Bundling and Aggregation of DNA by Cationic Dendrimers

On-Demand Aligned DNA Hydrogel Via Light Scanning

DNA is an anisotropic, water-attracting, and biocompatible material, an ideal building block for hydrogel. The alignment of the anisotropic DNA chains is essential to maximize hydrogel properties, which has been little explored. Here, we present a method to fabricate the anisotropic DNA hydrogel that allows precise control for the polymerization process of photoreactive cationic monomers. Scanning ultraviolet light enables the uniaxial alignment of DNA chains through the polymerization-induced diffusive mass flow using a concentration gradient. While studying anisotropic mechanical properties and orientation recovery according to the DNA chain alignment direction, we demonstrate the potential of directionally controlled DNA hydrogels as smart materials.

Deciphering the binding mechanism of an anti-cancer phytochemical plumbagin with calf thymus DNA using biophysical and in silico techniques

Plumbagin (PLM), a plant derivative, is well known for a wide range of therapeutic effects in humans including anti-cancer, anti-inflammatory, anti-oxidant, and anti-microbial. Cytotoxic and genotoxic potential of this phytochemical has been studied which demands further insight. DNA being a major target for several drugs was taken to study against PLM to understand its effects on the cellular system. UV-Vis spectroscopy has indicated the binding of PLM to ctDNA and dye displacement assays have confirmed the formation of PLM-ctDNA complex. The insignificant changes in circular dichroism spectra suggested that PLM is not affecting the structural makeup of the ctDNA, hence the binding could be peripheral and not intercalating. Further, the relative viscosity and minimal change in melting temperature upon the complex formation supported this finding and confirmed the groove binding of PLM. Molecular docking analysis and simulation studies also show PLM as a minor groove binder to DNA and provide details on the interaction dynamics of PLM-DNA complex. Docking followed by a 100 ns simulation reveals the negative Gibbs free energy change (∆G = -6.6 kcal mol-1), and the formation of a stable complex. The PLM- DNA complex with stable dynamics was further supported by different parameters including RMSD, RMSF, SASA, Rg, and the energy profile of interaction. This study provides an insight into the cytotoxic and genotoxic mechanism of PLM which can be a crucial step forward to exploit its therapeutic potential against several diseases including cancer.

Molecular Dynamics and Multi-Spectroscopic of the Interaction Behavior between Bladder Cancer Cells and Calf Thymus DNA with Rebeccamycin: Apoptosis through the Down Regulation of PI3K/AKT Signaling Pathway

The interaction of Rebeccamycin with calf thymus (ctDNA) in the absence and presence of H1 was investigated by molecular dynamics, multi-spectroscopic, and cellular techniques. According to fluorescence and circular dichroism spectroscopies, Rebeccamycin interacted with ctDNA in the absence of H1 through intercalator or binding modes, while the presence of H1 resulted in revealing theintercalator, as the dominant role, and groove binding modes of ctDNA-Rebeccamycin complex. The binding constants, which were calculated to be 1.22 × 104 M-1 and 7.92 × 105 M-1 in the absence and presence of H1, respectively, denoted the strong binding of Rebeccamycin with ctDNA. The binding constants of Rebeccamycin with ct DNA in the absence and presence of H1 were calculated at 298, 303 and 308 K. Considering the thermodynamic parameters (ΔH0 and ΔS0), both vander waals forces and hydrogen bonds played predominant roles throughout the binding of Rebeccamycin to ctDNA in the absence and presence of H1. The outcomes of circular dichroism suggested the lack of any major conformational changes in ctDNA upon interacting with Rebeccamycin, except some perturbations in native B-DNA at local level. Additionally, the effect of NaCl and KI on ctDNA-Rebeccamycin complex provided further evidence for the reliance of their interaction modes on substituted groups. The observed increase in the relative viscosity of ctDNA caused by the enhancement of Rebeccamycin confirmed their intercalation and groove binding modes in the absence and presence of H1. Moreover, the assessments of molecular docking simulation corroborated these experimental results and also elucidated the effectiveness of Rebeccamycinin inhibiting and proliferating T24 and 5637 cells. Meanwhile, the ability of Rebeccamycin in inhibiting cell proliferation and tumor growth through the induction of apoptosis by down regulating the PI3K/AKT signaling pathway were provided.

Bacteriophage-loaded functional nanofibers for treatment of P. aeruginosa and S. aureus wound infections

The increasing incidence of infected skin wounds poses a major challenge in clinical practice, especially when conventional antibiotic therapy fails. In this context, bacteriophages emerged as promising alternatives for the treatment of antibiotic-resistant bacteria. However, clinical implementation remains hampered by the lack of efficient delivery approaches to infected wound tissue. In this study, bacteriophage-loaded electrospun fiber mats were successfully developed as next-generation wound dressings for the treatment of infected wounds. We employed a coaxial electrospinning approach, creating fibers with a protective polymer shell, enveloping bacteriophages in the core while maintaining their antimicrobial activity. The novel fibers exhibited a reproducible fiber diameter range and morphology, while the mechanical fiber properties were ideal for application onto wounds. Further, immediate release kinetics for the phages were confirmed as well as the biocompatibility of the fibers with human skin cells. Antimicrobial activity was demonstrated against Staphylococcus aureus and Pseudomonas aeruginosa and the core/shell formulation maintained the bacteriophage activity for 4 weeks when stored at - 20 °C. Based on these promising characteristics, our approach holds great potential as a platform technology for the encapsulation of bioactive bacteriophages to enable the translation of phage therapy into clinical application.

