Topic: Molecular Dynamics of Oxazole Yellow Dye in its Ground and First Excited Electronic States in Solution and when Intercalated in dsDNA

Speaker: Chi Jin - Graduate Student, MSU - Chemistry

Host: Professor Bob Cukier

Date: Thursday, November 16, 2017

Time: 4:10 PM

Location: 136 CEM

More Information:

Oxazole yellow (YOPRO) is a cyanine dye consisting of benzoxazole and quinolone rings connected by a two dihedral linkers. YOPRO is almost non-fluorescent in water but its fluorescence is greatly enhanced after intercalation in double-stranded DNA, providing the basis of DNA concentration assays.1-4
To explore this difference, we introduce5 a new method to derive the linker two dihedral force field of S0 and S1 states of YOPRO with the IPolQ charge fitting protocol6. We then use umbrella sampling of YOPRO in water for S0 and S1 states with the new force fields to find energy minima of these states and obtain potentials of mean force along these dihedrals. The DNA intercalation simulations started at the minima of the S0 state were carried out to investigate the conformational changes of YOPRO of both states. We use a steepest decent algorithm to obtain the relaxation pathways on the S1 surfaces for both water solvated and intercalated YOPRO starting from the Franck Condon point and find an energy barrier on the intercalated pathway, and no barrier on the water pathway, which may explain the high fluorescent intensity of intercalated YOPRO.
1. Armitage, B. A., Cyanine Dye-DNA Interactions: Intercalation, Groove Binding, and Aggregation. DNA Binders and Related Subjects 2005, 253, 55-76.
2. Haugland, R. P., Nucleic Acid Stains. In Handbook of Fluorescent Probes and Research Products, Molecular Probes, Inc.: : Oregon, 2002;Vol. 8.
3. Ihmels, H.; Otto, D., Intercalation of Organic Dye Molecules into Double-Stranded DNA General Principles and Recent Developments. Supermolecular Dye Chemistry 2005, 258, 161-204.
4. Yarmoluk S. M. ; Kovalska, V. B.; D., V. K., Optimized Dyes for Protein and Nucleic Acid Detection. In Advanced Fluorescence Reporters in Chemistry and Biology Iii: Applications in Sensing and Imaging, P., D. A., Ed. Springer-Verlag: Berlin Heidelberg, 2011; Vol. 10, pp 1-352.
5. Jin, C.; Cerutti, D.; Cukier, R. I. Molecular Dynamics of Oxazole Yellow Dye in Its Ground and First Excited Electronic States in Solution and When Intercalated in dsDNA. The Journal of Physical Chemistry B 2017, 121, 10242-10248.
6. Cerutti, D. S., J. E. Rice, W. C. Swope and D. A. Case., Derivation of Fixed Partial Charges for Amino Acids Accommodating a Specific Water Model and Implicit Polarization. Journal of Physical Chemistry B, 2013,117, 2328-2338.