Recently, Prof. Mingpan Cheng's team in the Department of Biomedical Engineering, School of Engineering, published their latest research results entitled Deciphering and Predicting Thermal and pH Stabilities of Triplex DNA under Multifactorial Conditions. Shilong Zhang, a master's degree student in the class of 2023, is the first author of the paper, while Prof. Jean-Louis Mergny of Ecole Polytechnique and Prof. Mingpan Cheng are the co-corresponding authors, and China Pharmaceutical University (CPU) is the first corresponding author of the paper.
As an important atypical DNA structure, triple-stranded body DNA (TFO) plays an important role in physiological processes such as gene regulation and disease pathogenesis. In addition, TFO can target the target double-stranded DNA to form a stable triple-stranded structure, which in turn regulates the expression of target genes, and thus is also an important class of nucleic acid drugs. As an environmentally sensitive nucleic acid structure, the structural stability of the triple-stranded body is affected by pH, ionic strength and temperature. However, previous studies on the structural stability of triplexes have often considered only two of these three factors, lacking an effective means of comprehensively assessing their structural stability, as well as a mathematical model for predicting the structure of triplexes under different environmental conditions.
In order to solve the above scientific problems, this study first developed a novel high-throughput five-dimensional fluorescence resonance energy transfer melting annealing experiment (5DFRETMA) method to test the structural stability under no less than 414 conditions of environmental factor combinations, and found that monotonically negative correlations existed between the thermal stability and pH, as well as between the pH stability and temperature. In contrast, ionic strength has a dual effect on triple-stranded body stability: it enhances the stability of the A-T Hoogsteen base pair while destabilizing the G-C+ Hoogsteen base pair. Overall, the relationship between triple-stranded body stability and ionic strength gradually shifted from a monotonically positive correlation to a monotonically negative correlation as the G-C+ content in the triple-stranded body increased. Based on the large amount of stability data obtained by 5DFRETMA, the research team successfully established a prediction model for the first time in the international arena, which is able to quantitatively predict the thermal and pH stability of trichomes under multifactorial conditions. This work deepens the academic understanding of the mechanisms by which triple-stranded DNA performs various physiological functions in biologically complex environments, and also provides tools for the rational design of gene-targeted therapeutic drugs and synthetic biology applications.
This work was supported by the National Natural Science Foundation of China, the Natural Science Foundation of Jiangsu Province, Jiangsu Distinguished Professors, Jiangsu Frontier Technology Research and Development Program, Jiangsu Shuangchuang Team, and the High-level Talent Program of our university.
Original link: https://onlinelibrary.wiley.com/doi/10.1002/anie.202507190
Diagram