Functionalized PAMAM constructed nanosystems for biomacromolecule delivery

Polyamidoamines (PAMAMs) are a class of dendrimer with monodispersity and controlled topology, which can deliver biologically active macromolecules (e.g., genes and proteins) to specific regions with high efficiency and minimum side effects. In detail, PAMAMs can be functionalized easily by core modification or surface amendment to encapsulate a wide range of biomacromolecules. Besides, self-assembled, cross-linked and hybrid PAMAMs with customized therapeutic purposes are developed as delivery vehicles, which makes PAMAMs promising for biomacromolecule therapy. In this review, we comprehensively summarize the application of PAMAMs in biomacromolecule delivery from the synthesis of functionalized PAMAM carriers to the development of PAMAM-based drug delivery systems. The underlying strategies for PAMAM functionalization and assembly are first systematically discussed, and then the current applications of PAMAMs for biomacromolecule delivery are reviewed. Finally, a brief perspective on the further applications of PAMAMs concludes, aiming to provide insights into developing PAMAM-based biomacromolecule delivery systems.

Cu(II)-Catalysed Hydrocarboxylation of Imines Utilizing CO2 to Synthesize α-Unsaturated Aminocarboxylic Acids

Here, we report the Cu(II)-photocatalysed hydrocarboxylation of imines (C=N) from a series of synthesized Schiff Base derivatives, namely (E)-1-(4-((4-methylbenzylidene)amino)phenyl)ethanone, (E)-1-(3-((5-bromo-2-hydroxybenzylidene)amino)phenyl)ethanone, (E)-4-((5-bromo-2-hydroxybenzylidene)amino)-1,5-dimethyl-2-phenyl-1H-pyrazol-3(2H)-one, and (E)-1,5-dimethyl-4-((4-methylbenzylidene)amino)-2-phenyl-1H-pyrazol-3(2H)-one, with carbon dioxide (CO₂) to generate disubstituted amino acids. Under mild conditions (atmospheric pressure of CO₂, room temperature, and 30 W Blue LED light), good to excellent yields confirming the formation of substituted amino acid unsaturated acid derivatives were obtained. Single crystal X-ray diffraction (SC-XRD) and UV-Vis diffuse reflectance spectroscopy (UV-Vis-DRS) confirmed the square pyramidal geometry of the Cu(II) photocatalyst. Docking and DFT calculations of the substituted amino acid unsaturated acid derivatives showed their potential as antimicrobial molecules.

Brush-Structured Chitosan/PolyHEMA with Thymine and Its Synergistic Effect on the Specific Interaction with ssDNA and Cellular Uptake

Cationic polymers are known to attach on an anionic cell surface and favor gene transportation/transfection into the cells. However, when the positive charges accumulate, they tend to cause cell damage and delivery failure. Chitosan (CS) is a potential cationic bio-derived polymer whose chemical structures can be modified to fine-tune the charges as well as the add-on functions. The present work demonstrates (i) the decoration of a nucleic acid sequence-like brush structure on CS to allow the specific interaction with DNA and (ii) delivery into the cell. By simply applying mercaptoacetic acid as the chain transfer agent, the grafting of poly(hydroxyethyl methacrylate) (PHEMA) containing Thy (P(HEMA-Thy)) on CS is possible. The brush-like P(HEMA-Thy) leads Thy moieties to be in sequences. The Thy sequences perform as poly[T] for the specific interaction with ssDNA. The synergistic effect of CS and Thy sequences, i.e., electrostatic and base pairing interactions, results in an effective and efficient binding with ssDNA as well as significant delivery, especially in cellular uptake and cell viability. The use of CS in combination with Thy sequences in brush-like structures on CS is a model for other polysaccharides to be conjugated with the as-designed nucleic acid sequences for potential gene delivery.

Mode of interaction of altretamine with calf thymus DNA: biophysical insights

Insights into drug-DNA interactions have importance in medicinal chemistry as it has a major role in the evolution of new therapeutic drugs. Therefore, binding studies of small molecules with DNA are of significant interest. Spectroscopy, coupled with measurements of viscosity and molecular docking studies were employed to obtain mechanistic insights into the binding of altretamine with calf thymus DNA (CT-DNA). The UV-visible spectroscopic measurements study confirmed altretamine-CT-DNA complex formation with affinity constant ([15.68 ± 0.04] × 10³ M^-1), a value associated with groove binding phenomenon. The associated thermodynamic signatures suggest enthalpically driven interactions. The values of standard molar free energy change (ΔGmo) -(23.93 ± 0.23) kJ mol^-1, enthalpy change (ΔvHHmo) -(50.84 ± 0.19) kJ mol^-1 and entropy change (ΔSmo) -(90.29 ± 0.12) JK^-1 mol^-1 indicate the binding is thermodynamically favorable and an important role of the hydrogen bonds and Van der Waals interactions in the binding of altretamine with CT-DNA. Circular dichroism spectroscopy indicated insignificant conformational changes in the DNA backbone upon interaction with altretamine suggesting no distortion and/or unstacking of the base pairs in the DNA helix. UV-melting study suggested that the thermal stability of the DNA backbone is not affected by the binding of the drug. Competitive displacement assays with ethidium bromide, Hoechst-33258 and DAPI established the binding of altretamine with CT-DNA in the minor groove. The mode of binding was further confirmed by viscosity and molecular docking studies. Molecular docking further ascertained binding of altretamine in the minor groove of the CT-DNA, preferably with the A-T rich sequences.

