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TMPyP binding evokes a complex, tunable nanomechanical response in DNA.

Balázs Kretzer^1,2, Levente Herényi¹, Gabriella Csík¹

¹Department of Biophysics and Radiation Biology, Semmelweis University, Tűzoltó Str. 37-47, H1094 Budapest, Hungary.

Nucleic Acids Research

|June 29, 2024

Summary

This study reveals how TMPyP (tetraphenylporphyrin) affects DNA nanomechanics. TMPyP binding dynamically alters DNA length and stiffness, with significant effects observed within pharmacologically relevant concentrations.

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Area of Science:

Biophysics
Molecular Biology
Nanotechnology

Background:

Porphyrins like TMPyP are known for DNA binding and applications in photodynamic therapy and G-quadruplex stabilization.
The influence of TMPyP on DNA nanomechanics, however, remains largely unexplored.

Purpose of the Study:

To investigate the effects of TMPyP on the nanomechanical properties of DNA.
To understand how TMPyP concentration, ionic strength, and mechanical force modulate DNA structure and stability.

Main Methods:

Utilized optical tweezers and microfluidics to manipulate lambda-phage DNA.
Performed equilibrium and kinetic experiments across a range of TMPyP concentrations (5-5120 nM), forces (0-100 pN), NaCl concentrations (0.01-1 M), and pulling rates (0.2-20 μm/s).
Developed a mathematical model to analyze complex binding responses.

Main Results:

TMPyP binding dynamically lengthens and softens double-stranded DNA (dsDNA).
dsDNA stability initially increases at low TMPyP concentrations (<10 nM) but decreases with higher concentrations.
Overstretch cooperativity is reduced, likely due to TMPyP acting as a roadblock on single-stranded DNA (ssDNA), and ssDNA contour length increases.
High NaCl concentrations (1 M) interfere with TMPyP-induced nanomechanical changes.

Conclusions:

TMPyP significantly alters DNA nanomechanics, influencing dsDNA lengthening, softening, and stability.
The observed effects, particularly within pharmacologically relevant TMPyP concentrations, suggest its potential for tuning DNA structure.
This tunability could enable control over DNA-dependent biological processes such as replication, transcription, and repair.