3.1. Motivation
In the life science class, I learned the DNA sequence called TATA box. Specifically, the TATA box binds to the TATA junction protein and acts as a common promoter of genes. However, other promoter sequences are recognized only by specific transcription factors, which play an important role in cell differentiation during development. This TATA box was named because of the high ratio of A and T in the nucleotide sequence. The binding properties of this TATA box are explained in textbooks as ‘the number of hydrogen bonds, which is a chemical characteristic, is relatively small, so it is easily separated.’ Accordingly, the team thought, ‘Can’t the bonding and separation of the TATA box be explained by elasticity, which is a physical property?’, and decided to explore the difference in elastic modulus according to the base composition.
The study of the characteristics of DNA, which is the body of a gene, is an ongoing research field, and in particular, DNA is known as a dense data storage system. Biological information is stored in that small space. Because DNA can bend seamlessly, it has immediate access to the cell's special proteins. These properties enable DNA to regulate proteins in various life processes. Similarly, DNA is efficient, rapidly unwinding and replicating when RNA is made. A protein complex that makes RNA molecules used in DNA chaining from a gene template is sent to a 'molecular giant', it was recently reported in the journal Cell. Considering the importance of DNA in the cell, the elasticity of DNA has both the necessity and importance of research. In addition, this study was conducted with the expectation that this study would be of great help in understanding the properties of the TATA box based on the physical properties.
3.2. Purpose
Physicists at the Institute of Institut LaueLangevin (ILL) located in Grenoble, France, which is a previous study, investigated the flexibility of DNA by measuring how well it transmits sound waves (Physical Review Letters presentation). In the nanosimulation lab, we tried to measure the elasticity of DNA using optical forceps. In this study, unlike the experimental method of measuring elasticity, in this study, the change in DNA of the desired base composition is directly observed through molecular dynamics simulation, and the change in DNA is analyzed through physical modeling, and the elastic modulus (Bending modulus) and persistence length were directly obtained, and the correlation between these values and DNA binding strength was analyzed to study the characteristics of the TATA box.
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