Paper Citing NAMD - Abstract
Katti, Dinesh R.; Sharma, Anurag; Pradhan, Shashindra Man; Katti, Kalpana S.
Carbon nanotube proximity influences rice DNA
CHEMICAL PHYSICS, 455:17-22, JUL 9 2015
The uptake of carbon nanotubes (CNT) influences the output of plants, potentially through interactions between the DNA and CNTs. However, little is known about the changes in the plant DNA due to CNT proximity. We report changes in rice plant DNA in the proximity of single walled CNT (SWCNT) using molecular dynamics simulations. The DNA experiences breaking and forming of hydrogen bonds due to unzipping of Watson-Crick (WC) nucleobase pairs and wrapping onto SWCNT. The number of hydrogen bonds between water and DNA nucleobases decreases due to the presence of SWCNT. A higher number of guanine-cytosine (Gua-Cyt) WC hydrogen bonds break as compared to adenine-thymine (Ade-Thy), which suggests that Gua and Cyt bases play a dominant role in DNA-SWCNT interactions. We also find that changes to non-WC nucleobase pairs and van der Waals attractive interactions between WC nucleobase pairs and SWCNT cause significant changes in the conformation of the DNA. (C) 2015 Elsevier B.V. All rights reserved.
