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Minicircle DNA (mcDNA) is a smaller and safer version of non-viral DNA vectors that results from a cutting-edge in vivo recombination process to excise prokaryotic sequences from plasmid DNA (pDNA). Considering the molecule’s potential and increasing interest as a non-viral DNA-based therapeutic, biomanufacturing methodologies need to be improved, especially in downstream processing.

Trypanosomatida parasites, such as trypanosoma and lishmania, are the cause of deadly diseases in many third world countries. A distinctive feature of these organisms is the three dimensional organization of their mitochondrial DNA into maxi and minicircles. In some of these organisms minicircles are confined into a small disk volume and are topologically linked, forming a gigantic linked network. The origins of such a network as well as of its topological properties are mostly unknown. In this paper we quantify the effects of the confinement on the topology of such a minicircle network. We introduce a simple mathematical model in which a collection of randomly oriented minicircles are spread over a rectangular grid. We present analytical and computational results showing that a finite positive critical percolation density exists, that the probability of formation of a highly linked network increases exponentially fast when minicircles are confined, and that the mean minicircle valence (the number of minicircles that a particular minicircle is linked to) increases linearly with density. When these results are interpreted in the context of the mitochondrial DNA of the trypanosome they suggest that confinement plays a key role on the formation of the linked network. This hypothesis is supported by the agreement of our simulations with experimental results that show that the valence grows linearly with density. Our model predicts the existence of a percolation density and that the distribution of minicircle valences is more heterogeneous than initially thought.

To address the current lack of validated molecular standards for analytical ultracentrifugation (AUC), we investigated the suitability of double-stranded DNA molecules. We compared the hydrodynamic properties of linear and circular DNA as a function of temperature. Negatively supercoiled, nicked, and linearized 333 and 339 bp minicircles were studied. We quantified the hydrodynamic properties of these DNAs at five different temperatures, ranging from 4 to 37 °C. To enhance the precision of our measurements, each sample was globally fitted over triplicates and five rotor speeds. The exceptional stability of DNA allowed each sample to be sedimented repeatedly over the course of several months without aggregation or degradation, and with excellent reproducibility. The sedimentation and diffusion coefficients of linearized and nicked minicircle DNA demonstrated a highly homogeneous sample, and increased with temperature, indicating a decrease in friction. The sedimentation of linearized DNA was the slowest; supercoiled DNA sedimented the fastest. With increasing temperature, the supercoiled samples shifted to slower sedimentation, but sedimented faster than nicked minicircles. These results suggest that negatively supercoiled DNA becomes less compact at higher temperatures. The supercoiled minicircles, as purified from bacteria, displayed heterogeneity. Therefore, supercoiled DNA isolated from bacteria is unsuitable as a molecular standard. Linear and nicked samples are well suited as a molecular standard for AUC and have exceptional colloidal stability in an AUC cell. Even after sixty experiments at different speeds and temperatures, measured over the course of 4 months, all topological states of DNA remained colloidal, and their concentrations remained essentially unchanged.

Understanding how supercoiled DNA releases intramolecular stress is essential for its functional realization. However, the molecular mechanism underlying the relaxation process remains insufficiently explored. Here we employed MD simulations based on the oxDNA2 model to investigate the relaxation process of a 336-base pair supercoiled minicircular DNA under double-strand breaks with two fixed endpoints. Our simulations show that the conformational changes in the DNA occur continuously, with intramolecular stress release happening abruptly only when the DNA chain traverses the breakage site. The relaxation process is influenced not only by the separation distance between the fixed ends but also their angle. Importantly, we observe an inhibitory effect on the relaxation characterized by small angles, where short terminal loops impede DNA conformational adjustments, preserving the supercoiled structure. These findings elucidate the intricate interplay between DNA conformational change, DNA motion and intramolecular stress release, shedding light on the mechanisms governing the relaxation of supercoiled DNA at the molecular level.

