Recent developments in the chemistry of deoxyribonucleic acid (DNA) intercalators: principles, design, synthesis, applications and trends

Rod-like D-π-A-π-D Schiff base liquid crystal for continuous ion sensing, live cell imaging, fingerprint imaging and WLED

A series of rod-like D-π-A-π-D Schiff base liquid crystals were synthesized, featuring a BTD central acceptor unit connected to N-trialkoxybenzyl carbazole terminal donor groups through imine linkages at both ends. The series includes hydroxyl-containing derivatives BOH/n (n = 12, 14, 16), hydroxyl-free BH/12, and the corresponding boron complex BOB/12 derived from BOH/12. Among them, BOH/n can self-assemble into the Colrec/c2mm LC phase, while BH/12 can self-assemble into the Colrec/p2mm LC phase, and boron complex BOB/12 can self-assemble into the Colhex/p6mm LC phase. Further compound BOH/n can self-assemble into a luminescent organic gel in organic solvents with wrinkled sheet morphologies. Photophysical studies revealed that all compounds showed J-aggregation form. All compounds except BOB/12 exhibited the AIEE effect. The fluorescence quantum yield in solution and the absolute solid quantum yield of BOB/12, reached as high as 85 % and 41 % respectively which is 14 and 3 times higher than those of the corresponding BOH/12. Based on the ion recognition result of BOH/12, a non-conventional sequential detection method for the identification sequence of Fe3+-Cu2+-Al3+ was constructed and applied successfully as test paper detection. Additionally, BOH/12 was successfully utilized as live cell imaging, potential fingerprint imaging, and white light emitting devices (WLED).

Recent Advances in DNA Origami-Enabled Optical Biosensors for Multi-Scenario Application

Over the past few years, significant progress has been made in DNA origami technology due to the unrivaled self-assembly properties of DNA molecules. As a highly programmable, addressable, and biocompatible nanomaterial, DNA origami has found widespread applications in biomedicine, such as cell scaffold construction, antimicrobial drug delivery, and supramolecular enzyme assembly. To expand the scope of DNA origami application scenarios, researchers have developed DNA origami structures capable of actively identifying and quantitatively reporting targets. Optical DNA origami biosensors are promising due to their fast-to-use, sensitive, and easy implementation. However, the conversion of DNA origami to optical biosensors is still in its infancy stage, and related strategies have not been systematically summarized, increasing the difficulty of guiding subsequent researchers. Therefore, this review focuses on the universal strategies that endow DNA origami with dynamic responsiveness from both de novo design and current DNA origami modification. Various applications of DNA origami biosensors are also discussed. Additionally, we highlight the advantages of DNA origami biosensors, which offer a single-molecule resolution and high signal-to-noise ratio as an alternative to traditional analytical techniques. We believe that over the next decade, researchers will continue to transform DNA origami into optical biosensors and explore their infinite possible uses.

Predominant Binding Mode of Palmatine to DNA

Palmatine is a protoberberine alkaloid, which may produce singlet oxygen under visible light irradiation and binds to DNA. The fact that singlet oxygen activation in palmatine may be triggered by environmental conditions, and in particular its interaction with nucleic acids, makes it a most suitable candidate for photodynamic therapy and DNA-targeted noninvasive anticancer strategies. Despite these remarkable properties, the actual binding mode between palmatine and DNA has not been resolved, yet. Its elucidation has indeed led to contrasting hypotheses. In this contribution, by using long-range molecular dynamic simulations and enhanced sampling approaches, we unequivocally identify that intercalation is the dominant binding mode of palmatine with DNA, from both a thermodynamic and kinetic point of view.

Detoxification of aflatoxin B1 by a Bacillus subtilis spore coat protein through formation of the main metabolites AFQ1 and epi-AFQ1

A variety of important agricultural crops host fungi from the Aspergillus genus can produce cancerogenic secondary metabolites such as aflatoxins. Consequently, novel strategies for detoxification and their removal from food and feed chains are required. Here, detoxification of Aflatoxin B1 (AFB1) by the Bacillus subtilis multi-copper oxidase CotA (BsCotA) was investigated. This laccase was recombinantly produced in E. coli while codon optimization led to duplication of the amount of active protein obtained. CuCl2 was added to the cultivation medium leading to a 25-fold increase of V max corresponding to improved incorporation of Cu2+ into the enzyme protein which is essential for the catalytic reaction. To avoid potential cytotoxicity of Cu2+, cultivation was performed at microaerobic conditions indeed leading to 100x more functional protein when compared to standard aerobic conditions. This was indicated by an increase of V max from 0.30 ± 0.02 to 33.56 ± 2.02 U/mg. Degradation kinetics of AFB1 using HPLC with fluorescence detection (HPLC-FLD) analysis indicated a theoretical substrate saturation above solubility in water. At a relatively high concentration of 500 μg/L, AFB1 was decomposed at 10.75 μg/Lh (0.17 nmol*min-1*mg-1) at a dosage of 0.2 μM BsCotA. AFQ1 and epi-AFQ1 were identified as the initial oxidation products according to mass spectrometry (i.e., HPLC-MS, HPLC-QTOF). None of these molecules were substrates for laccase but both decomposed in buffer. However, decomposition does not seem to be due to hydration of the vinyl ether in the terminal furan ring. Genotoxicity of the formed AFB1 was assessed in several dilutions based on the de-repression of the bacterial SOS response to DNA damage indicating about 80-times reduction in toxicity when compared to AFQ1. The results of this study indicate that BsCotA has high potential for the biological detoxification of aflatoxin B1.

