Small-Molecule-Based Self-Assembled Ligands for G-Quadruplex DNA Surface Recognition

Quantifying and Modulating Protein Encapsulation in Guanosine-Based Supramolecular Particles

The encapsulation of proteins is an effective way to preserve their structure and enhance their function. One exciting possibility is adjusting the protective agent to match the specific protein's characteristics to influence its properties. In a recent study, we developed a flow cytometry-based method to quantify the encapsulation of small-molecule dyes in colloidal particles made from guanosine derivatives (supramolecular hacky sacks (SHS) particles). We aimed to determine whether this method could quantify protein encapsulation and track changes and if the particles could be tuned to bind to specific proteins. Our results showed that fluorescein isothiocyanate (FITC)-labeled proteins had apparent association constants in the micromolar range with hydrophobicity as the dominant factor enhancing the affinities. Confocal laser scanning microscopy (CLSM) imaging supported these results and provided additional information about the protein distribution within the particles. We also tested the feasibility of tuning the avidin affinity (AVI) for SHS particles with a biotin ligand. We found that increasing the amount of biotin initially enhanced AVI binding, but then reached saturation, which we hypothesize results from noncovalent cross-linking caused by strong biotin/AVI interactions. CLSM images showed that the linker also impacted the AVI distribution within the particles. Our strategy provides an advantage over other methods for quantifying protein encapsulation by being suitable for high-throughput analysis with high reproducibility. We anticipate that future efforts to use lower-affinity ligands would result in better strategies for modulating protein affinity for drug delivery applications.

Demir G, Demir D. Quantum tunneling time delay investigation of [Formula: see text] ion in human telomeric G-quadruplex systems

Guanine-rich quadruplex DNA (G-quadruplex) is of interest both in cell biology and nanotechnology. Its biological functions necessitate a G-quadruplex to be stabilized against escape of the monovalent metal cations. The potassium ion ([Formula: see text]) is particularly important as it experiences a potential energy barrier while it enters and exits the G-quadruplex systems which are normally found in human telomere. In the present work, we analyzed the time it takes for the [Formula: see text] cations to get in and out of the G-quadruplex. Our time estimate is based on entropic tunneling time-a time formula which gave biologically relevant results for DNA point mutation by proton tunneling. The potential energy barrier experienced by [Formula: see text] ions is determined from a quantum mechanical simulation study, Schrodinger equation is solved using MATLAB, and the computed eigenfunctions and eigenenergies are used in the entropic tunneling time formula to compute the time delay and charge accumulation rate during the tunneling of [Formula: see text] in G-quadruplex. The computations have shown that ion tunneling takes picosecond times. In addition, average [Formula: see text] accumulation rate is found to be in the picoampere range. Our results show that time delay during the [Formula: see text] ion tunneling is in the ballpark of the conformational transition times in biological systems, and it could be an important parameter for understanding its biological role in human DNA as well as for the possible applications in biotechnology. To our knowledge, for the first time in the literature, time delay during the ion tunneling from and into G-quadruplexes is computed.

Advancements in antimicrobial nanoscale materials and self-assembling systems

Antimicrobial resistance is directly responsible for more deaths per year than either HIV/AIDS or malaria and is predicted to incur a cumulative societal financial burden of at least $100 trillion between 2014 and 2050. Already heralded as one of the greatest threats to human health, the onset of the coronavirus pandemic has accelerated the prevalence of antimicrobial resistant bacterial infections due to factors including increased global antibiotic/antimicrobial use. Thus an urgent need for novel therapeutics to combat what some have termed the 'silent pandemic' is evident. This review acts as a repository of research and an overview of the novel therapeutic strategies being developed to overcome antimicrobial resistance, with a focus on self-assembling systems and nanoscale materials. The fundamental mechanisms of action, as well as the key advantages and disadvantages of each system are discussed, and attention is drawn to key examples within each field. As a result, this review provides a guide to the further design and development of antimicrobial systems, and outlines the interdisciplinary techniques required to translate this fundamental research towards the clinic.