Ovarian Cancer remains a significant global health concern, with high mortality rates, largely due to late-stage diagnosis and limited treatment options. These extrinsic factors are driven or exacerbated by intrinsic mechanisms such as persistent activation or upregulation of Signal Transducer and Activator of Transcription 3 (STAT3). STAT3 promotes tumor growth, inhibits apoptosis, accelerates angiogenesis and metastasis, facilitates immune evasion, and contributes to chemoresistance. Consequently, STAT3 activation fosters an aggressive ovarian cancer phenotype, contributing to treatment failure, poor prognosis and low survival rates, highlighting the urgent need for novel, safe, effective and affordable STAT3-targeted therapeutic strategies. In this study, we developed a novel double-stranded DNA minicircle (mcDNA) inhibitor, designed to act as a decoy for STAT3, preventing its binding to target gene promoters. Utilizing the SKOV3 ovarian cancer cell line, we evaluated the effects of our inhibitor on cell viability through MTS assay, its apoptotic and necrotic effects using flow cytometry and the expression modulation of downstream STAT3-regulated genes, assayed through RT-qPCR and Western blot analysis. We demonstrate that anti-STAT3 mcDNA significantly reduces the viability of SKOV3 cells at low nanomolar concentrations, while sparing the control group. The effect observed was dose-dependent. Mechanistically, anti-STAT3 mcDNA induces apoptosis and necrosis in treated cells, also revealing a certain dose-dependency, while also decreasing cell proliferation. Finally, our inhibitor significantly downregulates STAT3-dependent anti-apoptotic genes and . These findings suggest that anti-STAT3 mcDNA is a promising, effective and specific candidate for targeted STAT3 inhibition in SKOV3 ovarian cancer cells, warranting further validation in ovarian cancer, exploration and potential application in other types of malignancies, where STAT3 acts as an oncogenic factor.

Motivated by the problem of inferring the molecular dynamics of DNA in solution, and linking them with its base-pair composition, we consider the problem of comparing the dynamics of functional time series (FTS), and of localizing any inferred differences in frequency and along curvelength. The approach we take is one of Fourier analysis, where the complete second-order structure of the FTS is encoded by its spectral density operator, indexed by frequency and curvelength. The comparison is broken down to a hierarchy of stages: at a global level, we compare the spectral density operators of the two FTS, across frequencies and curvelength, based on a Hilbert-Schmidt criterion; then, we localize any differences to specific frequencies; and, finally, we further localize any differences along the length of the random curves, that is, in physical space. A hierarchical multiple testing approach guarantees control of the averaged false discovery rate over the selected frequencies. In this sense, we are able to attribute any differences to distinct dynamic (frequency) and spatial (curvelength) contributions. Our approach is presented and illustrated by means of a case study in molecular biophysics: how can one use molecular dynamics simulations of short strands of DNA to infer their temporal dynamics at the scaling limit, and probe whether these depend on the sequence encoded in these strands? Supplementary materials for this article are available online.

Recessive dystrophic epidermolysis bullosa (RDEB) is a rare autosomal inherited skin disorder caused by mutations in the COL7A1 gene that encodes type VII collagen (C7). The development of an efficient gene replacement strategy for RDEB is mainly hindered by the lack of vectors able to encapsulate and transfect the large cDNA size of this gene. To address this problem, our group has opted to use polymeric-based non-viral delivery systems and minicircle DNA. With this approach, safety is improved by avoiding the usage of viruses, the absence of bacterial backbone, and the replacement of the control viral cytomegalovirus (CMV) promoter of the gene with human promoters. All the promoters showed impressive C7 expression in RDEB skin cells, with eukaryotic translation elongation factor 1 α (EF1α) promoter producing higher C7 expression levels than CMV following minicircle induction, and COL7A1 tissue-specific promoter (C7P) generating C7 levels similar to normal human epidermal keratinocytes. The improved system developed here has a high potential for use as a non-viral topical treatment to restore C7 in RDEB patients efficiently and safely, and to be adapted to other genetic conditions.

