Critical assessment of interactions between ct-DNA and choline-based magnetic ionic liquids: evidences of compaction

Ionic liquids (ILs) have become an alternative green solvent for storage and for stability of DNA. However, an in-depth understanding of binding and molecular interactions between ILs and DNA is needed. In this respect, magnetic ILs (MILs) are promising due to their tunable physicochemical properties. Various spectroscopic techniques and molecular simulations have been employed to unravel the critical factors of the strength and binding mechanism of MILs with DNA. UV-vis spectra unravel the multimodal binding of MILs with DNA, and the intrusion of IL molecules into the minor groove of DNA has been observed from dye displacement studies. Fluorescence correlation spectroscopic studies and scanning electron microscopy confirm the compaction of the DNA. ITC and molecular docking studies estimate the binding affinity of DNA with MILs, of ∼7 kcal mol-1. The 1 μs long-MD simulations give insight into the structural changes in the DNA in the MIL environment. Due to strong interaction with choline ions in the close vicinity, DNA helixes bend or squeeze in length and dilate in diameter (elliptical → spherical), leading to compaction. The post-MD parameters suggest a stronger interaction with [Ch]2[Mn] IL than with [Ch][Fe] IL; hence, the former induces DNA compaction to a more significant extent. Furthermore, decompaction is observed with the addition of sodium salts and is characterized using spectroscopic methods.

Rigidification-Induced Emissive Metal-Carbene Complexes for Artificial Light Harvesting

A tetraphenylethylene (TPE)-based flexible imidazolium (L) salt was used to develop a di-nuclear silver(I)-tetracarbene (1) complex. Coordination-induced rigidity upon formation of 1 exhibited a 6-fold increase in emission intensity in acetonitrile compared to starting L. Despite TPE being a well-known aggregation-induced emissive moiety, Ag^I-N-heterocyclic carbene (NHC) complex 1 had a remarkably higher fluorescence emission (4-fold) in dilute solution when compared with L in its aggregated state. Finally, this enhanced emission was used to institute a new platform for an artificial light-harvesting system. 1 acted as an energy donor and efficiently transferred energy to Eosin Y (ESY) with a high saturation at a 67:1 (1/ESY) molar ratio. Use of rigidification-induced emission of the Ag^I-NHC complex to fabricate a light-harvesting scaffold is a new approach and can greatly impact the generation of smart materials.

Gradient Nanoconfinement Facilitates Binding of Transcriptional Factor NF-κB to Histone- and Protamine-DNA Complexes

Mechanically induced chromosome reorganization plays important roles in transcriptional regulation. However, the interplay between chromosome reorganization and transcription activities is complicated, such that it is difficult to decipher the regulatory effects of intranuclear geometrical cues. Here, we simplify the system by introducing DNA, packaging proteins (i.e., histone and protamine), and transcription factor NF-κB into a well-defined fluidic chip with changing spatical confinement ranging from 100 to 500 nm. It is uncovered that strong nanoconfinement suppresses higher-order folding of histone- and protamine-DNA complexes, the fracture of which exposes buried DNA segments and causes increased quantities of NF-κB binding to the DNA chain. Overall, these results reveal a pathway of how intranuclear geometrical cues alter the open/closed state of a DNA-protein complex and therefore affect transcription activities: i.e., NF-κB binding.

DNA condensation and formation of ultrathin nanosheets via DNA assisted self-assembly of an amphiphilic fullerene derivative

