Status : Verified
| Personal Name | Azucena, Alexis G. |
|---|---|
| Resource Title | Solvation effects as the main stabilizer for double helix structure of DNA : a molecular modeling approach |
| Date Issued | January 2023 |
| Abstract | Recent experimental studies proposed that hydrophobicity is the main stabilizing factor of DNA and the Watson-Crick (WC) hydrogen bonding only contributes weakly to its stability. However, this recent study cannot theoretically explain the mechanism behind longitudinal breathing under water-PEG conditions. A multiscale molecular modeling method was done to provide the solvation thermodynamic information of unstacking base pairs on the double helix structure of DNA in different solvent conditions. The B-DNA structure was solvated in ethylene glycol (EG) molecules with different mass concentrations increasing from 0% to 40% using a NaCl concentration of 150 mM at 310.15 K. The DNA retains its B-DNA conformer with an increase in the rise parameter value (3.3169 to 3.4997 Å at 0-30%, 3.2600 Å at 40%) as EG concentration increases. The persistence length of DNA increased (1180.2549 to 2367.9278 Å at 10-30%, 1845.8658 Å at 40%), stretching the DNA, and base pair flipping was observed as EG concentration increased, especially at the EG-crowded layer. 3D-RISM-KH analysis using the water-ions-EG continuum solvent system revealed the decrease in excess chemical potential (-415.7741 to -2368.5599 kcal/mol) of the DNA structure mainly contributes to the Helmholtz solvation energy (-403.4853 to -2127.1421 kcal/mol) in decreasing trend. At 30-40% mass EG, the formation of the EG-crowded layer leads to a decrease in the contribution of entropy (-920.0247 to -1055.0167 kcal/mol) in the excess chemical potential with favorable solute-solvent interaction contribution (-734.0113 to -1052.5248 kcal/mol). There is no significant difference in the DNA potential energy at increasing EG concentration. The decrease in the excess chemical potential at increasing EG concentrations makes the DNA structure in the water-EG system more favorable. The DNA potential energy increase is insufficient to have a difference in the Helmholtz free energy. |
| Degree Course | MS Chemical Engineering |
| Language | English |
| Keyword | DNA stability; base pairs parameters; 3D-RISM-KH; solvation thermodynamics |
| Material Type | Thesis/Dissertation |
Preliminary Pages
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Category : F - Regular work, i.e., it has no patentable invention or creation, the author does not wish for personal publication, there is no confidential information.
Access Permission : Open Access