Unraveling the interaction between doxorubicin and DNA origami nanostructures for customizable chemotherapeutic drug release

Abstract

Doxorubicin (DOX) is a commonly employed drug in cancer chemotherapy, and its high DNA-binding affinity can be harnessed in preparing programmable DOX-loaded DNA nanostructures that can be further tailored for targeted delivery and therapeutics. Although DOX has been widely studied, the existing literature of promising DOX-loaded DNA nanocarriers remains limited and incoherent. A number of reports have overlooked the fundamentals of the DOX-DNA interaction, let alone the peculiarities arising from the complexity of the system as a whole. Here, based on an in-depth spectroscopic analysis, we characterize and optimize the DOX loading into different 2D and 3D scaffolded DNA origami nanostructures. In our experimental conditions, all of our DNA origami designs show rather similar DOX binding capacities, which are, however, remarkably lower than previously reported. To simulate the possible physiological degradation pathways, we examine the stability and DOX release properties of the complexes upon DNase I digestion, which reveals that they disintegrate and release DOX into the surroundings at characteristic rates related to the DNA origami superstructure and the loaded DOX content. In addition, we identify DOX self-aggregation and precipitation mechanisms and spectral changes linked to pH, magnesium, and DOX concentration that have been largely ignored in experimenting with DNA nanostructures and in spectroscopic analysis performed with routine UV-Vis and fluorescence techniques. Nevertheless, we demonstrate the possibility of customizing drug release profiles through rational DNA origami design. Therefore, we believe this work can be used as a guide to tailor the release profiles and develop better drug delivery systems based on DNA nanostructures. DNA nanotechnology | DNA origami | drug delivery | intercalation | groove binding | drug release | stability | nucleases | enzymatic digestionIjäs et al. | bioRχiv | May 13, 2020 | 1-14

Thermophoresis of Molecules and Structures of different Sizes in Self-assembled Biomatrices

“…15 While OT, OR, and OR' are planar structures, the six-helix bundle (O6) and 24-helix bundle (O24) DNA origami are 3D structures. 16,17 As expected, OR, but not OR', forms aggregates in aqueous solution, thus preventing the MST measurement of OR in aqueous solution (figure 5B). While bluntend stacking is minimized in the OT design, it can nevertheless result in small aggregates via intermolecular contacts at the vertices, which interferes with the MST measurement in solution.…”

Challenges and Perspectives of DNA Nanostructures in Biomedicine

“…[17] Although the efficacyofDOX-loaded DNAnanocarriers was verified in several in-vivo models, [10,11,13,14,16] each approach has its own and different loading and purification strategy, environment, pH, as well as DOX and ion concentrations, thus making the results extremely hard to compare to each other. Not only are the spectroscopic [18] properties of DOX strongly ion-and pH-dependent, [19] but DOX is also commonly employed in substantial excess to DN in the loading process,a lthough it is known to self-aggregate at high concentrations. [20] Moreover,D OX can also bind to partially hybridized or self-hybridized staples that are used in excess to DO-scaffold strand during folding.A sthe binding affinity of DOX is only slightly DNA-sequence-dependent, [21] the effects of staples should not be ignored.…”

Construction of Smart Stimuli‐Responsive DNA Nanostructures for Biomedical Applications

“…For drug delivery, doxorubicin is known to be intercalated into DNA and is probably the most commonly employed drug in DNA nanostructure-based delivery.N ote that somed ispute exists regarding the loading and releasing of doxorubicin from DNA nanostructures as the concentration of doxorubicin could be heavily miss-estimated. The fluorescenceo fd oxorubicin strongly dependso nt he surrounding pH, ion strength,i on types, and doxorubicin concentration, [66,67] which may lead to misleading results of the actual drug efficacy.W ith the rapid development of dynamic DNA nanotechnology,n umerous smart DNA nanostructures have emerged in recenty ears. Among them, DNA hydrogels, HCR-dictated nanostructures,D NA origami,a nd wireframe DNA represent the characteristic DNA nanostructures with stimuli-responsive properties and are thus summarized herein.…”