Proper application of DNA dyes in agarose gel electrophoresis

Various dyes are used to visualize DNA bands in agarose gel electrophoresis (AGE) by the methods of pre- or post-staining. The DNA dye user's guides generally state that the binding of the dye to DNA will affect DNA mobility in electrophoresis, thus recommending post-staining for accurate measurement of DNA size. However, many AGE performers prefer pre-staining procedures for reasons such as convenience, real-time observation of DNA bands, and/or the use of a minimal amount of dye. The detrimental effect of the dye on DNA mobility and the associated risk for inaccurate measurement of DNA size are often overlooked by AGE performers. Here we quantitatively determine the impact on DNA migration imposed by frequently used dyes, including GelRed, ethidium bromide (EB), and Gold View. It was observed that pre-staining with GelRed and EB significantly slowed down DNA migration to cause as much as 39.1% overestimation on the size of sample DNA, whereas Gold View had little effect. The slowdown of DNA migration increased with dye concentration until it plateaued when the dye concentration reached a saturated level. Thus, to take advantage of pre-staining, saturated levels of DNA dyes should always be applied for both DNA samples and DNA markers to ensure a fair comparison of DNA sizes. In addition, GelRed and EB display much higher sensitivity than Gold View in the detection of DNA bands in post-staining. The saturated concentrations, cost considerations, and other useful features of these frequently used dyes are summarized for the information of AGE performers.

Evaluation of the Antitumor Effects of Platinum-Based [Pt(η1-C2H4-OR)(DMSO)(phen)]+ (R = Me, Et) Cationic Organometallic Complexes on Chemoresistant Pancreatic Cancer Cell Lines

Pancreatic cancer is one of the most lethal malignancies with an increasing incidence and a high mortality rate, due to its rapid progression, invasiveness, and resistance to anticancer therapies. In this work, we evaluated the antiproliferative and antimigratory activities of the two organometallic compounds, [Pt(η1-C2H4-OMe)(DMSO)(phen)]Cl (1) and [Pt(η1-C2H4-OEt)(DMSO)(phen)]Cl (2), on three human pancreatic ductal adenocarcinoma cell lines with different sensitivity to cisplatin (Mia PaCa-2, PANC-1, and YAPC). The two cationic analogues showed superimposable antiproliferative effects on the tested cells, without significant differences depending on alkyl chain length (Me or Et). On the other hand, they demonstrated to be more effective than cisplatin, especially on YAPC cancer cells. For the interesting cytotoxic activity observed on YAPC, further biological assays were performed, on this cancer cell line, to evaluate the apoptotic and antimetastatic properties of the considered platinum compounds (1 and 2). The cytotoxicity of 1 and 2 compounds appeared to be related to their intracellular accumulation, which was much faster than that of cisplatin. Both 1 and 2 compounds significantly induced apoptosis and cell cycle arrest, with a high accumulation of sub-G1 phase cells, compared to cisplatin. Moreover, phenanthroline-containing complexes caused a rapid loss of mitochondria membrane potential, ΔΨM, if compared to cisplatin, probably due to their cationic and lipophilic properties. On 3D tumor spheroids, 1 and 2 significantly reduced migrated area more than cisplatin, confirming an antimetastatic ability.

Label-free, ultra-low detection limit DNA biosensor using high quality optical microcavity functionalized by DNA tetrahedral nanostructure probes

This study proposes and demonstrates a novel label-free DNA biosensor using high quality optical microcavity functionalized by 3D DNA nanostructure probes. To achieve ultra-low limit DNA biosensing, optical sensing interface of the hollow-core, thin wall-thickness microcavity was functionalized by self-assembled DNA tetrahedral nanostructure (DTN) probes with size of 17 bp and length of ∼5.8 nm. High efficiency binding of the DTN probes with the optical sensor interface and the target ssDNA are achieved. Whispering gallery mode (WGM) spectra with high-Q factor of >107 are excited and traced for DNA detection inside the microfluidic channel of the microcavity, with a small sample volume of nL. Incorporation of nanoscale DTN probes onto surface of the optical microcavity makes it an effective way for increasing efficient probe density and eliminating entanglement between DNA probes, thus ∼1000 times lower detection limit is achieved as compared to using 1D ssDNA probes. Due to its desirable merits of label-free, ultra-low LoD, real time and compact size, the proposed DNA biosensor has broad application prospects in bioengineering and medical diagnosis.

Optimization of aflatoxin B1 removal efficiency of DNA by resonance light scattering spectroscopy

In this paper, firstly, the resonance light scattering spectra of aflatoxin B₁ (AFB₁) and DNA were measured by resonance light scattering spectroscopy (RLS), and the DNA binding saturation value (DBSV) of AFB₁ was calculated from their spectral results. Then the interaction intensity between DNA and AFB₁ and the effects of some external factors on the interaction between DNA and AFB₁ were evaluated by corresponding DBSVs, so as to establish and optimize a way for removing AFB₁ by DNA. DBSV of AFB₁ was 2.04 at 30℃ and pH 7.40. However, after adding sodium ion, calcium ion, vitamin E, vitamin C and D-glucose, DBSV of AFB₁ was changed to 2.72, 3.17, 2.67, 1.68 and 1.33 respectively. Correspondingly, the removal efficiency of AFB₁ by DNA was changed from 90.05% to 93.25%, 95.48%, 93.08%, 82.36% and 78.90% respectively. These results indicated that the external factors had a significant impact on the interaction between DNA and AFB₁. Among them, some factors enhanced the interaction between DNA and AFB₁, while some factors weakened the interaction between DNA and AFB1. The change of these external factors led to the corresponding changes in DBSV and the removal efficiency of AFB₁. DBSV of AFB₁ could really be used as an index to evaluate the intensity of the interaction between DNA and AFB₁, and to optimize the removal efficiency of AFB₁ by DNA. The experimental data also showed that the adsorption of AFB₁ to DNA was consistent with the pseudo-second-order kinetic model and the Freundlich isothermal model, was an exothermic and spontaneous process. All these results will give good references for establishing and optimizing a way of AFB₁ removal via DNA intercalation.

