Estimating Persistence Length of ssDNA using Fluorescence Correlation Spectroscopy and a Computer Simulation
School Name
Governor's School for Science and Mathematics
Grade Level
12th Grade
Presentation Topic
Physics
Presentation Type
Mentored
Oral Presentation Award
1st Place
Written Paper Award
3rd Place
Abstract
DNA molecules are critical to cell life and development, as they are the basis for cell replication and synthesis of crucial proteins. Due to the phosphate in the backbone of DNA, it is negatively charged, so, with positive particles in the solution, the overall charge of the DNA will be changed. This increase in the overall charge of the molecule allows it to bend as the negatively charged backbone held the helical DNA in a straight progression of the helix, but, without the negative charge, the helix contorts and folds over itself. Because of these effects, a model for the shape and interactions of the cations and the DNA is critical. For the simulation, experimental results of the diffusion coefficients of DNA at multiple cation concentration serve as a basis for the simulation. For experimentation, we used Fluorescence Correlation Spectroscopy to obtain the diffusion times of the molecules, and, by using a known dye with a known diffusion coefficient, converted the diffusion times to diffusion coefficients of the DNA molecules. The simulation then made multiple virtual chains of DNA and found their diffusion coefficients, which were then compared to those of the experimental results using a defined cost function. This simulation yielded results that express a clear pattern, but contains too much noise in data, so we could not be certain of the conclusions we obtained. From this, we saw that our data showed potential for improvement, but shows that we were not successful in making an accurate simulation.
Recommended Citation
Smith, Patrick, "Estimating Persistence Length of ssDNA using Fluorescence Correlation Spectroscopy and a Computer Simulation" (2018). South Carolina Junior Academy of Science. 74.
https://scholarexchange.furman.edu/scjas/2018/all/74
Location
Neville 306
Start Date
4-14-2018 10:45 AM
Presentation Format
Oral and Written
Estimating Persistence Length of ssDNA using Fluorescence Correlation Spectroscopy and a Computer Simulation
Neville 306
DNA molecules are critical to cell life and development, as they are the basis for cell replication and synthesis of crucial proteins. Due to the phosphate in the backbone of DNA, it is negatively charged, so, with positive particles in the solution, the overall charge of the DNA will be changed. This increase in the overall charge of the molecule allows it to bend as the negatively charged backbone held the helical DNA in a straight progression of the helix, but, without the negative charge, the helix contorts and folds over itself. Because of these effects, a model for the shape and interactions of the cations and the DNA is critical. For the simulation, experimental results of the diffusion coefficients of DNA at multiple cation concentration serve as a basis for the simulation. For experimentation, we used Fluorescence Correlation Spectroscopy to obtain the diffusion times of the molecules, and, by using a known dye with a known diffusion coefficient, converted the diffusion times to diffusion coefficients of the DNA molecules. The simulation then made multiple virtual chains of DNA and found their diffusion coefficients, which were then compared to those of the experimental results using a defined cost function. This simulation yielded results that express a clear pattern, but contains too much noise in data, so we could not be certain of the conclusions we obtained. From this, we saw that our data showed potential for improvement, but shows that we were not successful in making an accurate simulation.
