procedures have been performed at our Radiation Oncology Department of Gulhane Medical Faculty at University of Health Sciences. Prior to vaginal cuff SBRT, all included patients have been individually evaluated by a multidisciplinary team of experts from surgical oncology, radiation oncology, and medical oncology. Critical goal of vaginal cuff SBRT planning has been to achieve optimal target coverage without violation of critical organ dose constraints. IGRT techniques such as kilovoltage cone beam CT was used, and vaginal cuff SBRT has been delivered by Synergy (Elekta, UK) LINAC. We found that CT and MRI defined target definition resulted in differences. Thus, we utilized fused CT and MRI for ground truth target volume definition for vaginal cuff SBRT.

Endometrial cancer is a significant public health concern for women with its critical incidence around the globe [1]. Surgery, radiation therapy (RT), and systemic treatments may be used alone or in combination for management of endometrial cancer with respect to patient, disease, and treatment characteristics [2-7]. Recently, SBRT has emerged as a viable irradiation technique for management of a variety of cancers throughout the human body. Admittedly, recent years have witnessed critical advances in technology. Automatic segmentation techniques, molecular imaging methods, IGRT, IMRT, stereotactic RT, and ART techniques have been introduced for improved radiotherapeutic management of patients [8-49]. With improved stereotactic localization of well-defined targets under image guidance, SBRT offers a highly precise radiotherapeutic modality. High doses of radiation may be delivered in a single fraction or with a limited number of fractions, and highly conformal treatment with steep dose gradients around the target may allow for optimal irradiation with an acceptable toxicity profile. More recently, SBRT has been used for vaginal cuff boost as an alternative to brachytherapy [7]. The utilization of a vaginal cuff boost may be considered for patients deemed to be at a higher risk of vaginal recurrence. Cervical stromal invasion along with other factors including age, margin status, grade, extent of invasion, histology, and lower external beam RT doses may be regarded as critical issue to consider for optimal patient selection.

In the context of radiation oncology, improved target definition and critical organ sparing should be considered among the pertinent aspects of optimal stereotactic irradiation. Determination of larger target volumes may lead to radiation induced toxicity, and definition of smaller than actual target volumes may result in decreased local control of the disease. It should be mentioned that adaptive irradiation approaches and multimodality imaging-based target definition may be suggested to improve radiotherapeutic results [50-106]. The current study has assessed target definition for vaginal cuff SBRT with comparative analysis of CT and MRI. Stereotactic irradiation procedures have been performed at our Radiation Oncology Department of Gulhane Medical Faculty at the University of Health Sciences. Prior to vaginal cuff SBRT, all included patients have been individually evaluated by a multidisciplinary team of experts from surgical oncology, radiation oncology, and medical oncology. The critical goal of vaginal cuff SBRT planning has been to achieve optimal target coverage without violation of critical organ dose constraints. IGRT techniques such as kilovoltage cone beam CT were used, and vaginal cuff SBRT has been delivered by Synergy (Elekta, UK) LINAC. We found that CT and MRI defined target definition resulted in differences. Thus, we utilized fused CT and MRI for ground truth target volume definition for vaginal cuff SBRT. From a radiation oncology perspective, our results may have implications for increased adoption of multimodality imaging- based target definition for vaginal cuff SBRT, nevertheless, the need for future studies to shed light on this critical issue may not be neglected.

Figure 5

Because of the interaction with the polymer and how it relates to the poorer thermodynamic stability of the bonding section of DNA, this shift in the superhelicity of the DNA resulted in noticeable modifications in different DNAs. [39] Due to the great significance of procedures of biological importance, i.e., gene transport, the early research findings can provide very favourable and essential evidence in the elucidation of recognition complications existing between massive chains of polymers (Figure 5). By combining the necessary amount of PAs’ aqueous solution with the necessary amount of the plasmid’s aqueous solution, samples were obtained for biophysical characterization procedure measurements. The complex was stored for at least one hour before the measurement to guarantee that the DNA completely interacted with PEI and that the percentage of nitrogen/phosphorus in the chain of PAs and DNA was 9:1. Furthermore,

1. To collect samples for PAs and DNA characterization measurements, add the same amount of water as the other ingredient that was used to construct the complex. Before being included in the complex, the Ag/Au colloid had been activated [40].

2. To observe a robust characterization spectrum, this activation involved the colloid aggregation achieved by the addition of potassium nitrate solution prepared in water at the requisite concentration.

3. To get the spectra at various excitation wavelengths, the stimulated Ag/Au colloid was then mixed with the aforementioned solution of complex using glass capillaries.