In silico study of HASDI (high-affinity selective DNA intercalator) as a new agent capable of highly selective recognition of the DNA sequence

Cancer as an acquired genetic disease is based on changes both in the genome itself and in transcription processes. Accordingly, it is at the DNA level that it makes sense to search for and design agents capable of effective and selective anticancer action. In this study, we used an iterative approach based on a molecular dynamics simulation to design a highly selective DNA-intercalating agent called HASDI. To confirm its selective affinity to DNA, we conducted two simulation experiments: HASDI in a complex with a DNA fragment of the EBNA1 gene (it targets 16 nucleotide pairs of this gene) and HASDI in a complex with a random DNA fragment of the KCNH2 gene. The molecular dynamics simulation was carried out in the GROMACS 2019 package. The binding energy was calculated by gmx_MMPBSA 1.5.2. The further analysis was performed using the built-in utilities of GROMACS, gmx_MMPBSA and also XMGRACE and Pymol 1.8. As a result, we determined that the EBNA1-50nt/HASDI complex was stable throughout the whole simulation trajectory. HASDI, due to the presence of a linker modified depending on a specific pair of nitrogenous bases, formed an average of 32 hydrogen bonds with a sequence of 16 nucleotide pairs. Phenazine rings were stably intercalated every 2 base pairs. The root-mean-square deviation of HASDI in such a complex fluctuated around the value of 6.5 Å and had no tendency to increase. The calculated value of the binding free energy was - 235.3 ± 7.77 kcal/mol. The KCNH2-50nt/HASDI complex, as an example of the intercalation of the designed structure into a random part of the human genome, maintained the stability of its position at a level comparable to the EBNA1-50nt/HASDI complex. The phenazine rings were constantly intercalated in their original positions, and the root-mean-square deviation fluctuated around one value, although it had a tendency to chaotic changes. At the same time, this complex was characterized by 17-19 hydrogen bonds, on average, and the binding free energy was - 193.47 ± 14.09 kcal/mol. Moreover, the DNA duplex had local single-nucleotide melting in the region of the 4th linker. According to a significant decrease in the number of hydrogen bonds, a decrease in energy gain, as well as a decrease in the stability of the DNA duplex characteristic of the KCNH2-50nt/HASDI complex compared to the target EBNA1-50nt/HASDI complex, the molecule we designed can be considered a potentially selective DNA polyintercalating agent capable of relatively accurate recognition of 16 base pairs.

Bioactivity, molecular docking and anticancer behavior of pyrrolidine based Pt(II) complexes: Their kinetics, DNA and BSA binding study by spectroscopic methods

The complex [Pt(AEP)Cl₂]; C-1 (where, AEP = 1-(2-Aminoethyl) pyrrolidine) and its hydrolyzed diaqua form cis-[Pt(AEP)(H₂O)₂]²⁺; C-2 were synthesized for their bioactivity and in vitro kinetic study with bioactive thiol group (-SH) containing ligands (like; L- cysteine and N-ac-L- cysteine) for their biological importance for 'drug reservoir' activity. The Thermal Gravimetric Analysis (TGA) was executed to confirm about the weight loss due to coordinated water molecules at high temperature range. At pH 4.0, the substitution behavior of C-2 with the thiols was studied in pseudo-first order reaction condition. The interaction mechanism of thiols with complex C-2 to their corresponding thiol substituted C-3 [Pt(AEP)(L-cys)] and C-4 [Pt(AEP)(N-ac-L-cys)] (where L-cys = L-cysteine and N-ac-L-cys = N-ac-L- cysteine) were proposed from their thermodynamical activation parameters (ΔH^≠ and ΔS^≠), which were obtained from Eyring equation. DNA and BSA binding activity of the complexes C-1 to C-4 were investigated by gel electrophoresis technique, spectroscopic titration and viscosity methods. The binding activity of the complexes with DNA and BSA was evaluated using a theoretical approach molecular docking study. The drug-like nature of the complexes is supported by the prediction of activity spectra for substance (PASS) from 2D structure of the Pt(II) complexes. Structural optimization, HOMO-LUMO energy calculation, Molecular electrostatic potential surface, NBO and TD-DFT calculation were executed by using density functional theory (DFT) with Gaussian 09 software package to pre-assessment of biological activity of the complexes. DFT-based descriptors were determined from the HOMO-LUMA energy to be related with the ability of binding affinity of Pt(II) complexes towards DNA and BSA to the formation of their corresponding adducts. The anticancer property of the design complexes were examined on HCT116 (colorectal carcinoma) cancer cell lines and as well as human normal cell NKE (Normal Kidney Epithelial) and compared with the recognised anticancer drug cisplatin. The Reactive Oxygen Species (ROS) production was assessed by DCFDA assay in presence of the Pt(II) complexes.

"Technical Note:" Optimisation of Diamond™ Nucleic Acid Dye preparation, application, and visualisation, for latent DNA detection

A targeted sampling approach of latent DNA, deposited when a person makes contact with a surface, can prove challenging during crime scene or evidence processing, with the sampling of latent DNA often relying on the expert judgement from crime scene officers and forensic examiners. As such, the ability to use the quick and robust screening tool Diamond™ Nucleic Acid Dye (DD) was explored, with a focus on the visualisation of latent DNA on non-porous substrates, namely polypropylene, acrylic, aluminium, PVC composite material, glass, and crystalline silicon. The application of DD was performed according to methods reported in literature, where 10 µL of the dye solution (20-fold dilution of DD in 75% EtOH) was applied onto a variety of non-porous substrates via a micropipette and then subsequently visualised using a portable fluorescence microscope. It was discovered that there was scope for improvement in the reported methods due to the observation of crystal formations on all test substrates upon drying of the DD, resulting in the impaired visualisation of latent DNA and fingerprint detail. Thus, changes to the EtOH water ratio of the dye solution, and changes to the mode of dye application from a micropipette to a spray application, were explored to improve the drying time of the dye and mitigate the formation of crystals. While changes to the EtOH water ratio did not improve the overall drying time, the mode of dye application enhanced visualisation, with a spray application eliminating the formation of crystals no matter the EtOH water ratio. Visualisation with a portable Dino-Lite and Zeiss Widefield fluorescence microscope were also explored, with the Zeiss Widefield fluorescence microscope proving to be useful in whole print imaging and a more efficient imaging tool in a laboratory setting.