Studying the interaction of scopolamine with calf-thymus DNA: An in-vitro and in-silico approach and genotoxicity

Scopolamine is used to treat various CNS disorder like urinary incontinence, motion sickness, spasmic movements. Despite its pharmaceutical properties, its interaction with DNA is not yet reported. In this article, the interaction between scopolamine and ct-DNA is reported using a combination of biophysical techniques. UV-visible and steady-state fluorescence spectroscopy were used to study interaction and complex formation. Competitive displacement assays and potassium iodide quenching confirmed the mode of binding between scopolamine and DNA. Structural changes induced in the ct-DNA in the presence of scopolamine were evaluated by CD spectroscopy. The plasmid nicking and NBT assay confirmed the genotoxic effect of scopolamine. In-silico study by molecular docking and molecular dynamics simulation revealed the mode of interaction, major stabilizing forces as well as the nucleotide sequences to which the scopolamine binds.

Evaluation of the binding effect and cytotoxicity assay of 2-Ethyl-5-(4-methylphenyl) pyramido pyrazole ophthalazine trione on calf thymus DNA: spectroscopic, calorimetric, and molecular dynamics approaches

With advances in new drug therapies, it is essential to understand the interactions between drugs and target molecules. In this study, we applied multiple spectroscopic techniques including absorbance, fluorescence, circular dichroism spectroscopy, viscosity, thermal melting, calorimetric, and molecular dynamics (MD) simulation to study the interaction between 2-Ethyl-5-(4-methylphenyl) pyramido pyrazole ophthalazine trione (PPF) and calf thymus DNA (ct DNA) in the absence or presence of histone H1. PPF exhibits a high binding affinity towards ct DNA in binary and ternary systems. In addition, the result for the binding constant was observed within the range 10⁴  M^-1 achieved through fluorescence quenching data, while the values for enthalpy and entropy changes for ct DNA-PPF and (ct DNA-H1) PPF complexes were measured to be -72.54 kJ.mol^-1 , -161.14 J.mol^-1  K^-1 , -85.34 kJ.mol^-1 , and -19.023 J.mol^-1  K^-1 , respectively. Furthermore, in accordance with circular dichroism spectra, the inducement of ct DNA structural changes was observed during binding of PPF and H1 in binary and ternary system forms. The essential roles of hydrogen bonding and van der Waals forces throughout the interaction were suggested using thermodynamic parameters. According to the obtained data, the interaction mode of ct DNA-PPF and (ct DNA-H1) PPF complexes was intercalation binding. Suggested by the MD simulation study, the ct DNA-H1 complex caused a reduction in the stability of the DNA structure in the presence or absence of ligand, which demonstrated that PPF as an intercalating agent can further distort the structure. The information achieved from this study will be very helpful in understanding the effects of PPF on the conformational state of ct DNA in the absence or presence of the H1 molecule, which seems to be quite significant for clarifying the mechanisms of action and its pharmacokinetics.

FeII 4L4 tetrahedron binds and aggregates DNA G-quadruplexes

Since the discovery of the G-quadruplex (G4) structure in telomeres in 1980s, studies have established the role it plays in various biological processes. Here we report binding between DNA G4 and a self-assembled tetrahedral metal-organic cage 1 and consequent formation of aggregates, whereby the cage protects the DNA G4 from cleavage by S1 nuclease. We monitor DNA–cage interaction using fluorescence spectroscopy, firstly by quenching of a fluorescent label appended to the 5′ end of G4. Secondly, we detect the decrease in fluorescence of the G4-selective dyes thioflavin-T and Zn-PPIX bound to various DNA G4 sequences following the addition of cage 1. Our results demonstrate that 1 interacts with a wide range of G4s. Moreover, gel electrophoresis, circular dichroism and dynamic light scattering measurements establish the binding of 1 to G4 and indicate the formation of aggregate structures. Finally, we find that DNA G4 contained in an aggregate of cage 1 is protected from cleavage by S1 nuclease.

We find Fe^II₄L₄ binds to G-quadruplex and forms aggregates. G-quadruplex in the aggregates is protected from digestion by S₁ nuclease.

Attachment and in vitro transfection efficiency of an anti-rabies Chitosan-DNA nanoparticle vaccine

In Mexico, urban rabies has been reduced during the last decade thanks to intensive canine control and vaccination campaigns; however, rabies transmitted by wild animals, especially by bats, has been increasing due to vampire bats feeding on livestock. Vampire bat populations has been controlled by culling with vampiricides, reducing indiscriminately other bat species. Hence, bat vaccination for rabies offers an alternative for culling. Nevertheless, available rabies vaccines are not suitable for their use in wildlife from emerging countries. This project presents an alternative for the use of plasmid vaccines using bio-nanotechnology, to create low-cost and accessible vaccines. To accomplish this goal, chitosan nanoparticles were synthesized by ionic gelation and conjugated by coacervation with a pDNA rabies vaccine to test their attachment efficiency. Also, the conjugate was functionalized with Protoporphyrin IX and Folic acid as biomarkers. The nanoparticles complex was characterized by ultraviolet visible spectroscopy, infrared spectroscopy, transmission electron microscopy, dynamic light scattering, and the Z potential was obtained. In vitro tests were performed on cell viability and transfection. The nanoparticles possessed a low polydispersity, a mean size of 118.5 ± 13.6 nm and a Z potential of 17.3 mV. The attachment efficiency was of 100% independent of pDNA added. In contrast to functionalized nanoparticles which showed a max attachment efficiency of 99.6% dependent of pDNA concentration and the method of functionalization. The conjugate did not influence the viability and they improved the transfection efficiency. Results suggest that these nanoparticles are easy to prepare, inexpensive, and exhibit potential for plasmid delivery as it improves transfection efficiency of pDNA vaccines.

