Loading of DOX into a tetrahedral DNA nanostructure: the corner does matter

The unusual structural properties and potential biological relevance of switchback DNA

Synthetic DNA motifs form the basis of nucleic acid nanotechnology. The biochemical and biophysical properties of these motifs determine their applications. Here, we present a detailed characterization of switchback DNA, a globally left-handed structure composed of two parallel DNA strands. Compared to a conventional duplex, switchback DNA shows lower thermodynamic stability and requires higher magnesium concentration for assembly but exhibits enhanced biostability against some nucleases. Strand competition and strand displacement experiments show that component sequences have an absolute preference for duplex complements instead of their switchback partners. Further, we hypothesize a potential role for switchback DNA as an alternate structure in sequences containing short tandem repeats. Together with small molecule binding experiments and cell studies, our results open new avenues for switchback DNA in biology and nanotechnology.

Supramolecular self-assembly strategies of natural-based β-lactoglobulin modulating bitter perception of goat milk-derived bioactive peptides

Complete self-assembly and reassembly behavior of bitter peptide-protein necessitates multilevel theories that encompass phenomena ranging from the self-assembly of recombinant complex to atomic trajectories. An extension to the level of mechanism method was put forth, involves limited enzymatic digestion and bottom-up proteomics to dissect inherent heterogeneity within β-LG and β-LG-PPGLPDKY complex and uncover conformational and dynamic alterations occurring in specific local regions of the model protein. Bitter peptide PPGLPDKY spontaneously bound to IIAEKTK, IDALNENK, and YLLFCMENSAEPEQSLACQCLVR regions of β-LG in a 1:1 stoichiometric ratio to mask bitterness perception. Molecular dynamic simulation and free energy calculation provided time-varying atomic trajectories of the recombinant complex and found that a peptide was stabilized in the upper region of the hydrophobic cavity with the binding free energy of -30.56 kJ mol-1 through 4 hydrogen bonds (Glu74, Glu55, Lys69, and Ser116) and hydrophobic interactions (Asn88, Asn90, and Glu112). Current research aims to provide valuable physical insights into the macroscopic self-assembly behavior between proteins and bitter peptides, and the meticulous design of highly acceptable taste characteristics in goat milk products.

DNA Framework-Enabled 3D Organization of Antiarrhythmic Drugs for Radiofrequency Catheter Ablation

Preorganizing molecular drugs within a microenvironment is crucial for the development of efficient and controllable therapeutic systems. Here, the use of tetrahedral DNA framework (TDF) is reported to preorganize antiarrhythmic drugs (herein doxorubicin, Dox) in 3D for catheter ablation, a minimally invasive treatment for fast heartbeats, aiming to address potential complications linked to collateral tissue damage and the post-ablation atrial fibrillation (AF) recurrence resulting from incomplete ablation. Dox preorganization within TDF transforms its random distribution into a confined, regular spatial arrangement governed by DNA. This, combined with the high affinity between Dox and DNA, significantly increases local Dox concentration. The exceptional capacity of TDF for cellular internalization leads to a 5.5-fold increase in intracellular Dox amount within cardiomyocytes, effectively promoting cellular apoptosis. In vivo investigations demonstrate that administering TDF-Dox reduces the recurrence rate of electrical conduction after radiofrequency catheter ablation (RFCA) to 37.5%, compared with the 77.8% recurrence rate in the free Dox-treated group. Notably, the employed Dox dosage exhibits negligible adverse effects in vivo. This study presents a promising treatment paradigm that strengthens the efficacy of catheter ablation and opens a new avenue for reconciling the paradox of ablation efficacy and collateral damage.

Topology- and size-dependent binding of DNA nanostructures to the DNase I

The susceptibility of DNA nanomaterials to enzymatic degradation in biological environments is a significant obstacle limiting their broad applications in biomedicine. While DNA nanostructures exhibit some resistance to nuclease degradation, the underlying mechanism of this resistance remains elusive. In this study, the interaction of tetrahedral DNA nanostructures (TDNs) and double-stranded DNA (dsDNA) with DNase I is investigated using all-atom molecular dynamics simulations. Our results indicate that DNase I can effectively bind to all dsDNA molecules, and certain key residues strongly interact with the nucleic bases of DNA. However, the binding of DNase I to TDNs exhibits a non-monotonic behavior based on size; TDN15 and TDN26 interact weakly with DNase I (∼ - 75 kcal/mol), whereas TDN21 forms a strong binding with DNase I (∼ - 110 kcal/mol). Furthermore, the topological properties of the DNA nanostructures are analyzed, and an under-twisting (∼32°) of the DNA helix is observed in TDN15 and TDN26. Importantly, this under-twisting results in an increased width of the minor groove in TDN15 and TDN26, which primarily explains their reduced binding affinity to DNase I comparing to the dsDNA. Overall, this study demonstrated a novel mechanism for local structural control of DNA at the nanoscale by adjusting the twisting induced by length.

