Biological and catalytic evaluation of Ru(II)‐p‐cymene complexes of Schiff base ligands: Impact of ligand appended moiety on photo‐induced DNA and protein cleavage,cytotoxicity and C‐H activation

Two organometallic Ru(II)‐p‐cymene complexes of the type [Ru(η⁶‐p‐cymene)(L)Cl]PF₆ 1 and 2 , where L is N,N‐bis(4‐isopropylbenzylidene)ethane‐1,2‐diamine (bien, L1 ) or N,N‐bis (pyren‐2‐ylmethylene)ethane‐1,2‐diamine (bpen, L2 ) have been prepared and characterized well. Because of appended pyrenyl groups in coordinated bpen ligand, the complex 2 exhibits higher DNA and protein binding than complex 1 in which isopropylbenzyl groups are incorporated. Interestingly, the luminescent characteristic complex 2 is unique in displaying DNA cleavage after light activation by UVA light at 365 nm through oxygen dependent mechanism. AFM analysis attests the photo‐induced DNA fragmentation ability of complex 2 . Also, the complex 2 cleaves the protein after light exposure in a non‐specific manner suggesting that it can act as a protein photo cleaving agent. In contrast to the trend of DNA and protein interaction of complexes, the complex 1 exhibits cytotoxic activity against human breast carcinoma ( MCF‐7 ) and liver carcinoma ( HepG2 ) with potency higher than that of complex 2 due to enhanced hydrophobicity of isopropyl groups present in p‐cymene and bien ligands. Indeed, complex 2 is inactive against MCF‐7 and HepG2 cancer cell lines even up to 200 μM concentration. The AO/EB staining assay reveals that the complex 1 is able to induce late apoptotic mode of cell death in breast cancer cells, which is further confirmed by inter‐nucleosomal DNA cleavage. Furthermore, the complexes 1 and 2 are evaluated for their catalytic activities and found to be working well for the β‐carboline directed C–H arylation to afford the desired products in good yield (40–47%).     

Ligand Design to Acquire Specificity to Intended G-Quadruplex Structures

A G-quadruplex is a nucleic acid secondary structure that is adopted by guanine-rich sequences, and is considered to be relevant in various pharmacological and biological contexts. G-Quadruplexes have also attracted great attention in the field of DNA nanotechnology because of their extremely high thermal stability and the availability of many defined structures. To date, a large repertory of DNA/RNA G-quadruplex-interactive ligands has been developed by numerous laboratories. Several relevant reviews have also been published that have helped researchers to grasp the full scope of G-quadruplex research from its outset to the present. This review focuses on the G-quadruplex ligands that allow targeting of specific G-quadruplexes. Moreover, unique ligands, successful methodologies, and future perspectives in relation to specific G-quadruplex recognition are also addressed.     

Synthesis,crystal structure,DNA/bovine serum albumin binding and antitumor activity of two transition metal complexes with 4‐acylpyrazolone derivative

Two new complexes, namely [Cu₆L₆] ( 1 ) and [Zn(HL)₂] ( 2 ) (H₂L = N‐(1‐phenyl‐3‐methyl‐4‐propenylidene‐5‐pyrazolone)‐2‐furancarboxylic acid hydrazide), have been synthesized and characterized. Single crystal X‐ray analysis indicates that complex 1 has a hexanuclear structure and complex 2 exhibits a mononuclear structure. The DNA/bovine serum albumin (BSA) binding properties of complexes 1 and 2 were investigated by absorption spectroscopy and fluorescence quenching. Both complexes could effectively intercalate to DNA with calculated quenching constants of 2.6 × 10⁵ and 1.25 × 10⁵ M^?1, respectively. The quenching mechanism of the intrinsic fluorescence of BSA by the complexes was found to be a static one. The cytotoxicities of 1 and 2 were investigated in two human tumor cell lines, human esophageal cancer cells (Eca‐109) and cervical cancer cells (HeLa). Complex 1 exhibits higher antitumor activity than 2 . Furthermore, 1 can inhibit HeLa cells by inducing apoptosis and G0/G1 phase cell cycle arrest. All results demonstrate that 1 and 2 both have DNA/BSA binding capacity and antitumor activity.     