Polymeric Delivery of Therapeutic Nucleic Acids

The advent of genome editing has transformed the therapeutic landscape for several debilitating diseases, and the clinical outlook for gene therapeutics has never been more promising. The therapeutic potential of nucleic acids has been limited by a reliance on engineered viral vectors for delivery. Chemically defined polymers can remediate technological, regulatory, and clinical challenges associated with viral modes of gene delivery. Because of their scalability, versatility, and exquisite tunability, polymers are ideal biomaterial platforms for delivering nucleic acid payloads efficiently while minimizing immune response and cellular toxicity. While polymeric gene delivery has progressed significantly in the past four decades, clinical translation of polymeric vehicles faces several formidable challenges. The aim of our Account is to illustrate diverse concepts in designing polymeric vectors towards meeting therapeutic goals of in vivo and ex vivo gene therapy. Here, we highlight several classes of polymers employed in gene delivery and summarize the recent work on understanding the contributions of chemical and architectural design parameters. We touch upon characterization methods used to visualize and understand events transpiring at the interfaces between polymer, nucleic acids, and the physiological environment. We conclude that interdisciplinary approaches and methodologies motivated by fundamental questions are key to designing high-performing polymeric vehicles for gene therapy.

Novel indole-thiazole and indole-thiazolidinone derivatives as DNA groove binders

In this study, we report the synthesis of eight novel indole-thiazole and indole-thiazolidinone derivatives, as well as their ability to interact with DNA, analysed through the UV-vis absorption, fluorescence, circular dichroism (CD), viscosity techniques and molecular docking. The ctDNA interaction analysis demonstrated different spectroscopic effects and the affinity constants (Kb) calculated by the UV-vis absorption method were between 2.08 × 10⁵ and 6.99 × 10⁶ M^-1, whereas in the fluorescence suppression constants (Ksv) ranged between 0.38 and 0.77 × 10⁴ M^-1 and 0.60-7.59 × 10⁴ M^-1 using Ethidium Bromide (EB) and 4',6-Diamidino-2-phenylindole (DAPI) as fluorescent probes, respectively. Most derivatives did not alter significantly the secondary structure of the ctDNA according to the CD results. None of the compounds was able to change the relative viscosity of the ctDNA. These results prove that compounds interact with ctDNA via groove binding, which was confirmed by A-T rich oligonucleotide sequence assay with compound JF-252, suggesting the importance of both the phenyl ring coupled to C-4 thiazole ring and the bromo-unsubstituted indole nucleus.

Molecular complexes of calf thymus DNA with various bioactive compounds: Formation and characterization

The interaction between biomacromolecules and ligands has attracted great interest because of their biological properties. Calf thymus DNA (ctDNA) can interact with bioactive compounds to form complexes. Here, ctDNA-ligand complexes were studied using fluorescence, absorption, and infrared spectroscopy, circular dichroism, ABTS assay and competitive displacement. The binding constants of bioactive compounds at the intercalative site of ctDNA ranked in order kaempferol > apigenin > quercetin > curcumin > riboflavin, while the binding constants at minor groove sites ranked quercetin > kaempferol > naringenin ~ apigenin > hesperetin > curcumin ~ resveratrol ~ riboflavin > caffeic acid. CtDNA maintained stable B-form with an enhancement of base stacking and a decrease of right-handed helicity in the presence of these bioactive compounds, except for hesperetin and caffeic acid. Bioactive compounds preferentially bound to guanine bases and tended to transfer into a more hydrophobic environment upon complexation with ctDNA. The DNA complexation did not affect the ABTS·⁺ scavenging capacity of quercetin, kaempferol, resveratrol and apigenin but increased the ones of naringenin, caffeic acid, curcumin, hesperetin and riboflavin. The data gathered here should be useful to understand the binding modes of DNA with ligands for their potential application in pharmaceutical and food industries.

Probing the Strength and Mechanism of Binding Between Amifampridine and Calf Thymus DNA

In this work, we have investigated the strength and mechanism of amifampridine (3,4-Diaminopyridine/3,4-DAP) interaction with calf thymus DNA (ct-DNA). The existence and the strength of interaction are evaluated using circular dichroism (CD), UV-vis absorption, and differential pulse voltammogram studies. Results from UV-vis absorption technique indicate that amifampridine can significantly interact with DNA through a binding constant of Kb = 1.66 × 105 M-1 at 298 K. The mechanism of the interaction between amifampridine and DNA is also studied using ionic effect investigations, competitive fluorescence experiments, viscosity measurements, and molecular docking studies. The viscosity results indicate that amifampridine can bind to DNA via intercalation binding mode. Competitive fluorescence experiments using Acridine Orange (AO) and Hoechst 33258 (HO) probes also reveal that amifampridine binds to DNA via an intercalation mode of binding. Finally, the molecular docking studies also suggest that amifampridine tends to bind with the G-C rich region of DNA.

