Study on the de/stabilization of the phosphodiester bond of DNA (and RNA) nucleotides aiming at data storage

• Grant number: 23/11272-3
• Support Opportunities: Scholarships in Brazil - Scientific Initiation
• Start date: November 01, 2023
• End date: October 31, 2024
• Field of knowledge: Physical Sciences and Mathematics - Chemistry - Physical-Chemistry
• Principal Investigator: Alejandro López Castillo
• Grantee: Felipe Augusto Ribeiro
• Host Institution: Centro de Ciências Exatas e de Tecnologia (CCET). Universidade Federal de São Carlos (UFSCAR). São Carlos , SP, Brazil

Abstract

The DNA CGAT base sequence could be an alternative to the binary code to store digital information. Understanding DNA stability would be important to ensure the effective preservation of information. In this project, we intend to study the mechanism based on quantum mechanics of the de/stabilization of the phosphodiester bond of DNA and RNA nucleotides in some environments aiming to store digital data in safe conditions.We will study some details of the hydrolysis mechanism of the phosphodiester bond by redoing some theoretical studies using the DFT method (Density Functional Theory). After these studies, we will be able to infer better attack points such as: a) understanding the importance of different atoms, such as metals in hydrolysis; b) building minimal and functional models of the system; c) understanding the lability of DNA and RNA phosphodiester chains against hydrolysis or other mechanisms.We will study nucleotides (phosphate, pentose, and base groups) of DNA and RNA, which would be a relatively small but functional model to obtain the transition states associated with the mechanism of phosphodiester bond rupture.