Molecular dynamics simulation of telomeric single-stranded DNA and POT1

Kaburagi, Masaaki; Yamada, Hironao*; Miyakawa, Takeshi*; Morikawa, Ryota*; Takasu, Masako*; Kato, Takamitsu*; Uesaka, Mitsuru*

Polymer Journal, 48(2), p.189 - 195, 2016/02

AA2015-0476.pdf:1.08MB

https://doi.org/10.1038/pj.2015.82

We performed molecular dynamics (MD) simulations of telomeric single-stranded DNA and POT1 for 100 ns. The distance between (POT1) and O5' (telomeric ssDNA) is calculated to verify the binding system for 100 ns MD. We then calculated the distance between the bases of telomeric DNA ends and the root mean square deviation and gyration radius in single and binding states. We compared the root mean square fluctuations between single and binding states and calculated the number of hydrogen bonds between POT1 and telomeric DNA. There are many hydrogen bonds between Gln94 and the first guanine of the closest TTAGGG sequence in telomeric single-stranded DNA. These Gln94 and the guanine have a large difference in root mean square fluctuation between single and binding states. We found that Gln94 and guanine are important components of the binding system, and they are related to its stability.

The Possible interplanetary transfer of microbes; Assessing the viability of spp. under the ISS environmental conditions for performing exposure experiments of microbes in the Tanpopo mission

Kawaguchi, Yuko*; Yang, Y.*; Kawashiri, Narutoshi*; Shiraishi, Keisuke*; Takasu, Masako*; Narumi, Issey*; Sato, Katsuya; Hashimoto, Hirofumi*; Nakagawa, Kazumichi*; Tanigawa, Yoshiaki*; et al.

Origins of Life and Evolution of Biospheres, 43(4-5), p.411 - 428, 2013/10

https://doi.org/10.1007/s11084-013-9346-1