Synthesis,Characterization, Structural Description,Micellization Behavior,DNA Binding Study and Antioxidant Activity of 4, 5 and 6-Coordinated Copper(II) and Zinc(II) Complexes

Four mononuclear copper(II) and zinc(II) complexes were synthesized by the reaction of copper and zinc salts with 3,4-dichlorophenylactic acid, 2-bromophenylactic acid, biphenylacetic acid (O-donor ligand) and bipyridine (N-donor ligands) having the general formulae [(L)₂Cu(bp)(H₂O)] ( 1 ), [(BpA)₂Cu(bp)] ( 2 ), [(L)₂Zn(bp)(H₂O)] ( 3 ) and [(L*)₂Zn(bp)] ( 4 ) (L = 3,4-dichlorophenylacetate, L* = 2-bromophenylacetate bp = bipyridine, and BpA = biphenylacetate). Structures of all compounds were characterized through FT-IR spectroscopy and X-ray diffraction analysis. FT-IR spectra of all complexes confirmed the binding mode of Cu-O and Zn-O. XRD data revealed that complexes 1 – 3 exhibited distorted octahedral arrangement, whereas complex 4 has a distorted tetrahedral environment. Micellization behavior was examined with anionic surfactant (SDS) by conductance measurement as well as absorption spectral analysis. DNA binding study was assessed through viscosity measurement and UV/Vis spectrophotometry. DPPH free radical scavenging assay was measured by UV/Vis spectrophotometry. The results showed nice biological potential of all the complexes.     

In vitro biomolecular interaction studies and cytotoxic activities of copper(II) and zinc(II) complexes bearing ONS donor thiosemicarbazones

Among all the bio‐metals, zinc and copper derivatives of ONS donor thiosemicarbazone have aroused great interest because of their potential biological applications. Multisubstituted thiosemicarbazone ligand H₂dspt (3,5‐dichlorosalicylaldehyde‐N⁴‐phenylthiosemicarbazone) derived new ternary complexes like [Zn(dspt)(phen)]?DMF ( 1 ) and [Cu(dspt)(phen)]?DMF ( 2 ), and another thiosemicarbazone, H₂dsct (3,5‐dichlorosalicylaldehyde‐N⁴‐cyclohexylthiosemicarbazone), derived [Cu(dsct)(bipy)]?DMF ( 3 ). These complexes have been characterized by elemental analysis (CHNS), Fourier transform infrared (FT‐IR), ultraviolet–visible (UV–Vis) and proton nuclear magnetic resonance (¹H‐NMR) spectra. The structures of the complexes were obtained by single‐crystal X‐ray diffraction analysis. Compounds 1 and 2 got crystallized in the monoclinic P2₁/c space group. The complexes showed interesting supramolecular interaction, which in turn stabilizes the complexes. The ground state electronic configurations of the complexes were studied using the B3LYP/LANL2DZ basis set, and ESP plots of complexes were investigated. The interaction of the complexes with calf thymus DNA (CT‐DNA) was studied using absorption and fluorescence spectroscopic methods. A UV study of the interaction of the complexes with calf thymus DNA (CT‐DNA) has shown that the complexes can effectively bind to CT‐DNA, and [Cu(dspt)(phen)]·DMF ( 2 ) exhibited the highest binding constant to CT‐DNA (K_b = 3.7 × 10⁴). Fluorescence spectral studies also indicated that Complex 2 binds relatively stronger with CT DNA through intercalative mode, exhibiting higher binding constant (K_q = 4.7 × 10⁵). The DNA cleavage result showed that the complexes are capable of cleaving the DNA without the help of any external agent. Molecular docking studies were carried out to understand the binding of complexes with the molecular target DNA. Complex 2 exhibited the highest cytotoxicity against human breast cancer cell line MD‐MBA‐231 (IC₅₀ = 23.93 μg/mL) as compared to Complex 1 (IC₅₀ = 44.40 μg/mL) .     

Self-assembled free-floating nanomaterials from sequence-defined polymers

Sequence-defined polymers can be programmed to self-assemble into precise nanostructures for applications in biosensing, drug delivery, optics, and molecular computation. Inspired by the natural self-assembly processes present in biological protein and DNA systems, sets of molecular design rules have emerged across materials classes as instructions to build a variety of tunable structures. This review highlights recent advances in self-assembled sequence-defined and sequence-specific polymers across peptides, peptoids, DNA, and non-biological synthetic materials, with a focus on synthesis, assembly processes and overall structure. Specifically, these self-assembled structures are free-floating, as such constructs can potentially serve as a platform for the aforementioned applications. Emphasis is placed on the molecular design of polymers that self-assemble into zero-dimensional, one-dimensional, two-dimensional, or three-dimensional nanostructures. With the development of automated syntheses and increasing control over self-assembly, future work may focus on emerging classes of compatible hybrid materials with exciting directions toward new architectures and applications.     