Fluorometric Determination of DNA Nanostructure Biostability

The analysis and improvement of DNA nanostructure biostability is one of the keys areas of progress needed in DNA nanotechnology applications. Here, we present a plate-compatible fluorometric assay for measuring DNA nanostructure biostability using the common intercalator ethidium bromide. We demonstrate the assay by testing the biostability of duplex DNA, a double crossover DNA motif, and a DNA origami nanostructure against different nucleases and in fetal bovine serum. This method scales well to measure a large number of samples using a plate reader and can complement existing methods for assessing and developing robust DNA nanostructures.

Nanocomplexes of doxorubicin and DNA fragments for efficient and safe cancer chemotherapy

Cancer-targeted therapy by a chemotherapeutic agent formulated in a nanoscale platform has been challenged by complex and inefficient manufacturing, low drug loading, difficult characterization, and marginally improved therapeutic efficacy. This study investigated facile-to-produce nanocomplexes of doxorubicin (DOX), a widely used cancer drug, and clinically approved DNA fragments that are extracted from a natural source. DOX was found to self-assemble DNA fragments into relatively monodispersed nanocomplexes with a diameter of ∼70 nm at 14.3% (w/w) drug loading by simple and scalable mixing. The resulting DOX/DNA nanocomplexes showed sustained DOX release, unlike overly stable Doxil®, cellular uptake via multiple endocytosis pathways, and high hematological and immunological compatibility. DOX/DNA nanocomplexes eradicated EL4 T lymphoma cells in a time-dependent manner, eventually surpassing free DOX. Extended circulation of DOX/DNA nanocomplexes, while avoiding off-target accumulation in the lung and being cleared from the liver, resulted in rapid accumulation in tumor and lowered cardio toxicity. Finally, tumor growth of EL4-challenged C57BL/6 mice (syngeneic model) and OPM2-challenged NSG mice (human xenograft model) were efficiently inhibited by DOX/DNA nanocomplexes with enhanced overall survival, in comparison with free DOX and Doxil®, especially upon repeated administrations. DOX/DNA nanocomplexes are a promising chemotherapeutics delivery platform for their ease of manufacturing, high biocompatibility, desired drug release and accumulation, efficient tumor eradication with improved safety, and further engineering versatility for extended therapeutic applications.

Recent progress of aptamer‒drug conjugates in cancer therapy

Aptamers are single-stranded DNA or RNA sequences that can specifically bind with the target protein or molecule via specific secondary structures. Compared to antibody-drug conjugates (ADC), aptamer‒drug conjugate (ApDC) is also an efficient, targeted drug for cancer therapy with a smaller size, higher chemical stability, lower immunogenicity, faster tissue penetration, and facile engineering. Despite all these advantages, several key factors have delayed the clinical translation of ApDC, such as in vivo off-target effects and potential safety issues. In this review, we highlight the most recent progress in the development of ApDC and discuss solutions to the problems noted above.

Direct visualization of the drug loading of single DNA origami nanostructures by AFM-IR nanospectroscopy

The efficient loading of DNA nanostructures with intercalating or groove-binding drugs is an important prerequisite for various applications in drug delivery. However, unambiguous verification and quantification of successful drug loading is often rather challenging. In this work, AFM-IR nanospectroscopy is thus employed to directly visualize the loading of DNA origami nanostructures with the photosensitizer methylene blue (MB). Single MB-loaded DNA origami nanostructures can be clearly resolved in high-resolution infrared (IR) maps and the occurrence of MB-specific IR absorption correlates well with the topographic signals of the DNA origami nanostructures. The intensity of the recorded MB absorption bands furthermore scales with the MB concentration used for MB loading. By comparing single- and multilayer DNA origami nanostructures, it is also shown that the IR signal intensity of the loaded MB increases with the thickness of the DNA origami nanostructures. This indicates that also DNA double helices located in the core of bulky 3D DNA origami nanostructures are accessible for MB loading. AFM-IR nanospectroscopy thus has the potential to become an invaluable tool for quantifying drug loading of DNA origami nanostructures and optimizing drug loading protocols.