Title of Research Project
Exploring the Mechanism of the Electrostatic Denaturation of Double-Stranded DNA
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Major
Chemistry
Research Abstract
Electrostatic melting is an electrochemical tool that can be used to analyze the stability of the DNA double helix, allowing for the detection of the presence of various DNA mutations in double stranded DNA (dsDNA)1. Here we explore the effect of the formation of the double layer on the electrostatic melting of the DNA double helix in an effort to better understand the mechanism of the aforementioned category of melting. Previous studies by our lab have shown that the electrostatic melting curve produced can be used to distinguish between fully complementary 34-bp strands and single mismatch strands of the same length.2 Additionally, other papers have shown that when the potential on the electrode is pulsed at varying frequencies between an attractive and repulsive potential, at frequencies higher than a certain value, the ions in solution are unable to react quickly enough form the double layer.3 From this, we drew the conclusion that we could get a better insight on the exact mechanism of electrostatic DNA melting by replacing the melting step of our standard melting procedure with a fast potential pulse routine which alternates between a potential at which melting will occur and a potential too weak for melting to occur. The results of this research have shown that the time taken for melting to occur (τ) has remained constant regardless of frequency, which implies that the mechanism of electrostatic DNA melting is not due to the generation of the electric field caused by the formation of the electrical double layer thus indicating that the melting mechanism is not purely electrostatic. Additionally, we have verified that probe desorption does not have a significant impact on signal loss at the potentials used and that the ion response time is significantly slower than the fastest pulse time used in this work.
References
1. Mahajan, S.; Richardson, J.; Brown, T.; Bartlett, P. N.; SERS-Melting: A New Method for Discriminating Mutations in DNA Sequences, Journal of the American Chemical Society, 2008, 130(46), 15589-15601, https://pubs.acs.org/doi/abs/10.1021/ja805517q (Accessed 28th March 2020)
2. Ho, D.; Hetrick, W.; Le, N.; Chin, A; West, R. M.; Electric Field-Induced DNA Melting with Detection by Square Wave Voltammetry, Journal of The Electrochemical Society, 2019, 166(4), B236, https://iopscience.iop.org/article/10.1149/2.0671904jes/meta (Accessed on 16th February 2020)
3. Ulrich Rant et al., Dynamic Electrical Switching of DNA Layers on a Metal Surface, Nano Lett., 2004, 4, 12, 2441-2445, https://doi.org/10.1021/nl0484494 (Accessed 20th February 2020)
Faculty Mentor/Advisor
Ryan West
Exploring the Mechanism of the Electrostatic Denaturation of Double-Stranded DNA
Electrostatic melting is an electrochemical tool that can be used to analyze the stability of the DNA double helix, allowing for the detection of the presence of various DNA mutations in double stranded DNA (dsDNA)1. Here we explore the effect of the formation of the double layer on the electrostatic melting of the DNA double helix in an effort to better understand the mechanism of the aforementioned category of melting. Previous studies by our lab have shown that the electrostatic melting curve produced can be used to distinguish between fully complementary 34-bp strands and single mismatch strands of the same length.2 Additionally, other papers have shown that when the potential on the electrode is pulsed at varying frequencies between an attractive and repulsive potential, at frequencies higher than a certain value, the ions in solution are unable to react quickly enough form the double layer.3 From this, we drew the conclusion that we could get a better insight on the exact mechanism of electrostatic DNA melting by replacing the melting step of our standard melting procedure with a fast potential pulse routine which alternates between a potential at which melting will occur and a potential too weak for melting to occur. The results of this research have shown that the time taken for melting to occur (τ) has remained constant regardless of frequency, which implies that the mechanism of electrostatic DNA melting is not due to the generation of the electric field caused by the formation of the electrical double layer thus indicating that the melting mechanism is not purely electrostatic. Additionally, we have verified that probe desorption does not have a significant impact on signal loss at the potentials used and that the ion response time is significantly slower than the fastest pulse time used in this work.
References
1. Mahajan, S.; Richardson, J.; Brown, T.; Bartlett, P. N.; SERS-Melting: A New Method for Discriminating Mutations in DNA Sequences, Journal of the American Chemical Society, 2008, 130(46), 15589-15601, https://pubs.acs.org/doi/abs/10.1021/ja805517q (Accessed 28th March 2020)
2. Ho, D.; Hetrick, W.; Le, N.; Chin, A; West, R. M.; Electric Field-Induced DNA Melting with Detection by Square Wave Voltammetry, Journal of The Electrochemical Society, 2019, 166(4), B236, https://iopscience.iop.org/article/10.1149/2.0671904jes/meta (Accessed on 16th February 2020)
3. Ulrich Rant et al., Dynamic Electrical Switching of DNA Layers on a Metal Surface, Nano Lett., 2004, 4, 12, 2441-2445, https://doi.org/10.1021/nl0484494 (Accessed 20th February 2020)