Interaction of aflatoxin G1 with free DNA in vitro and possibility of its application in removing aflatoxin G1

The present study sought to evaluate the interaction between aflatoxin G₁ and free DNA in vitro through different analytical techniques. The UV-visible spectra results showed that the structure of DNA might be changed with a new aflatoxin G₁-DNA complex forming, which indicated that the interacting mode between them was the intercalating mode. The DNA melting temperature increased by 12.80 °C, suggesting that the DNA double helix structure was more compact and stable through intercalation. The circular dichroism (CD) spectra results indicated that the interaction of aflatoxin G₁ with DNA induced the DNA base stacking changes. The results of agarose gel electrophoresis and fluorescence microscope further verified that the interacting mode between aflatoxin G₁ and DNA was intercalation mode. According to the fluorescence spectrum data, the binding constant was calculated 6.24 × 10⁴ L·mol^-1. The thermodynamic results demonstrated that the reaction of aflatoxin G₁ intercalating to DNA was a spontaneous reaction. The elimination results suggested that aflatoxin G₁ could be enriched and removed by DNA intercalation through magnetic beads separation, with the removal efficiency of 93.73%. The study results would provide a theoretical basis for establishing a new aflatoxin removal method based on DNA intercalation.

Photochemical synthesis, intercalation with DNA and antitumor evaluation in vitro of benzo[d]thiazolo[3,2-a]quinolin-10-ium derivatives

A new anticancer benzo[d]thiazolo[3,2-a]quinolin-10-ium derivatives were synthesized and characterized. Anticancer evaluation in vitro against four cancer cell lines including adenocarcinomic human alveolar basal epithelial cells (A549), hepatocellular carcinoma (HepG2), prostate cancer (PC3) and breast cancer (MCF7) indicated that some of prepared compounds shows higher selectivity in comparison with doxorubicin. DNA interaction studies by optical, CD, NMR spectroscopies showed the high affinity of benzothiazole ligands towards the dsDNA. The ligand-DNA interaction occurs through the intercalation of benzo[d]thiazolo[3,2-a]quinolin-10-ium derivatives with nucleic acid. The investigation of formed ligand - DNA complexes by docking and molecular dynamic calculations was applied for analysis of the relationship between structure and anticancer activity. The results suggested that benzo[d]thiazolo[3,2-a]quinolin-10-ium derivatives might serve as a novel scaffold for the future development to new antitumor agents.

A Comprehensive Review on Fused Heterocyclic as DNA Intercalators: Promising Anticancer Agents

Since the discovery of DNA intercalating agents (by Lerman, 1961), a growing number of organic, inorganic, and metallic compounds have been developed to treat life-threatening microbial infections and cancers. Fused-heterocycles are amongst the most important group of compounds that have the ability to interact with DNA. DNA intercalators possess a planar aromatic ring structure that inserts itself between the base pairs of nucleic acids. Once inserted, the aromatic structure makes van der Waals interactions and hydrogen-bonding interactions with the base pairs. The DNA intercalator may also contain an ionizable group that can form ionic interactions with the negatively charged phosphate backbone. After the intercalation, other cellular processes could take place, leading ultimately to cell death. The heterocyclic nucleus present in the DNA intercalators can be considered as a pharmacophore that plays an instrumental role in dictating the affinity and selectivity exhibited by these compounds. In this work, we have carried out a revision of small organic molecules that bind to the DNA molecule via intercalation and cleaving and exert their antitumor activity. A general overview of the most recent results in this area, paying particular attention to compounds that are currently under clinical trials, is provided. Advancement in spectroscopic techniques studying DNA interaction can be examined in-depth, yielding important information on structure-activity relationships. In this comprehensive review, we have focused on the introduction to fused heterocyclic agents with DNA interacting features, from medicinal point of view. The structure-activity relationships points, cytotoxicity data, and binding data and future perspectives of medicinal compounds have been discussed in detail.

Novel Cytotoxic Phenanthro-triazine-3-thiol Derivatives as Potential DNA Intercalators and Bcl-2 Inhibitors

Novel phenanthro-triazine-3-thiol derivatives were designed as potential DNA intercalators and Bcl-2 inhibitors. After being synthesized, the compounds were evaluated for their cytotoxic activity against MOLT-4 (human acute lymphoblastic leukemia) and MCF-7 (human breast adenocarcinoma) cells by MTT assay. P1 (bearing hydrogen substitution) was the most potent derivative against MOLT-4 with an IC₅₀ value of 7.1 ± 1.1 μM, whereas P11 (bearing phenyl substitution) demonstrated considerable cytotoxicity against MCF-7 with an IC₅₀ value of 15.4 ± 2.9 μM. Compounds P7, P8, P14 and P15 exhibited moderate cytotoxic effects. Furthermore, to confirm the potential DNA intercalation and Bcl-2 inhibitory activities of phenanthro-triazine scaffolds, molecular docking analysis was performed. Molecular docking studies indicated that these compounds not only bind to DNA by intercalation mainly through stacking interactions but also are well accommodated in the active site of Bcl-2. Therefore, P1 and P11 having phenanthro-triazine-3-thiol scaffold could be presented as cytotoxic agents with dual DNA intercalation and Bcl-2 inhibitory activities.

Removal of 1,2-benzanthracene via the intercalation of 1,2-benzanthracene with DNA and magnetic bead-based separation

In this study, DNA-functionalize-magnetic beads were investigated as sorbent materials for effective removing 1,2-benzanthracene (BaA) from water. In order to reveal the removal mechanism, the interaction mode between BaA and DNA was evaluated by using various characterization tools such as UV-visible and circular dichroism spectroscopy, fluorescence and resonance scattering spectroscopy, and agarose gel electrophoresis. In the presence of BaA, the melting temperature of DNA increased from 76.2 °C to 82.3 °C, which closely related to the intercalating of BaA. It was found that a part of the ethidium bromide (EB) binding sites to DNA were occupied by BaA in EB competing study. The results indicated that a new complex appeared between hsDNA and BaA, and the number of the binding sites (n) and the binding constants (K_A) at different temperatures were obtained. DNA binding saturation value (≈0.80) was obtained by resonance scattering spectra study. BaA could be enriched and removed by DNA-functionalize-magnetic beads via the intercalation, and the removal efficiency was 97.73% when the initial concentration was 2.45 x10^-6mol·L^-1 (559.31 μg/L).