Osteoporosis is commonly treated via the long-term usage of anti-osteoporotic agents; however, poor drug compliance and undesirable side effects limit their treatment efficacy. The parathyroid hormone-related protein (PTHrP) is essential for normal bone formation and remodeling; thus, may be used as an anti-osteoporotic agent. Here, we developed a platform for the delivery of a single peptide composed of two regions of the PTHrP protein (1–34 and 107–139); mcPTHrP 1–34+107–139 using a minicircle vector. We also transfected mcPTHrP 1–34+107–139 into human mesenchymal stem cells (MSCs) and generated Thru 1–34+107–139-producing engineered MSCs (eMSCs) as an alternative delivery system. Osteoporosis was induced in 12-week-old C57BL/6 female mice via ovariectomy. The ovariectomized (OVX) mice were then treated with the two systems; (1) mcPTHrP 1–34+107–139 was intravenously administered three times (once per week); (2) eMSCs were intraperitoneally administered twice (on weeks four and six). Compared with the control OVX mice, the mcPTHrP 1–34+107–139-treated group showed better trabecular bone structure quality, increased bone formation, and decreased bone resorption. Similar results were observed in the eMSCs-treated OVX mice. Altogether, these results provide experimental evidence to support the potential of delivering PTHrP 1–34+107–139 using the minicircle technology for the treatment of osteoporosis.

DNA vaccines still represent an emergent area of research, giving rise to continuous progress towards several biomedicine demands. The formulation of delivery systems to specifically target mannose receptors, which are overexpressed on antigen presenting cells (APCs), is considered a suitable strategy to improve the DNA vaccine immunogenicity. The present study developed binary and ternary carriers, based on polyethylenimine (PEI), octa-arginine peptide (R8), and mannose ligands, to specifically deliver a minicircle DNA (mcDNA) vaccine to APCs. Systems were prepared at various nitrogen to phosphate group (N/P) ratios and characterized in terms of their morphology, size, surface charge, and complexation capacity. In vitro studies were conducted to assess the biocompatibility, cell internalization ability, and gene expression of formulated carriers. The high charge density and condensing capacity of both PEI and R8 enhance the interaction with the mcDNA, leading to the formation of smaller particles. The addition of PEI polymer to the R8-mannose/mcDNA binary system reduces the size and increases the zeta potential and system stability. Confocal microscopy studies confirmed intracellular localization of targeting systems, resulting in sustained mcDNA uptake. Furthermore, the efficiency of in vitro transfection can be influenced by the presence of R8-mannose, with great implications for gene expression. R8-mannose/PEI/mcDNA ternary systems can be considered valuable tools to instigate further research, aiming for advances in the DNA vaccine field.

Background Niosomes represent a promising non-viral gene delivery system, offering an alternative to viral vectors for the genetic modification of hard-to-transfect cells, such as mesenchymal stem cells (MSCs), which are pivotal in regenerative medicine. Specifically, SOX9 gene transfer is a valuable strategy for cartilage tissue repair, as it promotes chondrocyte differentiation while repressing hypertrophic and osteogenic markers. In this study, we investigated the potential of niosomes to deliver SOX9, using both parental and minicircle plasmids, to induce chondrogenic differentiation in primary bone marrow-derived human MSCs (hMSCs). Methods Niosomes were synthesised using the thin-film hydration method and complexed with either parental or minicircle SOX9 plasmids to form nioplexes. Physicochemical properties of niosomes and nioplexes were studied in terms of size, zeta potential, complexation, and protection capacity. Primary hMSCs were transfected in a 2D monolayer and 3D aggregate cultures using Lipofectamine as a positive control of transfection. Chondrogenic differentiation was assessed by gene expression (SOX9, ACAN, COLII, COLI, COLX), histological and immunohistochemical staining (Toluidine blue, haematoxylin & eosin and SOX9, COLII, COLI, COLX, respectively), and biochemical (proteoglycans, DNA and protein contents) analyses of main cartilage markers. Results SOX9 delivery via DP20CQ niosome systems significantly enhanced the expression of key chondrogenic markers (SOX9, ACAN, and COLII) and increased production of a characteristic hyaline-like cartilage matrix. In contrast, Lipofectamine-based complexes induced hypertrophic and fibrocartilaginous phenotypes, evidenced by increased expression of COLX and COLI. Quantification of proteoglycan production, along with proteins and DNA content, supported these findings. Both plasmid types promoted comparable chondrogenic outcomes, but parental plasmids yielded more consistent results than minicircles. Conclusions Delivery of SOX9 plasmids via niosomes promotes enhanced chondrogenic differentiation of primary hMSCs in a 3D aggregate culture system, leading to the formation of hyaline-like cartilage tissue. This non-viral strategy represents a promising gene delivery platform for cartilage reparative therapies.