Magnetic Field Effects and Biophysical Studies on DNA Charge Transport and Repair

Citation

Zwang, Theodore Joseph (2018) Magnetic Field Effects and Biophysical Studies on DNA Charge Transport and Repair. Dissertation (Ph.D.), California Institute of Technology. doi:10.7907/Z9TT4P4H. https://resolver.caltech.edu/CaltechTHESIS:07282017-141924517

Abstract

DNA-mediated charge transport (DNA CT) is well established in both ground and excited state systems. Although theoretical models are still being developed, it is clear that the integrity of the extended π-stack of the aromatic heterocycles, the nucleic acid bases, plays a critical role. Electron donors and acceptors must be electronically well coupled into the π-stack, typically via intercalation. Perturbations that distort the π-stack, such as single-base mismatches, abasic sites, base lesions, and protein binding that kinks the double helix, attenuate DNA CT dramatically.

This thesis encompasses work that first aims to understand how DNA duplex structure informs characteristics of DNA CT and then continues to develop an understanding of the role these structural features play in biological systems. To contextualize these advancements, this first chapter outlines foundational work that has shown ways that DNA structure influences its ability to conduct charge.

Next, experiments were conducted on magnetized DNA-modified electrodes to explore spin-selective electron transport through hydrated duplex DNA. These results show that the two spins migrate through duplex DNA with a different yield and that spin selectivity requires charge transport through the DNA duplex. Significantly, shifting the same duplex DNA between right-handed B- and left-handed Z-forms leads to a diode-like switch in spin selectivity; which spin moves more efficiently through the duplex depends upon the DNA helicity. With DNA, the supramolecular organization of chiral moieties, rather than the chirality of the individual monomers, determines the selectivity in spin, and thus a conformational change can switch the spin selectivity.

This exquisite spin selectivity begged the question: how might biology take advantage of such a spin filter? Photolyase and cryptochromes both have been shown to exhibit magnetosensitive chemistry nearby a DNA binding pocket, and photolyase had previously been shown capable of DNA CT. Thus, electrochemical studies were conducted to monitor the repair of cyclobutane pyrimidine dimer lesions by E coli photolyase and truncated A Thaliana Cryptochrome 1 with an applied magnetic field. We find that the yield of dimer repair is dependent on the strength and angle of the applied magnetic field even when using magnetic fields weaker than 1 Gauss, though spin selective DNA CT is not involved. These data illustrate how cyclobutane dimer repair could be used in a biological compass that is informed by the angles of Earth’s magnetic field.

Next DNA-mediated electrochemistry and atomic force microscopy studies were used to describe a role for redox active [4Fe4S] clusters in DNA-mediated charge transport signaling. DNA-modified electrochemistry shows that the [4Fe4S] cluster of DNA-bound DinG, an ATP-dependent helicase that repairs R-loops, is redox-active at cellular potentials and ATP hydrolysis increases DNA-mediated redox signaling. Atomic force microscopy experiments demonstrate that DinG and Endonuclease III, a base excision repair enzyme, cooperate at long range using DNA charge transport to redistribute to regions of DNA damage. These data are then described using an equilibrium model which elucidates fundamental characteristics of this redox chemistry that allow DNA CT to coordinate the activities of DNA repair enzymes across the genome.

The importance of the oxidation state of the redox-active [4Fe4S] cluster in the DNA damage detection process is then further explored. Together, these results show that the reduction and oxidation of [4Fe4S] clusters through DNA-mediated charge transport facilitates long-range signaling between [4Fe4S] repair proteins. The redox-modulated change in DNA-binding affinity regulates the ability of [4Fe4S] repair proteins to collaborate in the lesion detection process.

Thesis Files