Synthesis of novel calix[4]arene p-benzazole derivatives and investigation of their DNA binding and cleavage activities with molecular docking and experimental studies

In this study, novel p-benzimidazole-derived calix[4]arene compounds with different structures, and a benzothiazole-derived calix[4]arene compound, were synthesized by a microwave-assisted method and their structures were determined by FTIR, 1H NMR, 13C NMR, MALDI-TOF mass spectroscopy, and elemental analysis. The effects of functional calixarenes against bacterial (pBR322 plasmid DNA) and eukaryotic DNA (calf thymus DNA = CT-DNA) were investigated. The studies with plasmid DNA have shown that compounds 6 and 10 containing methyl and benzyl groups, respectively, have DNA cleavage activity at the highest concentrations (10 000 μM). Interactions with plasmid DNA using some restriction enzymes (BamHI and HindIII) were also investigated. The binding ability of p-substituted calix[4]arene compounds towards CT-DNA was examined using UV-vis and fluorescence spectroscopy and it was determined that some compounds showed efficiency. In particular, it was observed that the functional compounds (10 and 5) containing benzyl and chloro-groups had higher activity (K b binding constants were found to be 7.1 × 103 M-1 and 9.3 × 102 M-1 respectively) on DNA than other compounds. Competitive binding experiments using ethidium bromide also gave an idea about the binding properties. Docking studies of the synthesized compounds with DNA were performed to predict the binding modes, affinities and noncovalent interactions stabilizing the DNA-compound complexes at the molecular level. Docking results were in good agreement with the experimental findings on the DNA binding activities of compounds. Based on these results, this preliminary study could shed light on future experimental antibacterial and/or anticancer research.

DNA Origami as Emerging Technology for the Engineering of Fluorescent and Plasmonic-Based Biosensors

DNA nanotechnology is a powerful and promising tool for the development of nanoscale devices for numerous and diverse applications. One of the greatest potential fields of application for DNA nanotechnology is in biomedicine, in particular biosensing. Thanks to the control over their size, shape, and fabrication, DNA origami represents a unique opportunity to assemble dynamic and complex devices with precise and predictable structural characteristics. Combined with the addressability and flexibility of the chemistry for DNA functionalization, DNA origami allows the precise design of sensors capable of detecting a large range of different targets, encompassing RNA, DNA, proteins, small molecules, or changes in physico-chemical parameters, that could serve as diagnostic tools. Here, we review some recent, salient developments in DNA origami-based sensors centered on optical detection methods (readout) with a special emphasis on the sensitivity, the selectivity, and response time. We also discuss challenges that still need to be addressed before this approach can be translated into robust diagnostic devices for bio-medical applications.

Binding characteristics of aflatoxin B1 with free DNA in vitro

In this paper, the binding characteristics of aflatoxin B₁ (AFB₁) with the herring sperm deoxyribonucleic acid (DNA) in vitro were investigated through different analytical methods. The ultraviolet-visible spectroscopy (UV-vis), fluorescence, and circular dichroism (CD) spectra results showed that a new AFB₁-DNA complex was formed. All the results suggested that AFB₁ interacted with free DNA in vitro in an intercalating binding mode. The results of the DNA melting experiments also showed that the melting temperature of DNA increased by about 12.1 °C due to the addition of AFB₁, which was supposed to be closely related to the intercalation of AFB₁ into DNA. The agar gel electrophoresis experiments further confirmed that the binding mode of AFB₁ and free DNA in vitro was indeed intercalation. In addition, the fluorescence quenching induced by adding AFB₁ to the ethidium bromide-DNA (EB-DNA) mixture indicated the presence of competitive non-covalent intercalating binding interaction with a competitive binding constant of 5.58 L/mol between AFB₁, EB, and DNA. The thermodynamic data demonstrated that the main driving forces of the binding reaction were van der Waals forces and hydrogen bond. The resonance light scattering (RLS) assay results showed that the DNA binding saturation values of AFB₁, EB, psoralen (PSO), and angelicin (ANG) were 2.14, 15.59, 0.74, and 0.74, respectively. These results indicated that the DNA binding capacity of AFB₁ was weaker than that of EB, but stronger than those of PSO and ANG.

The 1,10-Phenanthroline Ligand Enhances the Antiproliferative Activity of DNA-Intercalating Thiourea-Pd(II) and -Pt(II) Complexes Against Cisplatin-Sensitive and -Resistant Human Ovarian Cancer Cell Lines

Ovarian cancer is the most lethal gynecological malignancy, often because of the frequent insurgence of chemoresistance to the drugs currently used. Thus, new therapeutical agents are needed. We tested the toxicity of 16 new DNA-intercalating agents to cisplatin (cDDP)-sensitive human ovarian carcinoma cell lines and their resistant counterparts. The compounds were the complexes of Pt(II) or Pd(II) with bipyridyl (bipy) and phenanthrolyl (phen) and with four different thiourea ancillary ligands. Within each of the four series of complexes characterized by the same thiourea ligand, the Pd(phen) drugs invariably showed the highest anti-proliferative efficacy. This paralleled both a higher intracellular drug accumulation and a more efficient DNA intercalation than all the other metal-bidentate ligand combinations. The consequent inhibition of topoisomerase II activity led to the greatest inhibition of DNA metabolism, evidenced by the inhibition of the expression of the folate cycle enzymes and a marked perturbation of cell-cycle distribution in both cell lines. These findings indicate that the particular interaction of Pd(II) with phenanthroline confers the best pharmacokinetic and pharmacodynamic properties that make this class of DNA intercalators remarkable inhibitors, even of the resistant cell growth.