Sodium valproate (VPA) interactions with DNA and histones

Valproic acid/sodium valproate (VPA) constitutes a widely prescribed drug for the treatment of seizure disorders and is a well-known epigenetic agent, inducing the acetylation of histones and affecting the methylation status of DNA and histones, with consequences on gene expression. Because this drug has been recently reported to exert affinity for histone H1, and to a minor degree for DNA, in this work, we investigated a possible interaction of sodium valproate with DNA and histones H1 and H3 using high-performance polarization microscopy and Fourier-transform infrared (FTIR) microspectroscopy. The preparations under examination consisted of hemispheres resulting from drop-casting samples containing VPA-DNA and VPA-histone mixtures. The results indicated that VPA may interact with DNA and histones, inducing changes in the textural superstructure and molecular order of the DNA possibly through van der Waals forces, and in histone H1 and H3 conformations, probably as a result of electrostatic binding between the drug and protein amino acid residues. These results contribute to a better understanding of the pharmacological potential of VPA. The precise sites and mechanisms involved in these interactions would certainly benefit from investigations provided by complementary methodologies.

Chitosan-Based Coacervate Polymers for Propolis Encapsulation: Release and Cytotoxicity Studies

Chitosan-DNA (CS-DNA) and Chitosan-Pectin (CS-P) hydrogels were formulated as a sustained drug delivery carrier for drug delivery. For this, hydrogels were prepared by emulsion technique: mixing aqueous phase of the CS and DNA or P solution with benzyl alcohol using a high-performance dispersing instrument. Green Propolis (GP) was incorporated by imbibition: hydrogels were placed in GP aqueous solution (70 µg/mL) for 2 h. The specimens were freeze-dried and then characterized using different techniques. In vitro cell viability and morphology were also performed using the MG63 cell line. The presence of P was evidenced by the occurrence of a strong band at 1745 cm-1, also occurring in the blend. DNA and CS-DNA showed a strong band at 1650 cm-1, slightly shifted from the chitosan band. The sorption of GP induced a significant modification of the gel surface morphology and some phase separation occurs between chitosan and DNA. Drug release kinetics in water and in saliva follow a two-step mechanism. Significant biocompatibility revealed that these hydrogels were non-toxic and provided acceptable support for cell survival. Thus, the hydrogel complexation of chitosan with DNA and with Pectin provides favorable micro-environment for cell growth and is a viable alternative drug delivery system for Green Propolis.

Elucidating the interaction of aminophylline with calf thymus DNA using multispectroscopic and molecular docking approach

Aminophylline (Am) is a methylxanthine compound clinically applied for chronic lung diseases like asthma, bronchitis or emphysema. Chemically, it comprises theophylline and ethylenediamine in a ratio 2:1. For the widening of the therapeutic window of any class of drug or for the designing of the newer therapeutic compound, an insight into the binding mechanics of available drugs with DNA is quite imperative. In view of that, here in this study we have investigated binding mechanics of aminophylline molecule with calf thymus DNA (Ct-DNA) using various spectroscopic techniques as well as molecular docking approach. Spectral analysis employing UV-visible and fluorescence approach confirmed the formation of aminophylline-Ct-DNA complex. The binding constant was calculated as 3.5 × 10⁴ M^-1 with 0.90 as the value of binding site suggestive of minor groove binding mode of aminophylline. The groove binding mode was further confirmed through spectrofluorimetric experiments like competitive displacement assay employing ethidium bromide, hoechst and rhodamine 6 G dyes as well as iodide quenching studies. The circular dichroic spectral evaluation and molecular docking study finally validated the minor groove binding mode of aminophylline with binding energy calculated as -4.5 Kcal/mol.

Highly Selective Fluorescence Sensing and Imaging of ATP Using a Boronic Acid Groups-Bearing Polythiophene Derivate

A boronic acid groups-bearing polythiophene derivate (L) was designed and synthesized for highly sensitive fluorescence detection of ATP based on a multisite-binding coupled with analyte-induced aggregation strategy. L has a polythiophene backbone as fluorophores and two functional side groups, i.e., quaternary ammonium group and boronic acid group, as multibinding sites for ATP. When various structural analogues such as ADP, AMP, and various inorganic phosphates were added into the aqueous solution of L, only ATP caused a remarkable fluorescence quenching of about 60-fold accompanied by obvious color changes of solution from yellow to purple. The detection limit is estimated to be 2 nM based on 3σ/slope. With the advantage of good water solubility, low toxicity, and highly selective response to ATP, L was successfully utilized as a probe to real-time assay activity of adenylate kinase (ADK) and map fluorescent imaging of ATP in living cells.

