Team member
Son Hye-Gang. Kim Myung-mo.
0.1. Motive
In the life science class, I learned the DNA sequence called TATA box. The TATA box is a part that is easily separated because there are many bonds between T and A in the nucleotide sequence and the number of hydrogen bonds is relatively small. In this way, the characteristics of the TATA box are explained by chemical bonding. Our team considered the helical structure as a single rod (worm-like chain), and to explain the characteristics of the TATA box with elasticity, which is a physical property, the elasticity according to the base composition of DNA was evaluated. explored.
0.2. Research content
DNA of four different base ratios was prepared using W3DNA and VMD, and two pairs of random base sequences were created for each ratio and molecular dynamics simulation was performed. In the process, DNA was implemented by creating PDB, PSF, CONF, and PARAMETER files. Reflecting the characteristics of DNA, which is a double helix structure, DNA was interpreted as a rod with elasticity. Based on this physical analysis process, a vast amount of data obtained through simulation was analyzed with MATLAB.
0.3. Result
According to the study results according to the base composition, it can be seen that the higher the ratio of A-T bonds, the more easily it is bent and twisted under the same conditions. Based on the results of this study, in addition to the textbook that explains that the TATA box is relatively well unraveled during transcription or replication by the number of hydrogen bonds, it seems possible that the more A-T bonds there are, the smaller the elastic modulus of DNA is and is more flexible. In addition, it is expected that we will be able to understand more about DNA based on its physical properties.
0. Summary[Characteristics study of TATA box through comparison of elastic modulus according to DNA sequence]
Team member Son Hye-Kang. Kim Myung-mo. 0.1. Motive In the life science class, I learned the DNA sequence called TATA box. The TATA box is a part that is easily separated because there are many bon..
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1. Things to read[Characteristics study of TATA box through comparison of elastic modulus according to DNA sequence]
1.1. DNA Additional Evidence That DNA Is the Genetic Material It was known that DNA is a polymer of nucleotides, each consisting of a nitrogenous base, a sugar, and a phosphate group In 1950, Erwin..
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2. Research plans[Characteristics study of TATA box through comparison of elastic modulus according to DNA sequence]
2.1. Introduction DNA is a field that is very frequently dealt with in the fields of chemistry and life sciences. Then, the question arises, “What are the physical properties of DNA?” “How about..
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3. Introduction[Characteristics study of TATA box through comparison of elastic modulus according to DNA sequence]
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 ..
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4. Theoretical background[Characteristics study of TATA box through comparison of elastic modulus according to DNA sequence]
4.1. Deoxyribonucleic acid (DNA) and deoxyribose DNA is a type of nucleic acid and is a substance that mainly stores genetic information of living things in the nucleus of a cell. The main funct..
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5. Research[Characteristics study of TATA box through comparison of elastic modulus according to DNA sequence]
5.1. Modeling A previous study, 'Helix's Elasticity Study', shows that in order to form a coordinate system necessary for the calculation process, a two-dimensional figure must be created using ato..
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6. Result[Characteristics study of TATA box through comparison of elastic modulus according to DNA sequence]
6.1. Graph(MATLAB) The horizontal axis of the log omega graph means the torsion angle w_i, and the vertical axis means -ln(P(w_i)). The graph should appear in the form of a parabo..
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7. Conclusion[Characteristics study of TATA box through comparison of elastic modulus according to DNA sequence]
7.1. Conclusion 물리학과 생물학이 융합된 생물물리학이라는 학문으로 DNA의 중요한 물리적 특성인 탄성에 대해 연구하였다. 본 연구에서는 다른 선행 연구와는 달리 염기조성에 따른 DNA의 탄성을
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8. Reference[Characteristics study of TATA box through comparison of elastic modulus according to DNA sequence]
Reference [1] NAMD User's Guide Version CVS-2016-09-08, M.Bhandarkar외 공저 [2] Seungho Choe and Sean X.Sun, “The elasticity of alpha-helices”, The Journal of Chemical Physics(2005)7 [3] VMD User..
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9. Note 1[Characteristics study of TATA box through comparison of elastic modulus according to DNA sequence]
Hydrogen atoms and bases were added to the PDB and PSF files made with autopsf to become normal DNA. When I ran namd in the command prompt window, nothing contained hydrogen atoms..
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10. Note 2[Characteristics study of TATA box through comparison of elastic modulus according to DNA sequence]
inp 파일은 원자들간의 퍼텐셜을 정의한 파일로 보통은 수정할 필요가 없음. 자신이 새로운 분자를 생성하고, 기존의 원자-원자간 퍼텐셜을 새롭게 정의할 필요가 있을 때는 수정을 해야됨. dna
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11. Note 3[Characteristics study of TATA box through comparison of elastic modulus according to DNA sequence]
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12. Note 4[Characteristics study of TATA box through comparison of elastic modulus according to DNA sequence]
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13. Note 5[Characteristics study of TATA box through comparison of elastic modulus according to DNA sequence]
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14. Note 6[Characteristics study of TATA box through comparison of elastic modulus according to DNA sequence]
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15. Note 7[Characteristics study of TATA box through comparison of elastic modulus according to DNA sequence]
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16. Note 8[Characteristics study of TATA box through comparison of elastic modulus according to DNA sequence]
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17. Presentation[Characteristics study of TATA box through comparison of elastic modulus according to DNA sequence]
For online posting
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