TMPyP binding evokes a complex, tunable nanomechanical response in DNA

Abstract

TMPyP is a porphyrin capable of DNA binding and used in photodynamic therapy and G-quadruplex stabilization. Despite its broad applications, the effect of TMPyP on DNA nanomechanics is unknown. Here we investigated, by manipulating lambda-phage DNA with optical tweezers combined with microfluidics, how TMPyP influences DNA nanomechanics across a wide range of TMPyP concentration (5-5120 nM), mechanical force (0-100 pN), NaCl concentration (0.01-1 M) and pulling rate (0.2-20 um/s). Complex responses were recorded, for the analysis of which we introduced a simple mathematical model. TMPyP binding leads to the lengthening and softening of dsDNA. dsDNA stability, measured as the force of DNA's overstretch transition, increased at low (<10 nM) TMPyP concentrations, then decreased progressively upon increasing TMPyP concentration. The cooperativity of the overstretch transition decreased, due most likely to mechanical roadblocks of ssDNA-bound TMPyP. TMPyP binding increased ssDNA's contour length. The addition of NaCl at high (1 M) concentration competed with many of the nanomechanical changes evoked by TMPyP. Because the largest amplitude of the nanomechanical changes are induced by TMPyP in the pharmacologically relevant nanomolar concentration range, this porphyrin derivative may be used to tune DNA's structure and properties, hence control the myriad of biomolecular processes associated with DNA.