Polymer networks are intricate structures made up of molecules. While most chemists have a good understanding of the properties of individual parts, the statistical and ill-defined nature of network structures makes it difficult to translate that chemical understanding into polymer networks. As a result, extrapolating from the molecular behaviour of components to the complete spectrum of performance and attributes of the entire polymer network is difficult, if not now impossible. [41] Therefore, polymer networks offer an untapped, significant, and interdisciplinary opportunity to exert chemical control at the molecular level over material macroscopic properties. [42] The fact that many scientists are typically inexperienced with the methods for characterizing the molecular structure of networks is a hurdle to advanced molecular approaches to polymer networks. In the absence of further fillers, we provide a critical evaluation of the existing characterization methods available to comprehend the relationship between molecular characteristics and the performance and behaviour of polymer networks [34].

We emphasise methods for characterizing the chemistry and molecular characteristics of individual polymer strands and junctions, the gelation process by which strands create networks, the topology of the resultant network, and the dynamics and mechanics of the finished product. Instead of acting as a comprehensive guide for carrying out these measurements, the aim is to harmonize the underlying concepts, identify unresolved issues, and offer chemists a succinct summary by which they may develop characterization procedures that are appropriate for their research goals. [43] Strategic pairings of several approaches are frequently needed for the molecular characterization of polymer networks since these networks are frequently difficult to properly characterize using a single technique. It has been investigated using biophysical characterization approaches to determine how to create an effective drug delivery system and how well it binds to biomacromolecules. On the one hand, it enables the spectroscopic spectral investigation of biomacromolecules at extremely low concentrations to investigate the physiological environment [44].

Contrarily, metals are substrates on which polymeric networks of amines are strongly attached in heterogeneous systems, such as the case of the proposed complexes, where multiple interactions are possible; as a result, the synthesis and design of novel polymeric networks of amines and their metal nanoparticles are discussed here. Structural investigations of PAs have been followed by some spectroscopic studies i.e. C, H, and N, electron impact mass spectra, 1H and 13C NMR spectra, and IR spectra. Circular dichroism (CD) spectroscopy has been used to conduct comprehensive research on the conformational properties of several optically active substances, from small molecules to natural (proteins, DNA, and RNA) or synthetically occurring macromolecules. Using biophysical characterization techniques, it has been determined that the chemical state of the discussed cationic polymers is on the ionic surfaces of cells, where equivalent adoption and contact processes may also occur. [45] Spectroscopic analysis can be performed by carefully observing the particular modifications that occur in the polymeric network of the amines and the plasmid after adsorption and complexation. When examining DNA/ nanoparticle systems, these techniques can be twice as helpful.

Different techniques, including circular dichroism, differential scanning calorimetry, potential measurements, atomic force microscopy, temperature-dependent UV, and light scattering, will be used to characterize the stability of the DNA in the cationic complexes, various altered features of the cationic complexes, conformational alterations, physical and chemical features of the cationic complexes. Isothermal titration calorimetry has been used to track the general thermodynamical characteristics of the binding event of these cationic complexes (ITC). These cationic complexes bind to DNA and strengthen the base-pair-stacking interactions, increasing the enthalpy occurring during the helix–coil transition. [46] The ability to bind is related to minor exothermic enthalpy modifications. Therefore, the binding route as a whole is entropically advantageous. A comparison of the thermodynamic parameters can help in understanding this.

With the help of this scientific foundation, the fields of gene therapy and drug delivery systems have evolved quickly and are today recognized as the most promising areas of medical study. Researchers will study the biophysical characterization of novel gene delivery systems that depend on the interaction of nanoparticles and biomacromolecules with the target tissue. [47] This research, will be studied how to detect the interaction between cationic complexes using biophysical technologies, which is a significant issue connected to gene therapy. To fully realize the promise and potential of gene therapeutics, the effective and targeted delivery of therapeutic genes to a target site must be addressed. By strategically using intracellular mechanisms, it may be necessary to analyze the binding affinity of enhanced synthetic vector designs and to look into innovative avenues for overcoming challenges in the field’s actual implementation. [48] However, what scientists now require is the creation and implementation of drug delivery systems essential for the building of efficient gene therapy methods using gene-related medicinal supplies. Despite this widespread understanding, there will be a lot of pressure to develop the vector to maximize the efficiency of gene expression, but the pharmacokinetics of its use have been overlooked.

The author (Rajiv Kumar) expresses gratitude to his younger brother, Bitto, for inspiring him.

Where applicable, the reference section contains pertinent citations.

The author has stated that they have no conflicting interests.

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