Effect of temperature on the structure and hydration layer of TATA-box DNA: A molecular dynamics simulation study

• Published in: Journal of molecular graphics & modelling Vol. 66; pp. 9 - 19
• Main Authors: Samanta, Sudipta, Raghunathan, Devanathan, Mukherjee, Sanchita
• Format: Journal Article
• Language: English
• Published: United States Elsevier Inc 01.05.2016
• Subjects: Deoxyribonucleic acid; DNA; DNA - chemistry; Dynamics; Flexibility; Grooves; Hydrogen Bonding; Major groove; Mathematical models; Minor groove; Models, Molecular; Molecular dynamics; Molecular Dynamics Simulation; Molecular dynamics simulations; Molecular structure; Nucleic Acid Conformation; Oligonucleotides - chemistry; Rigidity; TATA-box; Temperature; Water - chemistry; TATA-box; Molecular dynamics simulations; Minor groove; DNA; Major groove
• ISSN: 1093-3263; 1873-4243
• DOI: 10.1016/j.jmgm.2016.03.005

[Display omitted] •The structure of the DNA did not show any unusual properties within the studied range of temperatures.•Significant structural alteration was noticed between BI and BII forms at higher temperature.•Thermally induced expansion in minor groove width compares well with the experimental observations where TATA-box binding protein induces widening of the minor groove width in TATA box DNA.•The water dynamics around the major and minor groove of the DNA is highly sensitive towards temperature changes. DNA within the living cells experiences a diverse range of temperature, ranging from freezing condition to hot spring water. How the structure, the mechanical properties of DNA, and the solvation dynamics around DNA changes with the temperature is important to understand the functionality of DNA under those acute temperature conditions. In that notion, we have carried out molecular dynamics simulations of a DNA oligomer, containing TATA-box sequence for three different temperatures (250K, 300K and 350K). We observed that the structure of the DNA, in terms of backbone torsion angles, sugar pucker, base pair parameters, and base pair step parameters, did not show any unusual properties within the studied range of temperatures, but significant structural alteration was noticed between BI and BII forms at higher temperature. As expected, the flexibility of the DNA, in terms of the torsional rigidity and the bending rigidity is highly temperature dependent, confirming that flexibility increases with increase in temperature. Additionally, the groove widths of the studied DNA showed temperature sensitivity, specifically, the major groove width decreases and the minor groove width increases, respectively, with the increase in temperature. We observed that at higher temperature, water around both the major and the minor groove of the DNA is less structured. However, the water dynamics around the minor groove of the DNA is more restricted as compared to the water around the major groove throughout the studied range of temperatures, without any anomalous behavior.