ACCURATE MODELING OF SPECTRAL SIGNATURES IN EXCITONICALLY COUPLED CY3 DIMERS IN SOLUTION AND dsDNA

Abstract

Understanding the dynamics of proteins and DNA is of great importance in various fields of science. Labeling DNA and proteins with fluorescent probes is a powerful technique that allows researchers to visualize and track these molecules in various experimental contexts. Cyanine dyes, notably Cy3, are widely utilized for labeling DNA and proteins due to their unique spectral features. These dyes provide distinctive absorption and fluorescence signals, have a large Stokes shift, offer chemical stability, and can be used to label DNA and proteins with versatility. Excitonically coupled Cy3 aggregates present additional distinctive spectral characteristics that depend on the relative geometrical orientation of the constituting monomers and the surroundings, making Cy3 dimers invaluable tools in molecular imaging. Direct experimental interpretations of the spectral signatures of excitonically coupled systems are challenging mainly due to the complex nature of the energy landscapes. Theoretical and computational tools can offer explanations and they have been applied to the excitonic coupling problem. Despite the extensive theoretical research and literature on the indocarbocyanine dye Cy3, there are aspects of its spectral properties that remain unrevealed or subject to debate, particularly when it is excitonically coupled to other chromophores. This arises from limitations in the theories and models used to deal with the excitonic coupling phenomena and simulate the spectral signatures. In this dissertation, we used state-of-the-art quantum mechanical methods and hybrid classical mechanical molecular mechanical tools to (1) determine the methods that can accurately simulate and explain the spectral signatures of the Cy3 monomer; (2) apply the identified tools to the excitonic coupling problem in experimentally well-studied excitonically coupled Cy3 dimers in solution and DNA environments; (3) identify the components and factors needed for accurate modeling of the spectral signatures of Cy3 dimers in different environments. Using these tools and procedures, we were able to unravel the origin of the electronic and vibronic spectral signatures of the monomeric Cy3 and excitonically coupled Cy3 dimers. Our results offered robust quantum mechanical explanations and answers on multiple debatable fronts. The major finding of this work is that accurate modeling of the spectral signatures in excitonically coupled Cy3 dimers requires precise accountability for the events on the excited states, the environmental factors, and temperature effects. For simple excitonically coupled Cy3 systems solvated in solution, we found that the Franck-Condon approach can offer highly accurate predictions and interpretations of the spectral signatures. In more complex situations like Cy3 dimers covalently linked to dsDNA, a combination of classical mechanical and quantum mechanical tools is necessary.