Publication Date



Open access

Embargo Period


Degree Type


Degree Name

Doctor of Philosophy (PHD)


Chemistry (Arts and Sciences)

Date of Defense


First Committee Member

James Wilson

Second Committee Member

Francisco Raymo

Third Committee Member

Marc Knecht

Fourth Committee Member

James Baker


Flurorphores are an important class of compounds that are used as tools to better understand the processes that occur in cells. A subset of biologically useful fluorophores are nucleic acid binding probes. The inherent problems of many of the nucleic acid binding probes used on the market today is three-fold; (1) that the probes used produce some amount of autofluoresence from the biological sample due to the excitation wavelength needed for them to emit, (2) that most of the common probes lack cell membrane permeability, thus requiring fixation and pemeablization which limits the ability to observe dynamic processes of the biological sample and (3) that probes tend to have excitation maxima that poorly match commonly used visible laser lines. This research focuses on synthesizing probes that overcome these limitations by: exploiting the twisted intramolecular charge transfer (TICT) phenomena of probes to produce high on/off ratios when bound to nucleic acids, are membrane permeable, are live cell compatible, and match the major laser lines available for microscopy. Furthermore, with help from the development of these probes a new method for detecting DNA binding modes has been established through the use of two-photon spectroscopy.


Fluorophores; Nucleic Acids; Twisted Intramolecular Charge Transfer