Madhanagopal Bharath Raj, Talbot Hannah, Rodriguez Arlin, Louis Jiss Maria, Zeghal Hana, Vangaveti Sweta, Reddy Kaalak, Chandrasekaran Arun Richard
The RNA Institute, University at Albany, State University of New York, Albany, NY, USA.
Department of Biological Sciences, University at Albany, State University of New York, Albany, NY, USA.
bioRxiv. 2024 Apr 12:2023.11.15.563609. doi: 10.1101/2023.11.15.563609.
Synthetic DNA motifs form the basis of nucleic acid nanotechnology, and their biochemical and biophysical properties 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.
合成DNA基序构成了核酸纳米技术的基础，其生化和生物物理性质决定了它们的应用。在这里，我们对折返DNA进行了详细的表征，折返DNA是一种由两条平行DNA链组成的整体左旋结构。与传统双链体相比，折返DNA表现出较低的热力学稳定性，组装时需要更高的镁离子浓度，但对某些核酸酶具有增强的生物稳定性。链竞争和链置换实验表明，组成序列对双链互补序列有绝对偏好，而不是对其折返配对序列。此外，我们推测折返DNA在含有短串联重复序列的序列中作为一种替代结构可能发挥的作用。结合小分子结合实验和细胞研究，我们的结果为折返DNA在生物学和纳米技术中的应用开辟了新途径。
