Four-layered intramolecular parallel G-quadruplex with non-nucleotide loops: an ultra-stable self-folded DNA nano-scaffold

• Main Authors: Devi, Gitali, Winnerdy, Fernaldo Richtia, Ang, Jason Cheng Yu, Lim, Kah Wai, Phan, Anh Tuân
• Other Authors: School of Physical and Mathematical Sciences
• Format: Article
• Language: English
• Published: 2022
• Subjects: Science::Chemistry; Science::Biological sciences; Science::Physics; DNA; G-Quadruplex
• Online Access: https://hdl.handle.net/10356/158330
• Institution: Nanyang Technological University

A four-stranded scaffold of nucleic acids termed G-quadruplex (G4) has found growing applications in nano- and biotechnology. Propeller loops are a hallmark of the most stable intramolecular parallel-stranded G4s. To date, propeller loops have been observed to span only a maximum of three G-tetrad layers. Going beyond that would allow creation of more stable scaffolds useful for building robust nanodevices. Here we investigate the formation of propeller loops spanning more than three layers. We showed that native nucleotide sequences are incompatible to-wards this goal, and we identified synthetic non-nucleotide linkers that form propeller loop across four layers. With the established linkers, we constructed a four-layered intramolecular parallel-stranded G4, which exhibited ultra-high thermal stability. Control on loop design would augment the toolbox towards engineering of G4-based nano-scaffolds for diverse applications.