RNA targeting by an anthracycline drug: spectroscopic and in silico evaluation of epirubicin interaction with tRNA

Anthracyclines are putative anticancer agents used to treat a wide range of cancers. Among these anthracyclines, epirubicin is derived from the doxorubicin by the subtle difference in the orientation of C4-hydroxyl group at sugar molecule. Epirubicin has great significance as it has propitious anticancer potential with lesser cardiotoxicity and faster elimination from the body. The present study is done to understand the molecular aspect of epirubicin binding to tRNA. We have used various spectroscopic techniques like Fourier transform infrared spectroscopy (FTIR), absorption spectroscopy and circular dichroism to illustrate the binding sites, the extent of binding and conformational changes associated with tRNA after interacting with epirubicin. From infrared studies, we infer that epirubicin interacts with guanine and uracil bases of tRNA. Results obtained from infrared and CD studies suggest that epirubicin complexation with tRNA does not result in any conformational change in tRNA structure. Binding constant (2.1 × 10³ M^-1) calculated from the absorbance data illustrates that epirubicin has a weak interaction with tRNA molecule. These spectroscopic results like the binding site of epirubicin and binding energy of epirubicin-tRNA complex were also verified by the molecular docking. Results of the present study provide information that aids in the development of efficient RNA targeted drugs from the existing drugs by certain chemical modification in their structure resulting in lesser side effects and better efficacy.Communicated by Ramaswamy H. Sarma.

Eu3+ as a luminescence probe in DNA studies: Structural and conformational implications

Lanthanide ions are widely used as luminescent probes for structural studies of various biomolecules, including DNA. Latest developments of circularly polarized luminescence (CPL) methodology further boosted interest to luminescence techniques. However, an effect of the lanthanide probes themselves on the DNA structure and conformation was investigated only partially and not for all lanthanides. In the present work, we performed a detailed spectroscopic study of Eu³⁺ complexes with native double-stranded DNA and compared them to the relevant complexes with single-stranded DNA. We employed infrared (IR), vibrational circular dichroism (VCD) and electronic circular dichroism (ECD) spectroscopic methods to investigate Eu³⁺ effect on DNA structure and conformational transitions. It was shown that Eu³⁺ ions can induce significant alteration of the native DNA structure at the concentrations often used in luminescence studies. While no DNA denaturation was observed at these metal ion concentrations, significant unstacking of the base pairs and disordering of the sugar-phosphate backbone, partial appearance of the A-form backbone geometry, and DNA transition into condensed ψ-type form took place. Eu³⁺ binding to single-stranded DNA was more pronounced than the binding to double-stranded DNA. We detected the main Eu³⁺ binding sites and determined the metal ion concentration range in which DNA geometry remains largely unaltered. The results obtained in the current study could be used for tuning the luminescence and CPL structural studies of DNA utilizing Eu³⁺ ions as probes.

New Insights into the Interactions of a DNA Oligonucleotide with mPEGylated-PAMAM by Circular Dichroism and Solution NMR

Dendrimers are well-defined, highly branched, synthetic three-dimensional molecules with a large number of reactive end groups. PAMAM dendrimers form stable complexes with DNA chemistries and constitute an important class of nonviral, cationic vectors in gene delivery. The aim of this study is to examine the interactions of a 12 bp DNA oligonucletide with PAMAM-G2 and mPEG- b-PAMAM-G3 having eight surface amine groups under physiological conditions, using constant DNA concentration but varying dendrimer concentration. 1D ³¹P NMR, 2D NOESY, and CD spectroscopic methods were employed to investigate the interactions between the dendrimer and the DNA. The CD experiments carried out with a constant DNA concentration of 25 μM and dendrimer concentrations from 0 to 100 μM indicated minimal change to the chirality of the DNA for both types of dendrimers. While the PAMAM-G2 dendrimer caused aggregation of the majority of the DNA, the 2D NMR data of the DNA with an mPEG- b-PAMAM-G3 dendrimer indicated general broadening of the 1D ³¹P peaks from the DNA phosphates, a small number of ¹H chemical shift perturbations (CSPs), and reduction of specific ¹H-¹H NOE intensities. These data suggest there is minimal structural alteration of the DNA in the complex and indicate preferential binding of the dendrimer to the central AATT region of the DNA sequence. The results herein are the first such results demonstrating a soluble DNA complex with the mPEG- b-PAMAM-G3 dendrimer analyzed by multidimensional NMR.

PAMAM dendrimers as efficient drug and gene delivery nanosystems for cancer therapy

Drug delivery systems for cancer chemotherapy are employed to improve the effectiveness and decrease the side-effects of highly toxic drugs. Most chemotherapy agents have indiscriminate cytotoxicity that affects normal, as well as cancer cells. To overcome these problems, new more efficient nanosystems for drug delivery are increasingly being investigated. Polyamidoamine (PAMAM) dendrimers are an example of a versatile and reproducible type of nanocarrier that can be loaded with drugs, and modified by attaching target-specific ligands that recognize receptors that are over-expressed on cancer cells. PAMAM dendrimers with a high density of cationic charges display electrostatic interactions with nucleic acids (DNA, siRNA, miRNA, etc.), creating dendriplexes that can preserve the nucleic acids from degradation. Dendrimers are prepared by conducting several successive "generations" of synthetic reactions so their size can be easily controlled and they have good uniformity. Dendrimers are particularly well-suited to co-delivery applications (simultaneous delivery of drugs and/or genes). In the current review, we discuss dendrimer-based targeted delivery of drugs/genes and co-delivery systems mainly for cancer therapy.

