Supramolecular Architectures of Nucleic Acid/Peptide Hybrids

Intrinsic SERS Fingerprints of Aptamer-Peptide Conjugates for Direct High-Specific Profiling Abnormal Protein Levels in Cancer Patients

Surface-enhanced Raman spectroscopy (SERS) with ultrasensitive vibrational fingerprints enables quick identification and trace detection of various kinds of molecules. But proteins usually have low Raman cross sections and are difficult to generate recognizable signals in direct SERS detection. Recently, nucleic acid-peptide conjugates are emerging with great potential in structuring, assembling, catalyzing, sensing, etc., and the coupling of aptamers further enables superior biological recognition and programmability. Here, we develop the aptamer-peptide conjugates as a new kind of SERS probe for direct high-specific profiling abnormal protein levels in cancer patients. The aptamer conjugated with glutathione (GSH) functions as both the recognition element and the SERS reporters that can simultaneously generate SERS fingerprints of both peptides and nucleic acids. This kind of biocompatible probe appears to have excellent performance in high-salt environments and realizes rapid, simple, and multisignal detection of thrombin (TB). Data-driven soft independent modeling of class analogy (DD-SIMCA) is used to distinguish SERS profiles of actual blood samples and realize the identification and classification of cancer patients. Furthermore, the effect of low-temperature storage time on blood samples is analyzed by tracking the changes of SERS profiles; the results hint that plasma samples stored under 4 °C for more than 2 days could generate false negative results due to TB hydrolysis, which has important implications for clinical sample analysis. This kind of nucleic acid-peptide conjugate provides new ideas for SERS sensing strategy in the future.

Computer simulations as an effective way to distinguish supramolecular nanostructure in cyclic and phenyl alcohols

Molecular dynamics simulations supported by x-ray-diffraction experimental data were utilized to demonstrate how replacing the cyclic ring with the phenyl one in molecules of alcohols significantly differentiates their nanostructure by reducing the number of H-bonded clusters. Besides, molecules in the phenyl alcohols associate themselves in clusters via phenyl ring organization which likely is the result of OH⋯π and π⋯π interactions. Thus, at room temperature, the supramolecular structure of phenyl alcohols is more heterogeneous and governed by the formation of various clusters arising due to three types of interactions, while in cyclic alcohols, the H bonding controls the association of molecules. We believe that our methodology could be applied to better understand the fundamental process of association via H bonding and the competitive aggregation caused by phenyl rings.

Stabilization of Functional DNA Structures with Mild Photochemical Methods

A significant barrier to biological applications of DNA structures is their instability to nucleases. UV-mediated thymine dimerization can crosslink and stabilize DNA nanostructures, but its effect on DNA strand hybridization fidelity and function is unclear. In this work, we first compare a number of methods for DNA irradiation with different wavelengths of light and different photosensitizers. We demonstrate that all approaches can achieve nuclease protection; however, the levels of DNA off-target crosslinking and damage vary. We then describe mild irradiation conditions intended to safeguard DNA against nuclease degradation. We demonstrate up to 25× increase in serum stability while minimizing off-target damage and maintaining functions such as hybridization efficiency, gene silencing, aptamer binding, and DNA nanostructure formation. Our methodology requires no complex instruments beyond a UV light source and no synthetic modification of the DNA itself, allowing for applications in numerous areas of nucleic acid therapy and nanotechnology.

Design of supramolecular hybrid nanomaterials comprising peptide-based supramolecular nanofibers and in situ generated DNA nanoflowers through rolling circle amplification

The artificial construction of multicomponent supramolecular materials comprising plural supramolecular architectures that are assembled orthogonally from their constituent molecules has attracted growing attention. Here, we describe the design and development of multicomponent supramolecular materials by combining peptide-based self-assembled fibrous nanostructures with globular DNA nanoflowers constructed by the rolling circle amplification reaction. The orthogonally constructed architectures were dissected by fluorescence imaging using the selective fluorescence staining procedures adapted to this study. The present, unique hybrid materials developed by taking advantage of each supramolecular architecture based on their peptide and DNA functions may offer distinct opportunities to explore their bioapplications as a soft matrix.

Tuning dynamic DNA- and peptide-driven self-assembly in DNA-peptide conjugates

DNA-peptide conjugates offer an opportunity to marry the benefits of both biomolecular classes, combining the high level of programmability found with DNA, with the chemical diversity of peptides. These hybrid systems offer potential in fields such as therapeutics, nanotechnology, and robotics. Using the first DNA-β-turn peptide conjugate, we present three studies investigating the self-assembly of DNA-peptide conjugates over a period of 28 days. Time-course studies, such as these have not been previously conducted for DNA-peptide conjugates, although they are common in pure peptide assembly, for example in amyloid research. By using aging studies to assess the structures produced, we gain insights into the dynamic nature of these systems. The first study explores the influence varying amounts of DNA-peptide conjugates have on the self-assembly of our parent peptide. Study 2 explores how DNA and peptide can work together to change the structures observed during aging. Study 3 investigates the presence of orthogonality within our system by switching the DNA and peptide control on and off independently. These results show that two orthogonal self-assemblies can be combined and operated independently or in tandem within a single macromolecule, with both spatial and temporal effects upon the resultant nanostructures.

