DNA–Protein Noncovalent Cross-Linking: Ruthenium Dipyridophenazine Biotin Complex for the Assembly of Proteins and Gold Nanoparticles on DNA Templates

Utilizing peptide-anchored DNA templates for novel programmable nanoparticle assemblies in biological macromolecules: A review

Biological macromolecules such as proteins and DNA are known to self-assemble into various structural moieties with distinct functions. While nucleic acids are the structural building blocks, peptides exemplify diversity as tailorable biochemical units. Thus, combining the scaffold properties of the biomacromolecule DNA and the functionality of peptides could evolve into a powerful method to obtain tailorable nano assemblies. In this review, we discuss the assembly of non-DNA-coated colloidal NPs on DNA/peptide templates using functional anchors. We begin with strategies for directly attaching metallic NPs to DNA templates to ascertain the functional role of DNA as a scaffold. Followed by methods to assemble peptides onto DNA templates to emphasize the functional versatility of biologically abundant DNA-binding peptides. Next, we focus on studies corroborating peptide self-assembling into macromolecular templates onto which NPs can attach to emphasize the properties of NP-binding peptides. Finally, we discuss the assembly of NPs on a DNA template with a focus on the bifunctional DNA-binding peptides with NP-binding affinity (peptide anchors). This review aims to highlight the immense potential of combining the functional power of DNA scaffolds and tailorable functionalities of peptides for NP assembly and the need to utilize them effectively to obtain tailorable hierarchical NP assemblies.

Preparation, Functionalization, Modification, and Applications of Nanostructured Gold: A Critical Review

Gold nanoparticles (Au NPs) play a significant role in science and technology because of their unique size, shape, properties and broad range of potential applications. This review focuses on the various approaches employed for the synthesis, modification and functionalization of nanostructured Au. The potential catalytic applications and their enhancement upon modification of Au nanostructures have also been discussed in detail. The present analysis also offers brief summaries of the major Au nanomaterials synthetic procedures, such as hydrothermal, solvothermal, sol-gel, direct oxidation, chemical vapor deposition, sonochemical deposition, electrochemical deposition, microwave and laser pyrolysis. Among the various strategies used for improving the catalytic performance of nanostructured Au, the modification and functionalization of nanostructured Au produced better results. Therefore, various synthesis, modification and functionalization methods employed for better catalytic outcomes of nanostructured Au have been summarized in this review.

Functionalization of Gold Nanoparticles by Inorganic Entities

The great affinity of gold surface for numerous electron-donating groups has largely contributed to the rapid development of functionalized gold nanoparticles (Au-NPs). In the last years, a new subclass of nanocomposite has emerged, based on the association of inorganic molecular entities (IME) with Au-NPs. This highly extended and diversified subclass was promoted by the synergy between the intrinsic properties of the shell and the gold core. This review-divided into four main parts-focuses on an introductory section of the basic notions related to the stabilization of gold nanoparticles and defines in a second part the key role played by the functionalizing agent. Then, we present a wide range of inorganic molecular entities used to prepare these nanocomposites (NCs). In particular, we focus on four different types of inorganic systems, their topologies, and their current applications. Finally, the most recent applications are described before an overview of this new emerging field of research.

Nanosheets and 2D-nanonetworks by mutually assisted self-assembly of fullerene clusters and DNA three-way junctions

Programmable construction of two dimensional (2D) nanoarchitectures using short DNA strands is of utmost interest in the context of DNA nanotechnology. Previously, we have demonstrated fullerene-cluster assisted self-assembly of short oligonucleotide duplexes into micrometer long, semiconducting nanowires. This report demonstrates the construction of micrometer-sized nanosheets and 2D-nanonetworks from the mutual self-assembly of fullerene nanoclusters with three way junction DNA (3WJ-DNA) and 3WJ-DNA with a 12-mer overhang (3WJ-OH), respectively. The interaction of unique sized fullerene clusters prepared from an aniline appended fullerene derivative, F-An, with two 3WJ-DNAs, namely, 3WJ-20 and 3WJ-30, having 20 and 30 nucleobases, respectively at each strand was characterized using UV-visible absorption, circular dichroism and fluorescence techniques. The morphological characterization of nanosheets embedded with F-An clusters was performed via AFM, TEM and DLS analyses. The programmability and structural tunability of the resultant nanostructures were further demonstrated using 3WJ-OH containing a cytosine rich, single stranded DNA 12-mer overhang, which forms entangled 2D-nanonetwork structures instead of nanosheets due to the differential interaction of F-An nanoclusters with single and duplex strands of 3WJ-OH. Moreover, the selective modification of the cytosine rich sequence present in 3WJ-OH with silver nanoclusters (AgNCs) resulted in significant enhancement in silver nanocluster fluorescence (∼40%) compared to 3WJ-OH/AgNCs owing to the additional stability of AgNCs embedded in 2D nanostructures. This unique strategy of constructing DNA based 2D nanomaterials and their utilization in the integration of functional motifs could find application in the area of DNA nanotechnology and bio-molecular sensing.