Reversed Cation Selectivity of G8 -Octamer and G16 -Hexadecamer towards Monovalent and Divalent Cations

A reverse-binding-selectivity between monovalent and divalent cations was observed for two different self-assembly G16 -hexadecamer and G8 -octamer systems. The dissociation constant between G4 -quadruplex and monomer was calculated via VT-1 H NMR experiments. Quantitative energy profiles revealed entropy as the key factor for the weaker binding toward Ba2+ compared with K+ in the G8 -octamer system despite stronger ion-dipole interactions. This study is the first direct comparison of the G4 -quartet binding affinity between mono and divalent cations and will benefit future applications of G-quadruplex-related research. Further competition experiments between the G8 -octamer and 18-crown-6 with K+ demonstrated the potential of this G8 system as a new potassium receptor.

Ionophore constructed from non-covalent assembly of a G-quadruplex and liponucleoside transports K+-ion across biological membranes

The selective transport of ions across cell membranes, controlled by membrane proteins, is critical for a living organism. DNA-based systems have emerged as promising artificial ion transporters. However, the development of stable and selective artificial ion transporters remains a formidable task. We herein delineate the construction of an artificial ionophore using a telomeric DNA G-quadruplex (h-TELO) and a lipophilic guanosine (MG). MG stabilizes h-TELO by non-covalent interactions and, along with the lipophilic side chain, promotes the insertion of h-TELO within the hydrophobic lipid membrane. Fluorescence assays, electrophysiology measurements and molecular dynamics simulations reveal that MG/h-TELO preferentially transports K⁺-ions in a stimuli-responsive manner. The preferential K⁺-ion transport is presumably due to conformational changes of the ionophore in response to different ions. Moreover, the ionophore transports K⁺-ions across CHO and K-562 cell membranes. This study may serve as a design principle to generate selective DNA-based artificial transporters for therapeutic applications.

Construction of a cross-layer linked G-octamer via conformational control: a stable G-quadruplex in H-bond competitive solvents

Methanol soluble and stable guanosine octamers were successfully achieved via H-bond self-assembly. Through structural conformational design, we developed a new class of guanosine derivatives with modification on guanine (8-aryl) and ribose (2',3'-isopropylidene). This unique design led to the formation of the first discrete G8-octamer with its structure characterized by single crystal X-ray diffraction, MS and NMR spectroscopy. The G8-octamer showed unique cation recognition properties, including the formation of a stable Rb+ templated G-quadruplex. Based on this observation, further modification on the 8-aryl moiety was performed to incorporate a cross-layer H-bond or covalent linkage. Similar G-octamers were obtained in both cases with structures confirmed by single crystal X-ray diffraction. Furthermore, the covalently linked G-quadruplex exhibited excellent stability even in MeOH and DMSO, suggesting a promising future for this new H-bond self-assembly system in biological and material applications.

Hybrids Based on Graphene Oxide and Porphyrin as Tools for Detection and Stabilization of DNA G-Quadruplexes

Telomerase inhibition has been an important strategy in cancer therapies, but for which effective drugs are still required. Here, noncovalent hybrid nanoplatforms containing the tetracationic 5,10,15,20-tetrakis(1-methyl-pyridinium-4-yl)porphyrin (TMPyP) and graphene oxide (GO) were prepared for promoting telomerase inhibition through the selective detection and stabilization of DNA guanine-quadruplex (G-Q) structures. Upon binding TMPyP to the GO sheets, the typical absorption bands of porphyrin have been red-shifted and the fluorescence emission was quenched. Raman mapping was used for the first time to provide new insights into the role of the electrostatic and π-π stacking interactions in the formation of such hybrids. The selective recovery of fluorescence observed during the titration of TMPyP@GO with G-Q, resembles a selective "turn-off-on" fluorescence sensor for the detection of G-Q, paving the way for a new class of antitumor drugs.