Assessing G4-Binding Ligands In Vitro and in Cellulo Using Dimeric Carbocyanine Dye Displacement Assay

G-quadruplexes (G4) are the most actively studied non-canonical secondary structures formed by contiguous repeats of guanines in DNA or RNA strands. Small molecule mediated targeting of G-quadruplexes has emerged as an attractive tool for visualization and stabilization of these structures inside the cell. Limited number of DNA and RNA G4-selective assays have been reported for primary ligand screening. A combination of fluorescence spectroscopy, AFM, CD, PAGE, and confocal microscopy have been used to assess a dimeric carbocyanine dye B6,5 for screening G4-binding ligands in vitro and in cellulo. The dye B6,5 interacts with physiologically relevant DNA and RNA G4 structures, resulting in fluorescence enhancement of the molecule as an in vitro readout for G4 selectivity. Interaction of the dye with G4 is accompanied by quadruplex stabilization that extends its use in primary screening of G4 specific ligands. The molecule is cell permeable and enables visualization of quadruplex dominated cellular regions of nucleoli using confocal microscopy. The dye is displaced by quarfloxin in live cells. The dye B6,5 shows remarkable duplex to quadruplex selectivity in vitro along with ligand-like stabilization of DNA G4 structures. Cell permeability and response to RNA G4 structures project the dye with interesting theranostic potential. Our results validate that B6,5 can serve the dual purpose of visualization of DNA and RNA G4 structures and screening of G4 specific ligands, and adds to the limited number of probes with such potential.     

New insights into the anti-hepatoma mechanism of Alisol G-metal ions complexes based on c-myc DNA

This study investigated the anti-hepatoma molecular mechanism of Alisol G, which is an effective component of the Chinese medicine Alisma orientalis, in the presence of metal ions Cu²⁺ and Fe³⁺ based on c-myc DNA. Here, a combination of Alisol G and metal ions (Cu²⁺, Fe³⁺) to augment anti-hepatoma efficiencies of Alisol G has been identified by methyl thiazolyl tetrazolium (MTT) assay. Network pharmacology revealed that c-myc DNA was the potential target of Alisol G with respect to its anti-hepatoma effects. By performing multi-spectroscopic analyses, we showed that the interaction of Alisol G with c-myc DNA was a process of static quenching. The binding constants and thermodynamic constants indicated that a 1:1 complex was formed between Alisol G and c-myc DNA. Moreover, metal ions strengthened the interaction between Alisol G and c-myc DNA. Molecular docking and molecular dynamics simulation further unveiled that the higher binding affinity between Alisol G-Fe³⁺ complex and c-myc DNA as compared to Alisol G-Cu²⁺ complex. This probably resulted from the polarization of metal ions and the structural flexion of Alisol G. The C22-O31-H76 and C18-O32-H77 of Alisol G were key groups in the interaction with c-myc DNA. Addition of metal ion, had greatly changed the c-myc DNA-binding domain of Alisol G while didn’t affect the kinetic stability of the interaction, thus facilitating the insertion of Alisol G into c-myc DNA A-T base pair. Importantly, the DG113 of c-myc DNA was important for its binding to metal ions. Together, our findings suggested that Alisol G in combination with metal ions may be an efficient and promising option for the treatment of liver cancer.     

Topologically-Interlocked Minicircles as Probes of DNA Topology and DNA-Protein Interactions

DNA minicircles exist in biological contexts, such as kinetoplast DNA, and are promising components for creating functional nanodevices. They have been used to mimic the topological features of nucleosomal DNA and to probe DNA-protein interactions such as HIV-1 and PFV integrases, and DNA gyrase. Here, we synthesized the topologically-interlocked minicircle rotaxane and catenane inside a frame-shaped DNA origami. These minicircles are 183 bp in length, constitute six individual single-stranded DNAs that are ligated to realize duplex interlocking, and adopt temporary base pairing of single strands for interlocking. To probe the DNA-protein interactions, restriction reactions were carried out on DNAs with different topologies such as free linear duplex or duplex constrained inside origami and free or topologically-interlocked minicircles. Except the free linear duplex, all tested structures were resistant to restriction digestion, indicating that the topological features of DNA, such as flexibility, curvature, and groove orientation, play a major role in DNA-protein interactions.     

Multiplasmid DNA in agarose gel electrophoresis: Suitable dye and temperature is essential for prominent profiles

Nucleic acids dye Goldview is widely used in agarose gel electrophoresis (AGE). However, in this study, a sample of multiplasmid DNA (multi-pDNA) stained with Goldview analyzed by AGE showed its instability at low temperature. Three types of DNA samples were analyzed, including linear DNA (ladder), single-plasmid DNA (single-pDNA), and multi-pDNA, electrophoretic conditions were optimized by adjusting the dye, the buffer, and the temperature (1–50°C). The results showed that the light intensity of Gelred is 2.2-times higher than that of Goldview in staining multi-pDNA. Compared with the single-pDNA and the linear DNA, the multi-pDNA stained with Goldview was greatly affected by temperature. This short communication indicated that Gelred is a highly applicable dye for analyzing multiplasmid samples. The degree and the way of binding of Goldview to multi-pDNA are greatly affected by temperature.