DNA nanotechnology propose various assembly strategies to develop novel functional nanostructures utilizing unique interactions of DNA with small molecules, nanoparticles, polymers, and other biomolecules. Although, well defined nanostructures of DNA and amphiphilic small molecules were achieved through hybridization of covalently modified DNA, attaining precise organization of functional moieties through non-covalent interactions remain as a challenging task. Herein, we report mutually assisted assembly of an amphiphilic fullerene derivative and various DNA structures through non-covalent interactions, which leads to initial DNA condensation and subsequent assembly yielding ordered fullerene-DNA nanosheets. The molecular design of the cationic, amphiphilic fullerene derivative (FPy) ensures molecular solubility in the 10% DMSO-PBS buffer system and facile interactions with DNA through groove binding and electrostatic interactions of fullerene moiety and positively charged pyridinium moiety, respectively. The formation of FPy/DNA nanostructures were thoroughly investigated in the presence of λ-DNA, pBR322 plasmid DNA, and single and double stranded 20-mer oligonucleotides using UV-visible spectroscopy, AFM and TEM analysis. λ-DNA and pBR322 plasmid DNA readily condense in presence of FPy leading to micrometer sized few layer nanosheets with significant crystallinity due to ordered arrangement of fullerenes. Similarly, single and double stranded 20-mer oligonucleotides also interact efficiently with FPy and form highly crystalline nanosheets, signifying the role of electrostatic interaction and subsequent charge neutralization in the condensation triggered assembly. However, there is significant differences in the crystallinity and ordered arrangements of fullerenes between these two cases, where longer DNA form condensed structures and less ordered nanosheets while short oligonucleotides lead to more ordered and highly crystalline nanosheets, which could be attributed to the differential DNA condensation. Finally, we have demonstrated the addressability of the assembly using a cyanine modified single strand DNA, which also forms highly crystalline nanosheets and exhibit efficient quenching of the cyanine fluorescence upon self-assembly. These results open up new prospects in the development of functional DNA nanostructures through non-covalent interactions and hence have potential applications in the context of DNA nanotechnology.

How to Prepare Kinetically Stable Self-assembled Pt12 L24 Nanocages while Circumventing Kinetic Traps

Supramolecular coordination-based self-assembled nanostructures have been widely studied, and currently various applications are being explored. For several applications, the stability of the nanostructure is of key importance, and this strongly depends on the metal used in the self-assembly process. Herein, design strategies and synthetic protocols to access desirable kinetically stable Pt12 L24 nanospheres are reported, and it is demonstrated that these are stable under conditions under which the palladium counterparts decompose. Descriptors previously used for palladium nanospheres are insufficient for platinum analogues, as the stronger metal-ligand bond results in a mixture of kinetically trapped structures. We report that next to the dihedral angle, the rigidity of the ditopic ligand is also a key parameter for the controlled formation of Pt12 L24 nanospheres. Catalytic amounts of coordinating additives to labilise the platinum-pyridyl bond to some extent are needed to selectively form Pt12 L24 assemblies. The formed Pt12 L24 nanospheres were demonstrated to be stable in the presence of chloride, amines and acids, unlike the palladium analogues.

Boronated Condensed DNA as a Heterochromatic Radiation Target Model

The compound 4-dihydroxyboryl-l-phenylalanine (BPA) has found use in clinical trials of boron neutron capture therapy (BNCT). Here, we have examined the interaction with DNA of an amide-blocked BPA derivative of hexa-l-arginine (Ac-BPA-Arg6-NH2). Physical and spectroscopic assays show that this peptide binds to and condenses DNA. The resulting condensates are highly resistant to the effects of nuclease incubation (68-fold) and gamma (38-fold) irradiation. Radioprotection was modeled by Monte Carlo track structure simulations of DNA single strand breaks (SSBs) with TOPAS-nBio. The differences between experimental and simulated SSB yields for uncondensed and condensed DNAs were ca. 2 and 18%, respectively. These observations indicate that the combination of a plasmid DNA target, the BPA-containing peptide, and track structure simulation provides a powerful approach to characterize DNA damage by the high-LET radiation associated with neutron capture on boron.

