How Do DNA Molecular\nSprings Modulate Protein–Protein\nInteractions: Experimental and Theoretical Results

Deoxyribonucleic acid (DNA) nanomachines have been widely\nexploited\nin enzyme activity regulation, protein crystallization, protein assembly,\nand control of the protein–protein interaction (PPI). Yet,\nthe fundamental biophysical framework of DNA nanomachines in the case\nof regulating protein–protein interactions remains elusive.\nHere, we established a DNA nanospring-mCherry model with mCherry homodimers\nof different <i>K</i><sub>d</sub>. Using size exclusion\nchromatography and fluorescence polarization, we profiled the DNA\nnanospring-mediated manipulation of PPI as an entropy-reducing process.\nThe energy transfer efficiency was a function of the length of the\ncomplementary sequence and the geometry of the DNA nanospring construction.\nWith basic force analysis and physical chemistry calculation, we proposed\na unified model of the correlation between the dissociation constant,\nlocal concentration, construction of DNA nanospring, and kinetics\nof protein dimerization. Overall, we demonstrated that the DNA nanospring-mCherry\nconjugate was a simple and practical model to analyze DNA-controlled\nprotein–protein interaction.