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.

Programmable Assembly of Iron Oxide Nanoparticles Using DNA Origami

Magnetic iron oxide nanoparticles (IONPs) have received significant interest for the use in biomedical applications. The assembly of IONPs into larger superstructures has been used to modify the properties and functionality of these particles. For example, the clustering of IONPs can lead to improvements in MRI contrast generation, changes in heat generation during magnetic fluid hyperthermia, and alterations to pharmacokinetics and biodistribution. Nevertheless, the IONP clustering leads to significant heterogeneity in the assembly. Here, we demonstrate a method for using DNA origami to precisely control the number and positions of IONPs. We also showed how this technique can be used to module the functionality of IONP clusters by showing how MRI contrast generation efficiency can be tuned by altering the number and spacing of IONPs. Finally, we show that these property changes can be dynamically regulated, demonstrating the possibility for this technology to be used in biosensing applications.

PEGylated Bilirubin-coated Iron Oxide Nanoparticles as a Biosensor for Magnetic Relaxation Switching-based ROS Detection in Whole Blood

Rationale: Magnetic relaxation switching (MRSw) induced by target-triggered aggregation or dissociation of superparamagnetic iron oxide nanoparticles (SPIONs) have been utilized for detection of diverse biomarkers. However, an MRSw-based biosensor for reactive oxygen species (ROS) has never been documented.

Methods: To this end, we constructed a biosensor for ROS detection based on PEGylated bilirubin (PEG-BR)-coated SPIONs (PEG-BR@SPIONs) that were prepared by simple sonication via ligand exchange. In addition, near infra-red (NIR) fluorescent dye was loaded onto PEG-BR@SPIONs as a secondary option for fluorescence-based ROS detection.

Results: PEG-BR@SPIONs showed high colloidal stability under physiological conditions, but upon exposure to the model ROS, NaOCl, in vitro, they aggregated, causing a decrease in signal intensity in T2-weighted MR images. Furthermore, ROS-responsive PEG-BR@SPIONs were taken up by lipopolysaccharide (LPS)-activated macrophages to a much greater extent than ROS-unresponsive control nanoparticles (PEG-DSPE@SPIONs). In a sepsis-mimetic clinical setting, PEG-BR@SPIONs were able to directly detect the concentrations of ROS in whole blood samples through a clear change in T2 MR signals and a 'turn-on' signal of fluorescence.

Conclusions: These findings suggest that PEG-BR@SPIONs have the potential as a new type of dual mode (MRSw-based and fluorescence-based) biosensors for ROS detection and could be used to diagnose many diseases associated with ROS overproduction.

Size-Tunable Targeting-Triggered Nanophotosensitizers Based on Self-Assembly of a Phthalocyanine-Biotin Conjugate for Photodynamic Therapy

Self-assembled phototheranostic nanomaterials used for photodynamic therapy (PDT) have attracted increasing attention owing to their several advantages. Herein, we developed a novel strategy for size-tunable self-assembled nanophotosensitizers for PDT through a simple method. A series of switchable self-assembled nanophotosensitizers (NanoPc90, NanoPc40, NanoPc20, and NanoPc10) of different particle sizes were readily prepared based on an amphiphilic silicon(IV) phthalocyanine (SiPc)-biotin conjugate by regulating the amount of the Cremophor EL surfactant used. The photoactivities, including fluorescence and reactive oxygen species (ROS), of the self-assemblies could be regulated by the particle size. The self-assemblies could be specifically disassembled by tumor-overexpressing biotin receptors, leading to the recovery of quenched photoactivities. Demonstrated by the competitive assay, the self-assemblies were able to enter HepG2 cells through a biotin-receptor-mediated pathway, followed by biotin-receptor-triggered fluorescence recovery at the cellular level. Moreover, the particle size could also affect the in vitro and in vivo PDT effects and tumor targeting. The photocytotoxicity of NanoPc20 against HepG2 cells was more potent compared to that of NanoPc90 because of its strong intracellular fluorescence, higher intracellular ROS generation, and different subcellular localization. In addition, NanoPc20 showed higher in vivo tumor targeting and photodynamic therapeutic efficacy than NanoPc90. This work would provide a valuable reference for the development of self-assembled nanophotosensitizers for cancer diagnosis and therapy.

