Squaraine Rotaxanes: Highly Stable Fluorescent Bioimaging Probes

Doctoral Dissertation


Squaraine dyes are intensely colored fluorescent dyes that absorb and emit in the red and near infrared wavelengths which are valuable wavelength regions for bioimaging. However, squaraine dyes have tendency to form aggregates and they are susceptible to nucleophilic attack. Encapsulation of a squaraine dye inside a tetralactam macrocycle makes a squaraine rotaxane and avoids both problems simultaneously while retaining the favorable photophysical properties of the squaraine dye. This dissertation describes a series of structural investigations of squaraine rotaxanes and their fluorescent properties. Rotaxanes with structural variations in the terminal regions of the encapsulated squaraine thread were synthesized and studied. They show high stability in the presence of nucleophiles, and extreme pH values. Introducing a hydroxyl group on the anilinium ring of the squaraine thread leads to a congested squaraine rotaxane. Dynamic NMR studies of this rotaxane allow measurement of the hindered C-N bond rotation in the squaraine thread. The rotaxane mechanical stability also was found to be affected by the macrocycle structure. A series of squaraine rotaxanes with a pyridyl-containing macrocycle adopt an unusual boat conformation in the solid state. It was deduced that the macrocycle underwent a very fast chair/boat conformational exchange in solution. The photophysical properties of squaraine rotaxanes, especially the fluorescence quantum yield, are affected by the chair/boat conformational exchange of macrocycle. A truncated squaraine rotaxane was synthesized and shown to have enhanced fluorescence. Therefore, mechanical encapsulation can be employed as a rational design parameter to fine tune the chemical and photochemical properties of squaraine dyes. In addition, bioconjugation methods were developed to attach the squaraine rotaxanes to targeting ligands. A Zn-DPA conjugate could be used to efficiently label various strains of bacteria. The intense fluorescence, photostability, and specific interaction allow the detection of the bacteria infection in vitro and in vivo. Furthermore, rotaxanes were explored to label proteins in both non-specific and specific manners. Compared to conventional NIR fluorophores such as Cy5, squaraine rotaxanes are brighter, much more stable, and do not self-quench, thus they are superior replacements in many bioimaging applications.


Attribute NameValues
  • etd-08282009-140336

Author Na Fu
Advisor Marya Lieberman
Contributor Prashant Kamat , Committee Member
Contributor Marya Lieberman, Committee Member
Contributor Xavier Creary, Committee Member
Degree Level Doctoral Dissertation
Degree Discipline Chemistry and Biochemistry
Degree Name PhD
Defense Date
  • 2009-08-12

Submission Date 2009-08-28
  • United States of America

  • optical bioimaging

  • near-IR dye

  • fluorescence

  • bioconjugation

  • squaraine rotaxane

  • University of Notre Dame

  • English

Record Visibility Public
Content License
  • All rights reserved

Departments and Units


Please Note: You may encounter a delay before a download begins. Large or infrequently accessed files can take several minutes to retrieve from our archival storage system.