title: Effect of temperature on the structure and hydration layer of TATA-box DNA: A molecular dynamics simulation study.
abstract: 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.
authors.affiliation: BioSystems and Micromechanics IRG (BioSyM), Singapore-MIT Alliance for Research and Technology (SMART), 1 Create Way, 117543, Republic of Singapore; Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA 02139, USA. Electronic address: sudipta@smart.mit.edu.
authors.forename: Sudipta
authors.initials: S
authors.lastname: Samanta
authors.affiliation: Prochem Solutions Pte. Ltd., 89C Science Park Drive, The Rutherford, # 04-13, Singapore Science Park 1, 118261, Singapore.
authors.forename: Devanathan
authors.initials: D
authors.lastname: Raghunathan
authors.affiliation: Indian Institute of Science Education and Research, Kolkata, Mohanpur, West Bengal, 741246, India.
authors.forename: Sanchita
authors.initials: S
authors.lastname: Mukherjee
mesh_terms: D004247:DNA / Q000737:chemistry*; D006860:Hydrogen Bonding; D008958:Models, Molecular; D056004:Molecular Dynamics Simulation; D009690:Nucleic Acid Conformation; D009841:Oligonucleotides / Q000737:chemistry*; D013696:Temperature; D014867:Water / Q000737:chemistry
chemical_list: D009841:Oligonucleotides; D014867:Water; D004247:DNA
keywords: DNA; Major groove; Minor groove; Molecular dynamics simulations; TATA-box