Designing DNA Triplexes with High Affinity and Specific Recognition Based on Multiple Biophysical Mechanisms

As a multifunctional nucleic acid structure, the DNA triplex has potential applications in targeted gene regulation, nanoscale switch design, and the development of functional nanomaterials. However, certain limitations related to affinity, specificity, and design efficiency affect the targeting precision and accuracy of current DNA triplex designs. This paper proposes an approach for designing DNA triplexes with high affinity and specific recognition based on multiple biophysical mechanisms. First, we designed multiple biophysical mechanisms informed by the intermolecular interaction energy of DNA triplexes by combining chemical kinetic aggregation and structural symmetry distortion to enhance the affinity and specific recognition of DNA triplexes. On this basis, the intermolecular interaction energy was employed as the fitness function and evaluation index. Subsequently, we used a memetic algorithm (named "HGARO") based on the Hunger Games strategy and Artificial Rabbits Optimization to perform parallel optimization of DNA triplexes at multiple scales. Through a series of wet-lab validations, our approach improved the binding affinity and specific recognition performance of DNA triplexes. The dissociation constant (Kd) was reduced by 28-44%; the melting temperature (Tm) increased by 3-6 °C, and, under optimal conditions, the specific recognition of the target sequence by the DNA triplex improved by more than 35%. The run time required for DNA triplex design was reduced by approximately 80%. In summary, our approach improved the performance and design efficiency of DNA triplexes, thus expanding its applications in areas such as molecular recognition and smart sensing.