Biotin-conjugated tumour-targeting photocytotoxic iron(III) complexes

Iron(III) complexes [FeL(B)] (1-4) of a tetradentate phenolate-based ligand (H3L) and biotin-conjugated dipyridophenazine bases (B), viz. 7-aminodipyrido [3,2-a:2',3'-c]-phenazine (dppza in 1), (N-dipyrido[3,2-a:2',3'-c]-phenazino)amidobiotin (dppzNB in 2), dipyrido [3,2-a:2',3'-c]-phenazine-11-carboxylic acid (dppzc in 3) and 2-((2-biotinamido)ethyl) amido-dipyrido[3,2-a:2',3'-c]-phenazine (dppzCB in 4) are prepared, characterized and their interaction with streptavidin and DNA and their photocytotoxicity and cellular uptake in various cells studied. The high-spin iron(III) complexes display Fe(III)/Fe(II) redox couple near -0.7 V versus saturated calomel electrode in dimethyl sulfoxide-0.1 M tetrabutylammonium perchlorate. The complexes show non-specific interaction with DNA as determined from the binding studies. Complexes with appended biotin moiety show similar binding to streptavidin as that of free biotin, suggesting biotin conjugation to dppz does not cause any loss in its binding affinity to streptavidin. The photocytotoxicity of the complexes is tested in HepG2, HeLa and HEK293 cell lines. Complex 2 shows higher photocytotoxicity in HepG2 cells than in HeLa or HEK293, forming reactive oxygen species. This effect is attributed to the presence of overexpressed sodium-dependent multi-vitamin transporters in HepG2 cells. Microscopic studies in HepG2 cells show internalization of the biotin complexes 2 and 4 essentially occurring by receptor-mediated endocytosis, which is similar to that of native biotin and biotin fluorescein isothiocyanate conjugate.

"Light Switch" Effect Upon Binding of Ru-dppz to Water-Soluble Conjugated Polyelectrolyte Dendrimers

We report the "light switch" effect of [Ru(bpy)2(dppz)](2+) (where bpy = 2,2'-bipyridine and dppz = dipyrido[3,2-a:2',3'-c] phenazine, Ru-dppz) in the presence of anionic conjugated polyelectrolyte dendrimers (CPDs). The metal-to-ligand charge-transfer luminescence from Ru-dppz is efficient in the presence of CPD because the complex is shielded from water by binding to the hydrophobic dendrimer core.

Helical Conjugated Polyelectrolyte Aggregation Induced by Biotin-Avidin Interaction

Fluorescence correlation spectroscopy (FCS) is applied to demonstrate avidin-induced cross-linking in a system consisting of a helical anionic conjugated polyelectrolyte (P1) and a biotin-tetramethylrhodamine (TMR) conjugate (2). In a previous study, we used fluorescence spectroscopy to demonstrate that 2 binds to P1 via intercalation of the TMR chromophore into the P1 helix. Addition of avidin to the P1/2 complex induces little change in the fluorescence of the system; however, FCS reveals a remarkable increase in the diffusion time of the P1/2 complex in the presence of avidin. This change is attributed to supramolecular polymer aggregates produced by cross-link formation between the biotin unit of intercalated 2 and avidin. Atomic force microscopy imaging provides evidence supporting the existence of these aggregates. The highly sensitive FCS method is used to develop a novel sensor for the biotin-avidin interaction, with a detection limit of <100 pM for avidin.

Luminescent Ir(III) complex exclusively made of polypyridine ligands capable of intercalating into calf-thymus DNA

Efficient intercalation of a luminescent Ir(III) complex exclusively made of polypyridine ligands in natural and synthetic biopolymers is reported for the first time. The emission of the complex is largely enhanced in the presence of [poly(dA-dT)(2)] and strongly quenched in the presence of [poly(dG-dC)(2)]. By comparing the emission decays in DNA and in synthetic polynucleotides, it is proposed that the emission quenching of the title compound by guanine residues in DNA is no longer effective over a distance of four dA-dT base pairs.

Intercalation-FRET biosensor with a helical conjugated polyelectrolyte

A biotin-tetramethylrhodamine (biotin-TMR) quencher-ligand interacts with a (phenylene-ethynylene) based helical conjugated polyelectrolyte (poly-1) via intercalation of the TMR unit into the helix. The interaction is signaled by efficient fluorescence resonance energy transfer (FRET) from the polymer to the TMR chromophore. Avidin addition to the poly-1/biotin-TMR intercalation complex does not interrupt FRET, instead resulting in the formation of avidin-biotin "cross-links". Mixing of biotin-TMR with avidin prior to addition of the polymer efficiently disrupts the FRET signal, giving rise to a sensor with a detection limit of 100 pM for avidin. Study of the FRET response as a function of biotin-TMR and avidin concentration affords insight into the interaction of the protein with the poly-1/biotin-TMR intercalation complex.

Two base pair duplexes suffice to build a novel material

Tetrahedral DNA hybrids with tetrakis(p-hydroxyphenyl)methane cores hybridize in a sequence-specific fashion at much higher temperatures than isolated linear duplexes. Dinucleotide DNA arms suffice to induce the formation of a solid at room temperature; this demonstrates the strength of multivalent binding. The graphic shows a view of a modeled assembly.