Screening and investigation of triplex DNA binders from Stephania tetrandra S. Moore by a combination of peak area-fading ultra high-performance liquid chromatography with orbitrap mass spectrometry and optical spectroscopies

The identification and screening of triplex DNA binders are important because these compounds, in many cases, are potential anticancer agents as well as promising drug candidates. Therefore, the ability to screen for these compounds in a high-throughput mode could dramatically improve the drug screening process. A method involving a combination of 96-well plate format and peak area-fading ultra high-performance liquid chromatography coupled with Orbitrap mass spectrometry was employed for screening bioactive compounds binding to the triplex DNA from the extracts of Stephania tetrandra S. Moore. Two compounds were screened out and identified as fangchinoline and tetrandrine based on the comparison of retention time and tandem mass spectrometry data with those of standards. The binding mechanisms of fangchinoline and tetrandrine at the molecular level were explored using tandem mass spectrometry, fluorescence spectroscopy, ultraviolet-visible spectroscopy, and circular dichroism. Collision-induced dissociation experiments showed that the complexes with fangchinoline and tetrandrine were dissociated by ligand elimination. According to these measurements, an intercalating binding is the most appropriate binding mode of these two alkaloids to the triplex DNA. The current work provides not only deep insight into alkaloid-triplex DNA complexes but also useful guidelines for the design of efficient anticancer agents.

Modifications of quinolones and fluoroquinolones: hybrid compounds and dual-action molecules

ABSTRACT

This review is aimed to provide extensive survey of quinolones and fluoroquinolones for a variety of applications ranging from metal complexes and nanoparticle development to hybrid conjugates with therapeutic uses. The review covers the literature from the past 10 years with emphasis placed on new applications and mechanisms of pharmacological action of quinolone derivatives. The following are considered: metal complexes, nanoparticles and nanodrugs, polymers, proteins and peptides, NO donors and analogs, anionic compounds, siderophores, phosphonates, and prodrugs with enhanced lipophilicity, phototherapeutics, fluorescent compounds, triazoles, hybrid drugs, bis-quinolones, and other modifications. This review provides a comprehensive resource, summarizing a broad range of important quinolone applications with great utility as a resource concerning both chemical modifications and also novel hybrid bifunctional therapeutic agents.

GRAPHICAL ABSTRACT

Effect of Dendrigraft Generation on the Interaction between Anionic Polyelectrolytes and Dendrigraft Poly(l-Lysine)

In this present work, three generations of dendrigraft poly(l-Lysine) (DGL) were studied regarding their ability to interact with linear poly (acrylamide-co-2-acrylamido-2-methyl-1-propanesulfonate) (PAMAMPS) of different chemical charge densities (30% and 100%). Frontal analysis continuous capillary electrophoresis (FACCE) was successfully applied to determine binding constants and binding stoichiometries. The effect of DGL generation on the interaction was evaluated for the first three generations (G2, G3, and G4) at different ionic strengths, and the effect of ligand topology (linear PLL vs. dendrigraft DGL) on binding parameters was evaluated. An increase of the biding site constants accompanied with a decrease of the DGL-PAMAMPS (n:1) stoichiometry was observed for increasing DGL generation. The logarithm of the global binding constants decreased linearly with the logarithm of the ionic strength. This double logarithmic representation allowed determining the extent of counter-ions released from the association of DGL molecules onto one PAMAMPS chain that was compared to the total entropic reservoir constituted by the total number of condensed counter-ions before the association.

Synthesis and characterisation of arsenic nanoparticles and its interaction with DNA and cytotoxic potential on breast cancer cells

Therapeutic applications of arsenic trioxide (ATO) are limited due to their severe adverse effects. However, nanoparticles of ATO might possess inimitable biologic effects based on their structure and size which differ from their parent molecules. Based on this conception, AsNPs were synthesized from ATO and comparatively analysed for their interaction mechanism with DNA using spectroscopic & electrochemical techniques. Finally, anti-proliferative activity was assessed against different breast cancer cells (MDA-MB-231 & MCF-7) and normal non-cancerous cells (HEK-293). The DNA interaction study revealed that AsNPs and ATO exhibit binding constant values in the order of 10⁶ which indicates strong binding interaction. Binding of AsNPs did not disturb the structural integrity of DNA, on the other hand an opposing effect was observed with ATO through biophysical techniques. Further, in vitro study, confirms cytotoxicity of ATO and AsNPs against different cells, however at particular concentration ATO exhibits more cytotoxicity than that of AsNPs. Furthermore, cytotoxicity was confirmed through acridine orange and comet assay. In conclusion, AsNPs are safer than ATO with comparable efficacy and might be a suitable candidate for the development of novel therapeutic agent against breast cancer and other solid tumours.

Collapse of DNA in packaging and cellular transport

The dawn of molecular biology and recombinant DNA technology arose from our ability to manipulate DNA, including the process of collapse of long extended DNA molecules into nanoparticles of approximately 100 nm diameter. This condensation process is important for the packaging of DNA in the cell and for transporting DNA through the cell membrane for gene therapy. Multivalent cations, such as natural polyamines (spermidine and spermine), were initially recognized for their ability to provoke DNA condensation. Current research is targeted on molecules such as linear and branched polymers, oligopeptides, polypeptides and dendrimers that promote collapse of DNA to nanometric particles for gene therapy and on the energetics of DNA packaging.