Hierarchical Assemblies of Supramolecular Coordination Complexes

Hierarchical self-assembly (HAS) is a multilevel organization process that first assembles elementary molecular units into ordered secondary structures via noncovalent interactions, which further act as the building blocks to form more complex multifunctional superstructures at the next level(s). The HAS strategy has been used as a versatile method for the preparation of soft-matter nanoarchitectures of defined size and morphologies, tunable luminescence, and biological importance. However, such preparation can be greatly simplified if well-defined dynamic structures are employed as the cores that upon linking form the desired nanoarchitectures. Discrete supramolecular coordination complexes (SCCs) with well-defined shapes, sizes, and internal cavities have been widely employed to construct hierarchical systems with functional diversity. This Account summarizes the prevailing strategies used in recent years in the preparation of SCC-based HASs and illustrates how the combination of dynamic metal-ligand coordination with other interactions was used to obtain hierarchical systems with interesting properties. HASs with dual orthogonal interactions involving coordination-driven self-assembly and hydrogen bonding/host-guest interaction generally result in robust and flexible supramolecular gels. Likewise, hybridization of SCCs with a suitable dynamic covalent network via a hierarchical strategy is useful to prepare materials with self-healing properties. The intrinsic positive charges of the SCCs also make them suitable precursors for the construction of HASs via electrostatic interactions with negatively charged biological/abiological molecules. Furthermore, the interplay between the hydrophilic and lipophilic characters of HASs by varying the number and spacial orientation of alkyl/oxyethylene chains of the SCC is a simple yet controllable approach to prepare ordered and tunable nanostructures. Certain SCC-cored hierarchical systems exhibit reversible polymorphism, typically between micellar, nanofiber, and vesicular phases, in response to various external perturbations: heat, photoirradiation, pH-variance, redox-active agents, etc. At the same time, multiple noncovalent interaction mediated HASs are growing in numbers and are promising candidates for obtaining functionally diverse materials. The photophysical properties of SCC-based HASs have been used in many analytical applications. For example, embedding tetraphenylethene (TPE)-based pyridyl ligands within metallo-supramolecular structures partially restricts the molecular rotations of its phenyl rings, endowing the resultant SCCs with weak emissions. Further aggregation of such HASs in suitable solvents results in a marked enhancement in emission intensity along with quantum yields. They act as sensitive sensors for different analytes, including pathogens, drugs, etc. HASs are also useful to develop multidrug systems with cooperative chemotherapeutic effects. Hence, the use of HASs with theranostic SCCs combining cell-imaging agents and chemotherapeutic scaffolds is a promising drug delivery strategy for cancer theranostics. At the same time, their responsiveness to stimuli, oftentimes due to the dynamic nature of the metal-ligand interactions, play an important role in drug release via a disassembly mechanism.

Synthetic Approach to biomolecular science by cyborg supramolecular chemistry

BACKGROUND

To imitate the essence of living systems via synthetic chemistry approaches has been attempted. With the progress in supramolecular chemistry, it has become possible to synthesize molecules of a size and complexity close to those of biomacromolecules. Recently, the combination of precisely designed supramolecules with biomolecules has generated structural platforms for designing and creating unique molecular systems. Bridging between synthetic chemistry and biomolecular science is also developing methodologies for the creation of artificial cellular systems.

SCOPE OF REVIEW

This paper provides an overview of the recently expanding interdisciplinary research to fuse artificial molecules with biomolecules, that can deepen our understanding of the dynamical ordering of biomolecules.

MAJOR CONCLUSIONS AND GENERAL SIGNIFICANCE

Using bottom-up approaches based on the precise chemical design, synthesis and hybridization of artificial molecules with biological materials have been realizing the construction of sophisticated platforms having the fundamental functions of living systems. The effective hybrid, molecular cyborg, approaches enable not only the establishment of dynamic systems mimicking nature and thus well-defined models for biophysical understanding, but also the creation of those with highly advanced, integrated functions. This article is part of a Special Issue entitled "Biophysical Exploration of Dynamical Ordering of Biomolecular Systems" edited by Dr. Koichi Kato.