Intercalating Electron Dyes for TEM Visualization of DNA at the Single-Molecule Level

Staining compounds containing heavy elements (electron dyes) can facilitate the visualization of DNA and related biomolecules by using TEM. However, research into the synthesis and utilization of alternative electron dyes has been limited. Here, we report the synthesis of a novel DNA intercalator molecule, bis-acridine uranyl (BAU). NMR spectroscopy and MS confirmed the validity of the synthetic strategy and gel electrophoresis verified the binding of BAU to DNA. For TEM imaging of DNA, two-dimensional DNA origami nanostructures were used as a robust microscopy test object. By using scanning transmission electron microscopy (STEM) imaging, which is favored over conventional wide-field TEM for improved contrast, and therefore, quantitative image analysis, it is found that the synthesized BAU intercalator can render DNA visible, even at the single-molecule scale. For comparison, other staining compounds with a purported affinity towards DNA, such as dichloroplatinum, cisplatin, osmium tetroxide, and uranyl acetate, have been evaluated. The STEM contrast is discussed in terms of the DNA-dye association constants, number of dye molecules bound per base pair, and the electron-scattering capacity of the metal-containing ligands. These findings pave the way for the future development of electron dyes with specific DNA-binding motifs for high-resolution TEM imaging.

Recent Developments in the Interactions of Classic Intercalated Ruthenium Compounds: [Ru(bpy)₂dppz]2+ and [Ru(phen)₂dppz]2+ with a DNA Molecule

[Ru(bpy)₂dppz]²⁺ and [Ru(phen)₂dppz]²⁺ as the light switches of the deoxyribose nucleic acid (DNA) molecule have attracted much attention and have become a powerful tool for exploring the structure of the DNA helix. Their interactions have been intensively studied because of the excellent photophysical and photochemical properties of ruthenium compounds. In this perspective, this review describes the recent developments in the interactions of these two classic intercalated compounds with a DNA helix. The mechanism of the molecular light switch effect and the selectivity of these two compounds to different forms of a DNA helix has been discussed. In addition, the specific binding modes between them have been discussed in detail, for a better understanding the mechanism of the light switch and the luminescence difference. Finally, recent studies of single molecule force spectroscopy have also been included so as to precisely interpret the kinetics, equilibrium constants, and the energy landscape during the process of the dynamic assembly of ligands into a single DNA helix.

Energetic, Topological and Electric Field Analyses of Cation-Cation Nucleic Acid Interactions in Watson-Crick Disposition

A theoretical study of the effect of the diprotonation on the nucleic acid bases (A : U, A : T and G : C) in Watson-Crick conformation has been carried out by means of DFT computational methods in vacuum. In addition, the corresponding neutral and monoprotonated binary complexes have been considered. Most of the diprotonated species studied are stable, even though the binding energy is positive due to the overall repulsive electrostatic term. Local electrostatic attractive forces in the regions of hydrogen bonds (HBs) are responsible for equilibrium geometries, as shown by the electric field lines connecting the electrophilic and nucleophilic sites involved in the HB interactions. Secondary electrostatic effects also affect the assembling of the nucleic acid complexes in either neutral or cationic form. In particular, the electric field lines flowing from electrophilic sites in one base to nucleophilic sites in the other reinforce the linking between them. Hence, when the nucleophilic site concerns the free lone pair of the heteroatom involved in the HB interaction as acceptor, the HB distance shortens. However, if the free lone pair of the HB acceptor interacts with an electrophilic site in the same molecule, the HB distance elongates, weakening the HB interaction. The topological analysis of the electron density distribution in HB regions indicates that neutral, monoprotonated and diprotonated complexes show no differences in the nature of their HB's.

Interactions of Substituted Nitroaromatics with Model Graphene Systems: Applicability of Hammett Substituent Constants To Predict Binding Energies

Applicability of Hammett parameters (σ m and σ p ) was tested in extended π-systems in gas phase. Three different model graphene systems, viz. 5,5-graphene (GR), 3-B-5,5-graphene (3BGR), and 3-N-5,5-graphene (3NGR), were designed as extended π-systems, and interactions of various nitrobenzene derivatives (mainly m- and p-substituted together with some multiple substitutions) on such platforms were monitored using density functional theory (M06/cc-pVDZ, M06/cc-pVTZ, M06/sp-aug-cc-pVTZ) and Møller-Plesset second-order perturbation (MP2/cc-pV-DZ) theory. Offset face to face (OSFF) stackings were found to be the favored orientations, and reasonable correlations were found between binding energies (ΔE B) and the ∑|σ m | values of the substituted nitrobenzenes. It was proposed previously that |σ m | contains information about the substituents' polarizability and controls electrostatic and dispersion interactions. The combination of ∑|σ m | and molar refractivity (as ∑M r) or change in polarizability (Δα: with respect to benzene) of nitrobenzene derivatives generated statistically significant correlation with respect to ΔE B, thereby supporting the hypothesis related to the validity of |σ m | correlations. The |σ p | parameters also maintain similar correlations for the various p-substituted nitrobenzene derivatives together with several multiply-substituted nitrobenzene derivatives. The correlation properties in such cases are similar to the |σ m | cases, and the energy partition analysis for both the situations reveled importance of electrostatic and dispersion contributions in such interactions. The applicability of Hammett parameters was observed previously on the restricted parallel face to face orientation of benzene···substituted benzene systems, and the present results show that such an idea could be used to predict ΔE B values in OSFF orientations, if the scaffolds are designed in such a way that substituted benzene systems cannot escape their π-clouds.

