The labelling of proteins and nucleic acids with fluorescent probes is a powerful approach to map out the site-specific structure of such systems. The Marcus group has performed spectroscopic studies on duplex DNA constructs containing cyanine (Cy3) dimers, in which monomer probes are incorporated into the sugar-phosphate backbones at opposite positions within complementary single-strands. These experiments are sensitive to the exciton coupling within the Cy3 dimer, and thereby provide information about the local conformation and dynamics of the sugar-phosphate backbones at the labeling positions. The separation between Cy3 monomers and their relative orientation are among the main structural parameters that affect these measurements. In order to gain further insights into the local conformations of the Cy3 dimers, we computationally simulate this system using molecular dynamics (MD), and estimate the exciton coupling between the chromophores. We used AMBER99SB-ildn and AMBER99SB-dye force fields to run MD simulations of the Cy3 DNA system at 298 K, which accounts for the aqueous ionic environment. The small separation between the Cy3 chromophores calls into question the simple point-dipole approximation (PDA) for estimating the exciton coupling. Instead, we use a Mulliken Population Analysis to decompose the optical S<sub>1</sub> transition density into “transition charges,” which are localized to the atomic centers of the Cy3. The exciton coupling is thus calculated as the sum of pairwise electrostatic interactions between atomic transition charges local to each Cy3 monomer. These calculations add important dimensionality to the exciton coupling model, and address the proximity limitations of the PDA. The MD simulation shows that the dimer conformation is largely affected by the intra-dimer (Cy3-Cy3) stacking and vicinal Cy3-DNA base stacking. We see two main behaviors where the Cy3s either diverge away from, or are closely stacked with one another. We present the couplings resulting from a variety of equilibrated simulation structures.

Simulation of duplex DNA containing internally labeled Cy3 dimers

Macromolecular Chemistry: The Second Century

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ACS Spring 2020 National Meeting & Expo

The official archive and repository for all ACS Meetings & Expositions abstracts and select posters or presentations.