Block Co-PolyMOCs by Stepwise Self-Assembly

We report a stepwise assembly strategy for the integration of metal-organic cages (MOCs) into block copolymers (BCPs). This approach creates "block co-polyMOC" (BCPMOC) materials whose microscopic structures and mechanical properties are readily tunable by adjusting the size and geometry of the MOCs and the composition of the BCPs. In the first assembly step, BCPs functionalized with a pyridyl ligand on the chain end form star-shaped polymers triggered by metal-coordination-induced MOC assembly. The type of MOC junction employed precisely determines the number of arms for the star polymer. In the second step, microphase separation of the BCP is induced, physically cross-linking the star polymers and producing the desired BCPMOC networks in the bulk or gel state. We demonstrate that large spherical M12L24 MOCs, small paddlewheel M2L4 MOCs, or a mixture of both can be incorporated into BCPMOCs to provide materials with tailored branch functionality, phase separation, microdomain spacing, and mechanical properties. Given the synthetic and functional diversity of MOCs and BCPs, our method should enable access to BCPMOCs for a wide range of applications.

A Simple Zn2+ Complex-Based Composite System for Efficient Gene Delivery

Metal complexes might become a new type of promising gene delivery systems because of their low cytotoxicity, structural diversity, controllable aqua- and lipo-solubility, and appropriate density and distribution of positive charges. In this study, Zn2+ complexes (1-10) formed with a series of ligands contained benzimidazole(bzim)were prepared and characterized. They were observed to have different affinities for DNA, dependent on their numbers of positive charges, bzim groups, and coordination structures around Zn2+. The binding induced DNA to condensate into spherical nanoparticles with ~ 50 nm in diameter. The cell transfection efficiency of the DNA nanoparticles was poor, although they were low toxic. The sequential addition of the cell-penetrating peptide (CPP) TAT(48-60) and polyethylene glycol (PEG) resulted in the large DNA condensates (~ 100 nm in diameter) and the increased cellular uptake. The clathrin-mediated endocytosis was found to be a key cellular uptake pathway of the nanoparticles formed with or without TAT(48-60) or/and PEG. The DNA nanoparticles with TAT(48-60) and PEG was found to have the cell transfection efficiency up to 20% of the commercial carrier Lipofect. These results indicated that a simple Zn2+-bzim complex-based composite system can be developed for efficient and low toxic gene delivery through the combination with PEG and CPPs such as TAT.

Bridging Adhesion of a Protein onto an Inorganic Surface Using Self-Assembled Dual-Functionalized Spheres

For the bridging adhesion of different classes of materials in their intact functional states, the adhesion of biomolecules onto inorganic surfaces is a necessity. A new molecular design strategy for bridging adhesion was demonstrated by the introduction of two independent recognition groups on the periphery of spherical complexes self-assembled from metal ions (M) and bidentate ligands (L). These dual-functionalized M12L24 spheres were quantitatively synthesized in one step from two ligands, bearing either a biotin for streptavidin recognition or a titania-binding aptamer, and Pd(II) ions. The selective recognition of titania surfaces was achieved by ligands with hexapeptide aptamers (Arg-Lys-Leu-Pro-Asp-Ala: minTBP-1), whose fixation ability was enhanced by the accumulation effect on the surface of the M12L24 spheres. These well-defined spherical structures can be specifically tailored to promote interactions with both titania and streptavidin simultaneously without detrimentally affecting either recognition motif. The irreversible immobilization of the spheres onto titania was revealed quantitatively by quartz crystal microbalance measurements, and the adhesion of streptavidin to the titania surface mediated by the biotin surrounding the spheres was visually demonstrated by lithographic patterning experiments.

A dendritic nano-sized hexanuclear ruthenium(II) complex as a one- and two-photon luminescent tracking non-viral gene vector

Fluorescent tracking gene delivery could provide us with a better understanding of the critical steps in the transfection process. However, for in vivo tracking applications, a small diameter (<10 nm) is one of the rigorous requirements for tracking vectors. Herein, we have demonstrated a new paradigm for two-photon tracking gene delivery based on a dendritic nano-sized hexanuclear ruthenium(II) polypyridyl complex. Because this metallodendrimer has a multivalent periphery, the complex, which is 6.1 nm, showed high stability and excellent dispersibility and could stepwise condense DNA in vitro. With the outstanding photochemical properties of Ru(II) polypyridyl, this complex could track gene delivery in vivo using one- and two-photon imaging.