Ultrasonic effect on RuO2 nanostructures prepared by direct calcination of two new Ru(II)-organic supramolecular polymers

Two novel Ru(II) complexes [(η⁶-p-cymene)RuCl(L1)]PF₆ (R1) and [(η⁶-C₆H₆)RuCl(L1)]PF₆ (R3) with ligand (E)-4-(methylthio)-N-((quinolin-2-yl)methylene)benzenamine (L1), were synthesized and investigated using elemental analysis, IR, ¹H NMR, ¹³C NMR spectroscopy and X-ray crystallography. Complexes R1 and R3 have coordination environments with formulated (η⁶-p-cymene)Ru(N₂Cl) and (η⁶-C₆H₆)Ru(N₂Cl) respectively. The thermal stabilities of compounds R1 and R3 were studied by thermal gravimetric (TG) and differential scanning calorimetry (DSC). The binding of the complexes R1 and R3 to calf thymus DNA (CT DNA) was investigated by using electronic absorption spectra, fluorescence and redox behavior studies. Such experimental data showed that there are interactions between complexes and CT-DNA and the nature of this binding is electrostatic interaction type. Calcination of ultrasonic treated R1 and R3 results in the formation of nanoparticles of RuO₂. The nanoparticles were characterized by IR spectroscopy and X-ray diffraction (XRD). Also size and morphology of nanoparticles were investigated by scanning electron microscopy (SEM).

New insights into the mechanism of action of pyrazolo[1,2-a]benzo[1,2,3,4]tetrazin-3-one derivatives endowed with anticancer potential

Due to the scarce biological profile, the pyrazolo[1,2-a]benzo[1,2,3,4]tetrazine-3-one scaffold (PBT) has been recently explored as promising core for potential anticancer candidates. Several suitably decorated derivatives (PBTs) exhibited antiproliferative activity in the low-micromolar range associated with apoptosis induction and cell cycle arrest on S phase. Herein, we selected the most active derivatives and submitted them to further biological explorations to deepen the mechanism of action. At first, a DNA targeting is approached by means of flow Linear Dichroism experiments so as to evaluate how small planar molecules might interact with DNA, including the interference with the catalytic cycle of topoisomerase II and the influence on the cleavable complex stabilization (poisoning effect). In support of the experimental data, in silico studies have been achieved to better understand the chemical space of the interactions. Interestingly some meaningful structural features, useful for further developments, were found. The 8,9-di-Cl substituted derivative revealed as the most effective in the intercalative process, as well as on the inhibition of catalytic activity of topoisomerase II. Predicted ADME studies confirm that PBTs are promising as potential drug candidates.

Synthesis, structure, and biological active evaluation of a new cyclic tetranuclear copper(II) complex bridged both by oxamido and carboxylate groups

A new tetracopper(II) complex bridged both by oxamido and carboxylato groups, namely [Cu₄ (dmaepox)₂ (bpy)₂ ](NO₃ )₂ ·2H₂ O, where H₃ dmaepox and bpy represent N-benzoato-N'- (3-methylaminopropyl)oxamide and 2,2'-bipyridine, was synthesized, and its structure reveals the presence of a centrosymmetric cyclic tetracopper(II) cation assembled by a pair of cis-dmaepox^3- - bridged dicopper(II) units through the carboxylato groups, in which the endo- and exo-copper(II) ions bridged by the oxamido group have a square-planar and a square-pyramidal coordination geometries, respectively. The aromatic packing interactions assemble the complex molecules to a two-dimensional supramolecular structure. The reactivity toward DNA and protein bovine serum albumin (BSA) indicates that the complex can interact with herring sperm DNA through the intercalation mode and the binding affinity is dominated by the hydrophobicity and chelate ring arrangement around copper(II) ions and quenches the intrinsic fluorescence of BSA via a static process. The cytotoxicity of the complex shows selective cancer cell antiproliferative activity.

Elucidating the interaction of sulindac with calf thymus DNA: biophysical and in silico molecular modelling approach

Sulindac is one of the most effective NSAIDs and belongs to the arylalkanoic acid class.

Synthesis and structure of a new trinuclear nickel(II) complex bridged by N-[3-(Dimethylamino)propyl]-N'-(2-hydroxyphenyl)oxamido: in vitro anticancer activities, and reactivities toward DNA and protein

A new trinickel(II) complex bridged by N-[3-(dimethylamino)propyl]- N'-(2-hydroxylphenyl)oxamido (H₃ pdmapo), namely [Ni₃ (pdmapo)₂ (H₂ O)₂ ]⋅4CH₃ OH, was synthesized and characterized by X-ray single-crystal diffraction and other methods. In the molecule, two symmetric cis-pdmapo^3- mononickel(II) complexes as a "complex ligand" using the carbonyl oxygen atoms coordinate to the center nickel(II) ion situated on an inversion point. The Ni···Ni distance through the oxamido bridge is 5.2624(4) Å. The center nickel(II) ion and the lateral ones have octahedral and square-planar coordination geometries, respectively. In the crystal, a three-dimensional supramolecular network dominated by hydrogen bonds is observed. The reactivity toward DNA/protein bovine serum albumin (BSA) revealed that the complex could interact with herring sperm DNA (HS-DNA) through the intercalation mode and quench the intrinsic fluorescence of BSA via a static mechanism. The in vitro anticancer activities suggested that the complex is active against the selected tumor cell lines.