Study on the interaction between the 1,4,5,8-naphthalene diimide-spermine conjugate (NDIS) and DNA using a spectroscopic approach and molecular docking

The interaction of herring sperm DNA with the 1,4,5,8-naphthalene diimide-spermine conjugate (NDIS) was studied by UV/vis absorption, fluorescence and CD spectroscopic methods. Compared with the 1,8-naphthalimide-spermidine conjugate (NIS), the values of KSV (quenching constant) and Kb (binding constant) of NDIS were larger, and the hypochromic effect in the UV/vis spectra and the quenching effect in the fluorescence of NDIS were more significant. The interaction mode between NDIS and DNA was mainly groove binding. The fluorescence experiments at varying temperatures showed that the binding process of NDIS and DNA was static, as both hydrogen bonds and hydrophobic forces played a major role in the binding of NDIS and DNA. The CD spectrum indicated that NDIS caused a conformational change, like the B to A-DNA transition, and the tests using KI and NaCl and 1H NMR spectroscopy indicated that NDIS was not a classical DNA inserter. All the results demonstrated that both the polyamine side chain and the aromatic rings affect the process of NDIS binding to DNA, which is thus obviously different from that of NIS. The conclusion was confirmed by the in silico molecular docking experiments.

Monitoring wheat mitochondrial compositional and respiratory changes using Fourier transform mid-infrared spectroscopy in response to agrochemical treatments

Fungicides and plant growth regulators can impact plant growth outside of their effects on fungal pathogens. Although many of these chemicals are inhibitors of mitochondrial oxygen uptake, information remains limited as to whether they are able to modify other mitochondrial constituents. Fourier transform mid-infrared spectroscopy (FT-mIR) offers a high sample throughput method to comparatively and qualitatively evaluate the effects of exogenously added compounds on mitochondrial components. Therefore the objective of this study was to determine the ability of FT-mIR to detect effects mitochondrial fractions isolated from wheat (Triticum aestivum L.) seedlings in response to several agrochemical treatments, with an emphasis on fungicides. The accessed need was to develop FT-mIR analytical and statistical routines as an effective approach to differentiate spectra obtained from chemically-treated or untreated mitochondria. An NADH-dependent oxygen uptake approach was initially used as a comparative method to determine whether the fungicides (azoxystrobin, boscalid, cyazofamid, fluazinam, isopyrazam, and pyraclostrobin) and the plant growth regulator, (trinexapac-ethyl) reduced respiration inhibition on isolated mitochondria. Pyraclostrobin was the most effective inhibitor, whereas amisulbrom did not impact oxygen uptake. However, hierarchical clustering of FT-mIR spectra of isolated mitochondria treated with these different compounds separated into clades consistent with each of their expected mode of action. Analysis of the FT-mIR amide protein region indicated that amisulbrom and pyraclostrobin interacted with the isolated wheat mitochondria. Both chemicals were statistically different from the control signifying that respiration was indeed influenced by these treatments. Moreover, the entire FT-mIR region showed differences in various biological bands thereby providing additional information on mitochondria responses to agrochemicals, if so warranted.

A new FRET-based ratiometric probe for fluorescence and colorimetric analyses of adenosine 5′-triphosphate

A new ratiometric probe for ATP was designed based on the binding-induced modulation of FRET coupled with the ACQ sensing mechanism.

Interactions of a biocompatible water-soluble anthracenyl polymer derivative with double-stranded DNA

We have studied the interaction of a polymeric water soluble anthracenyl derivative () with salmon testes DNA. The results from UV-Vis, fluorescence, Fourier transform infrared (FT-IR) and circular dichroism spectroscopies indicate that the groove binding process regulates the interaction between and DNA. The binding constants, calculated by absorption spectroscopy at 298, 304 and 310 K, were equal to 3.2 × 10(5) M(-1), 4.7 × 10(5) M(-1), and 6.6 × 10(5) M(-1) respectively, proving a relatively high affinity of for salmon testes DNA. Results of Hoechst 33258 displacement assays strongly support the groove binding mode of to DNA. The association stoichiometry of the :DNA adduct was found to be 1 for every 5 base pairs. FT-IR spectra, recorded at different /DNA molar ratios, indicate the involvement of the phosphate groups and adenine and thymine DNA bases in the association process. Thermodynamic results suggest that hydrophobic forces regulate the binding of with DNA without excluding some extent of involvement of van der Waals forces and hydrogen bonding arising due to surface binding between the hydrophilic polymeric arms of the ligand and the functional groups positioned on the edge of the groove. The resulting composite biomaterial could constitute a valuable candidate for future biological and/or photonic applications.

Recent progress in gene therapy to deliver nucleic acids with multivalent cationic vectors

Due to the potential use as transfecting agents of nucleic acids (DNA or RNA), multivalent cationic non-viral vectors have received special attention in the last decade. Much effort has been addressed to synthesize more efficient and biocompatible gene vectors able to transport nucleic acids into the cells without provoking an immune response. Among them, the mostly explored to compact and transfect nucleic acids are: (a) gemini and multivalent cationic lipids, mixed with a helper lipid, by forming lipoplexes; and (b) cationic polymers, polycations, and polyrotaxanes, by forming polyplexes. This review is focused on the progress and recent advances experimented in this area, mainly during the present decade, devoting special attention to the lipoplexes and polyplexes, as follows: (a) to its biophysical characterization (mainly electrostatics, structure, size and morphology) using a wide variety of experimental methods; and (b) to its biological activity (transfection efficacy and cytotoxicity) addressed to confirm the optimum formulations and viability of these complexes as very promising gene vectors of nucleic acids in nanomedicine.