Synthesis of magnetite hybrid nanocomplexes to eliminate bacteria and enhance biofilm disruption

Bacteria can increase drug resistance by forming bacterial biofilms. Once the biofilm is formed, it becomes difficult to remove or kill the related bacteria completely by antibiotics and other antibacterial agents because these antibacterial agents cannot easily break through the biofilm matrix barrier and reach the internal bacteria. Therefore, we synthesized magnetite hybrid nanocomplexes that can penetrate and disrupt bacterial biofilms. The obtained nanocomposites are composed of multinucleated iron oxides and Ag seeds. The outer iron oxides can help the internal Ag nanoparticles penetrate the bacterial biofilms, hence killing the internal bacteria and disrupting the biofilms. We took advantage of E. coli and P. aeruginosa bacteria to test the antibacterial properties of the magnetite hybrid nanocomplexes. When planktonic E. coli and P. aeruginosa bacteria were incubated with 100 μg mL-1 magnetite hybrid nanocomplexes for 30 min, almost all the bacteria were killed. When the obtained biofilms of E. coli and P. aeruginosa were treated with magnetite hybrid nanocomplexes (10 μg mL-1 and 100 μg mL-1), the survival of E. coli and P. aeruginosa biofilms with a magnetic field showed a big decrease compared with that without a magnetic field. Therefore, the as-synthesized nanocomposites have promising potential as antimicrobial agents for killing bacteria and disrupting biofilms in the presence of a magnetic field, and thus should be further studied for a wide range of antibacterial applications.

Programed Assembly of Nucleoprotein Nanoparticles Using DNA and Zinc Fingers for Targeted Protein Delivery

With a growing number of intracellular drug targets and the high efficacy of protein therapeutics, the targeted delivery of active proteins with negligible toxicity is a challenging issue in the field of precision medicine. Herein, a programed assembly of nucleoprotein nanoparticles (NNPs) using DNA and zinc fingers (ZnFs) for targeted protein delivery is presented. Two types of ZnFs with different sequence specificities are genetically fused to a targeting moiety and a protein cargo, respectively. Double-stranded DNA with multiple ZnF-binding sequences is grafted onto inorganic nanoparticles, followed by conjugation with the ZnF-fused proteins, generating the assembly of NNPs with a uniform size distribution and high stability. The approach enables controlled loading of a protein cargo on the NNPs, offering a high cytosolic delivery efficiency and target specificity. The utility and potential of the assembly as a versatile protein delivery vehicle is demonstrated based on their remarkable antitumor activity and target specificity with negligible toxicity in a xenograft mice model.

DNA-Grafted Poly(acrylic acid) for One-Step DNA Functionalization of Iron Oxide Nanoparticles

Here, we report one-step DNA functionalization of hydrophobic iron oxide nanoparticles (IONPs) using DNA-grafted poly(acrylic acid) (PAA- g-DNA). PAA- g-DNA was synthesized by coupling PAA to amine-modified oligonucleotides via solid-phase amide chemistry, which yielded PAA grafted with multiple DNA strands with high graft efficiencies. Synthesized PAA- g-DNA was utilized as a phase-transfer and DNA functionalization agent for hydrophobic IONPs, taking advantage of unreacted carboxylic acid groups. The resulting DNA-modified IONPs were well dispersed in aqueous solutions and possessed DNA binding properties characteristic of polyvalent DNA nanostructures, showing that this approach provides a simple one-step method for DNA functionalization of hydrophobic IONPs.

Facile fabrication of water-dispersible nanocomposites based on hexa-peri-hexabenzocoronene and Fe3O4 for dual mode imaging (fluorescent/MR) and drug delivery

Water-dispersible, stable and biocompatible dandelion-like Fe₃O₄/HBC@F127 nanocomposites were facilely developed for dual mode imaging (fluorescent/MR) and drug delivery.

The principles and applications of avidin-based nanoparticles in drug delivery and diagnosis

Avidin-biotin interaction is one of the strongest non-covalent interactions in the nature. Avidin and its analogues have therefore been extensively utilized as probes and affinity matrices for a wide variety of applications in biochemical assays, diagnosis, affinity purification, and drug delivery. Recently, there has been a growing interest in exploring this non-covalent interaction in nanoscale drug delivery systems for pharmaceutical agents, including small molecules, proteins, vaccines, monoclonal antibodies, and nucleic acids. Particularly, the ease of fabrication without losing the chemical and biological properties of the coupled moieties makes the avidin-biotin system a versatile platform for nanotechnology. In addition, avidin-based nanoparticles have been investigated as diagnostic systems for various tumors and surface antigens. In this review, we will highlight the various fabrication principles and biomedical applications of avidin-based nanoparticles in drug delivery and diagnosis. The structures and biochemical properties of avidin, biotin and their respective analogues will also be discussed.