Morphological and Optoelectronic Characteristics of Double and Triple Lanthanide Ion-Doped DNA Thin Films

Double and triple lanthanide ion (Ln(3+))-doped synthetic double crossover (DX) DNA lattices and natural salmon DNA (SDNA) thin films are fabricated by the substrate assisted growth and drop-casting methods on given substrates. We employed three combinations of double Ln(3+)-dopant pairs (Tb(3+)-Tm(3+), Tb(3+)-Eu(3+), and Tm(3+)-Eu(3+)) and a triple Ln(3+)-dopant pair (Tb(3+)-Tm(3+)-Eu(3+)) with different types of Ln(3+), (i.e., Tb(3+) chosen for green emission, Tm(3+) for blue, and Eu(3+) for red), as well as various concentrations of Ln(3+) for enhancement of specific functionalities. We estimate the optimum concentration of Ln(3+) ([Ln(3+)]O) wherein the phase transition of Ln(3+)-doped DX DNA lattices occurs from crystalline to amorphous. The phase change of DX DNA lattices at [Ln(3+)]O and a phase diagram controlled by combinations of [Ln(3+)] were verified by atomic force microscope measurement. We also developed a theoretical method to obtain a phase diagram by identifying a simple relationship between [Ln(3+)] and [Ln(3+)]O that in practice was found to be in agreement with experimental results. Finally, we address significance of physical characteristics-current for evaluating [Ln(3+)]O, absorption for understanding the modes of Ln(3+) binding, and photoluminescence for studying energy transfer mechanisms-of double and triple Ln(3+)-doped SDNA thin films. Current and photoluminescence in the visible region increased as the varying [Ln(3+)] increased up to a certain [Ln(3+)]O, then decreased with further increases in [Ln(3+)]. In contrast, the absorbance peak intensity at 260 nm showed the opposite trend, as compared with current and photoluminescence behaviors as a function of varying [Ln(3+)]. A DNA thin film with varying combinations of [Ln(3+)] might provide immense potential for the development of efficient devices or sensors with increasingly complex functionality.

Discriminating Intercalative Effects of Threading Intercalator Nogalamycin, from Classical Intercalator Daunomycin, Using Single Molecule Atomic Force Spectroscopy

DNA threading intercalators are a unique class of intercalating agents, albeit little biophysical information is available on their intercalative actions. Herein, the intercalative effects of nogalamycin, which is a naturally-occurring DNA threading intercalator, have been investigated by high-resolution atomic force microscopy (AFM) and spectroscopy (AFS). The results have been compared with those of the well-known chemotherapeutic drug daunomycin, which is a non-threading classical intercalator bearing structural similarity to nogalamycin. A comparative AFM assessment revealed a greater increase in DNA contour length over the entire incubation period of 48 h for nogalamycin treatment, whereas the contour length increase manifested faster in case of daunomycin. The elastic response of single DNA molecules to an externally applied force was investigated by the single molecule AFS approach. Characteristic mechanical fingerprints in the overstretching behaviour clearly distinguished the nogalamycin/daunomycin-treated dsDNA from untreated dsDNA—the former appearing less elastic than the latter, and the nogalamycin-treated DNA distinguished from the daunomycin-treated DNA—the classically intercalated dsDNA appearing the least elastic. A single molecule AFS-based discrimination of threading intercalation from the classical type is being reported for the first time.

Mechanisms of small molecule-DNA interactions probed by single-molecule force spectroscopy

There is a wide range of applications for non-covalent DNA binding ligands, and optimization of such interactions requires detailed understanding of the binding mechanisms. One important class of these ligands is that of intercalators, which bind DNA by inserting aromatic moieties between adjacent DNA base pairs. Characterizing the dynamic and equilibrium aspects of DNA-intercalator complex assembly may allow optimization of DNA binding for specific functions. Single-molecule force spectroscopy studies have recently revealed new details about the molecular mechanisms governing DNA intercalation. These studies can provide the binding kinetics and affinity as well as determining the magnitude of the double helix structural deformations during the dynamic assembly of DNA–ligand complexes. These results may in turn guide the rational design of intercalators synthesized for DNA-targeted drugs, optical probes, or integrated biological self-assembly processes. Herein, we survey the progress in experimental methods as well as the corresponding analysis framework for understanding single molecule DNA binding mechanisms. We discuss briefly minor and major groove binding ligands, and then focus on intercalators, which have been probed extensively with these methods. Conventional mono-intercalators and bis-intercalators are discussed, followed by unconventional DNA intercalation. We then consider the prospects for using these methods in optimizing conventional and unconventional DNA-intercalating small molecules.

Fluorescent Labeling of Plasmid DNA and mRNA: Gains and Losses of Current Labeling Strategies

Live-cell imaging has provided the life sciences with insights into the cell biology and dynamics. Fluorescent labeling of target molecules proves to be indispensable in this regard. In this Review, we focus on the current fluorescent labeling strategies for nucleic acids, and in particular mRNA (mRNA) and plasmid DNA (pDNA), which are of interest to a broad range of scientific fields. By giving a background of the available techniques and an evaluation of the pros and cons, we try to supply scientists with all the information needed to come to an informed choice of nucleic acid labeling strategy aimed at their particular needs.

Synthesis and structure elucidation of new μ-oxamido-bridged dicopper(II) complex with in vitro anticancer activity: A combined study from experiment verification and docking calculation on DNA/protein-binding property

A new oxamido-bridged dicopper(II) complex with formula of [Cu2(deap)(pic)2], where H2deap and pic represent N,N'-bis[3-(diethylamino)propyl]oxamide and picrate, respectively, was synthesized and characterized by elemental analyses, molar conductance measurements, IR and electronic spectral study, and single-crystal X-ray diffraction. The crystal structure analyses revealed that the two copper(II) atoms in the dicopper(II) complex are bridged by the trans-deap(2-) ligand with the distances of 5.2116(17)Å, and the coordination environment around the copper(II) atoms can be described as a square-planar geometry. Hydrogen bonding and π-π stacking interactions link the dicopper(II) complex into a three-dimensional infinite network. The DNA/protein-binding properties of the complex are investigated by molecular docking and experimental assays. The results indicate that the dicopper(II) complex can interact with HS-DNA in the mode of intercalation and effectively quench the intrinsic fluorescence of protein BSA by 1:1 binding with the most possible binding site in the proximity of Trp134. The in vitro anticancer activities suggest that the complex is active against the selected tumor cell lines, and IC50 values for SMMC-7721 and HepG2 are lower than cisplatin. The effects of the electron density distribution of the terminal ligand and the chelate ring arrangement around copper(II) ions bridged by symmetric N,N'-bis(substituted)oxamides on DNA/BSA-binding ability and in vitro anticancer activity are preliminarily discussed.