Biomimetic and Biological Nanoarchitectonics

A post-nanotechnology concept has been assigned to an emerging concept, nanoarchitectonics. Nanoarchitectonics aims to establish a discipline in which functional materials are fabricated from nano-scale components such as atoms, molecules, and nanomaterials using various techniques. Nanoarchitectonics opens ways to form a more unified paradigm by integrating nanotechnology with organic chemistry, supramolecular chemistry, material chemistry, microfabrication technology, and biotechnology. On the other hand, biological systems consist of rational organization of constituent molecules. Their structures have highly asymmetric and hierarchical features that allow for chained functional coordination, signal amplification, and vector-like energy and signal flow. The process of nanoarchitectonics is based on the premise of combining several different processes, which makes it easier to obtain a hierarchical structure. Therefore, nanoarchitectonics is a more suitable methodology for creating highly functional systems based on structural asymmetry and hierarchy like biosystems. The creation of functional materials by nanoarchitectonics is somewhat similar to the creation of functional systems in biological systems. It can be said that the goal of nanoarchitectonics is to create highly functional systems similar to those found in biological systems. This review article summarizes the synthesis of biomimetic and biological molecules and their functional structure formation from various viewpoints, from the molecular level to the cellular level. Several recent examples are arranged and categorized to illustrate such a trend with sections of (i) synthetic nanoarchitectonics for bio-related units, (ii) self-assembly nanoarchitectonics with bio-related units, (iii) nanoarchitectonics with nucleic acids, (iv) nanoarchitectonics with peptides, (v) nanoarchitectonics with proteins, and (vi) bio-related nanoarchitectonics in conjugation with materials.

Programmed Macromolecular Assembly by Dipole-Dipole Interactions with Aggregation-Induced Enhanced Emission in Aqueous Medium

Self-assembling polymers by bioinspired directional supramolecular interactions currently hold great scientific and technological interests. Herein, we report an unorthodox strategy based on a dipole-dipole interaction-mediated extended antiparallel dipolar assembly of a model merocyanine (MC) dye for maneuvering the self-assembly of a highly water-soluble MC-functionalized block copolymer (P2). Unlike traditional amphiphilic block copolymers featuring distinct hydrophobic segments (flexible aliphatic hydrocarbon chains or rigid nonpolar aromatic scaffolds), P2 comprises polyethylene glycol monomethyl ether (PEG) as a hydrophilic block and an unconventional structure-directing acrylate block functionalized with polar MC-dyes in the side chains of every repeat unit. In the absence of any additional hydrophobic assistance, P2 spontaneously self-assembles in water through the continuous opposite alignment of its pendant MCs by multiple dipole-dipole interactions to cancel out their ground state dipole moments, which initially generates an H-aggregated species with ill-defined morphology (Aggregate 1). Upon thermal annealing, Aggregate 1 reorganizes into higher-order core-shell nanodisc-like structures (Aggregate 2) driven by the orthogonal π-stacking interactions of the rigid aromatic framework derived from the extended cofacial MC-stacks. The aromatic interiors of the nanodiscs gain colloidal stability from the externally decorated hydrophilic PEG chains. While the initially formed Aggregate 1, predominantly by dipole-dipole interactions, showed remarkable thermal stability due to the cooperative effect of the polymer chain, the hierarchical assembly guided by relatively weaker dispersion forces of the MC-stacked π-surfaces could be tailored by dilution or thermal treatment. Such organized packing of pendant MCs by the dual effect of dipole-dipole interactions and π-stacking conferred several exciting properties to the P2 assembly in water. Long-range ordered antiparallel stacking of the pendant MCs rendered outstanding aggregation-induced enhanced emission (AIEE) properties to the resultant nanostructures in water with increased fluorescence lifetime, quantum yield, and Stokes shift compared to nonaggregating P2 in CHCl₃. The remarkable thermal and kinetic stability of the nanodiscs, their guest loading ability, and very low critical aggregation concentration (CAC) were demonstrated by Förster resonance energy transfer (FRET) studies with an encapsulated donor-acceptor dye pair.

Self-Assembling Peptides and Carbon Nanomaterials Join Forces for Innovative Biomedical Applications

Self-assembling peptides and carbon nanomaterials have attracted great interest for their respective potential to bring innovation in the biomedical field. Combination of these two types of building blocks is not trivial in light of their very different physico-chemical properties, yet great progress has been made over the years at the interface between these two research areas. This concise review will analyze the latest developments at the forefront of research that combines self-assembling peptides with carbon nanostructures for biological use. Applications span from tissue regeneration, to biosensing and imaging, and bioelectronics.