Shape-tailored colloidal molecules obtained by self-assembly of model gold nanoparticles with flexible polyelectrolyte

We study for the first time the structure of stable finite size clusters (i.e., colloidal molecules) obtained by self-assembly of cationic gold nanoparticles (i.e., atoms) mediated by a flexible polyanion. We reveal with nondenaturizing techniques a striking structural transition from 1D small chains of 12 gold nanoparticles (AuNPs) with a self-avoiding conformation to 3D fractal clusters of 130 AuNPs with short-range ordering around the charge inversion threshold. Interestingly, these well-defined structures are obtained by simple mixing in water without anisotropic functionalization or external forces. As a preliminary step, we introduce a new synthesis pathway leading to well-defined cationic AuNPs of controllable size that can be dispersed in H2O or D2O without aggregation and ligands' self-assemblies. On this occasion, we point for the first time that usual procedures do not enable to eliminate cationic ligands' self-assemblies that could play an undesired role in AuNPs' self-assembly through electrostatic interactions.

Organometallic rotaxane dendrimers with fourth-generation mechanically interlocked branches

Mechanically interlocked molecules, such as catenanes, rotaxanes, and knots, have applications in information storage, switching devices, and chemical catalysis. Rotaxanes are dumbbell-shaped molecules that are threaded through a large ring, and the relative motion of the two components along each other can respond to external stimuli. Multiple rotaxane units can amplify responsiveness, and repetitively branched molecules--dendrimers--can serve as vehicles for assembly of many rotaxanes on single, monodisperse compounds. Here, we report the synthesis of higher-generation rotaxane dendrimers by a divergent approach. Linkages were introduced as spacer elements to reduce crowding and to facilitate rotaxane motion, even at the congested periphery of the compounds up to the fourth generation. The structures were characterized by 1D multinuclear ((1)H, (13)C, and (31)P) and 2D NMR spectroscopy, MALDI-TOF-MS, gel permeation chromatography (GPC), and microscopy-based methods including atomic force microscopy (AFM) and transmission electron microscopy (TEM). AFM and TEM studies of rotaxane dendrimers vs. model dendrimers show that the rotaxane units enhance the rigidity and reduce the tendency of these assemblies to collapse by self-folding. Surface functionalization of the dendrimers with ferrocenes as termini produced electrochemically active assemblies. The preparation of dendrimers with a well-defined topological structure, enhanced rigidity, and diverse functional groups opens previously unidentified avenues for the application of these materials in molecular electronics and materials science.

A Green Solvent Induced DNA Package

Mechanistic details of DNA compaction is essential blue print for gene regulation in living organisms. Many in vitro studies have been implemented using several compaction agents. However, these compacting agents may have some kinds of cytotoxic effects to the cells. To minimize this aspect, several research works had been performed, but people have never focused green solvent, i.e. room temperature ionic liquid as DNA compaction agent. To the best of our knowledge, this is the first ever report where we have shown that guanidinium tris(pentafluoroethyl)trifluorophosphate (Gua-IL) acts as a DNA compacting agent. The compaction ability of Gua-IL has been verified by different spectroscopic techniques, like steady state emission, circular dichroism, dynamic light scattering and UV melting. Notably, we have extensively probed this compaction by Gua-IL through field emission scanning electron microscopy (FE-SEM) and fluorescence microscopy images. We also have discussed the plausible compaction mechanism process of DNA by Gua-IL. Our results suggest that Gua-IL forms a micellar kind of self aggregation above a certain concentration (≥1 mM), which instigates this compaction process. This study divulges the specific details of DNA compaction mechanism by a new class of compaction agent, which is highly biodegradable and eco friendly in nature.

Nanoscale metallogel via self-assembly of self-assembled trinuclear coordination rings: multi-stimuli-responsive soft materials

A multi-stimuli-responsive metallogel is obtained by the self-assembly of an already self-assembled trinuclear palladium(ii) based coordination ring of the rare M₃L₆ composition.