Ducani, C. | bioRxiv Science

bioRxiv2025

Circularization of Single-Stranded DNA Donor Template Unleashes the Power of Non-Viral Gene Delivery for Long-Term HSCs editing

Over the past decade, non-viral DNA template delivery has been used with engineered nucleases to target single-stranded DNA sequences in hematopoietic stem and progenitor cells. While effective for gene therapy, this method has been limited to short DNA donor templates, restricting its applications to gene corrections. To expand its scope, we developed an editing process using kilobase-long circular single-stranded DNA donor templates and TALEN technology. Our results show that the CssDNA editing process achieves high gene insertion frequency in viable HSPCs. Compared to a conventional AAV-editing process, CssDNA-edited HSPCs show a higher propensity to engraft and maintain gene edits in a murine model. This positive outcome is partly due to higher levels of primitive edited HSPCs, a more quiescent metabolic state, and elevated expression of bone marrow niche adhesion markers. Our findings highlight the strong potential of CssDNA as a universal and efficient non-viral DNA template for gene therapy applications.

bioengineering↗

bioRxiv2023

Predicting the Three-dimensional Structure of the c-KIT Oncogene Promoter and the Dynamics of Strongly Coupled Guanine-Quadruplexes

Guanine-quadruplexes (G4s) are non-canonical DNA structures that play important protective and regulatory roles within cells, influencing, for instance, gene expression. Although the secondary structure of many human G4s is well characterized, in several gene-promoter regions multiple G4s are located in close proximity and may form three-dimensional structures which could ultimately influence their biological roles. In this contribution, we analyze the interplay between the three neighboring G4s present in the c-KIT proto-oncogene promoter, namely WK1, WSP and WK2. In particular, we highlight how these three G4s are structurally linked and how their crosstalk favors the formation of a parallel structure for WSP, differently from what observed for this isolated G4 in solution. Relying on all-atom molecular dynamic simulations exceeding the s time-scale and using enhanced sampling methods, we provide the first computationally-resolved structure of a well-organized G4 cluster in the promoter of a crucial gene involved in cancer development. Our results indicate that neighboring G4s influence their mutual three-dimensional arrangement and provide a powerful tool to predict and interpret complex DNA structures that ultimately can be used as starting point for drug discovery purposes.

biophysics↗