[18p-P5-1~22] 12.6 Nanobiotechnology

[18p-P5-8] The interaction between a single-stranded DNA and binding protein viewed by the fragment molecular orbital (FMO) method

Yuto Komeiji¹, Yosiho Okiyama², 〇Yuji Mochizuki^3,4, Kaori Fukuzawa^4,5 (1.AIST/BMDRI, 2.NIHS, 3.Rikkyo Univ., 4.Univ. Tokyo, IIS, 5.Hoshi Univ.)

Keywords:Fragment Molecular Orbital (FMO) Method, Single-stranded DNA, DNA-protein complex

The fragment molecular orbital (FMO) method is one of electronic state calculation methods usable for large scale molecules such as proteins, where the notable advantage of FMO is its high ability to do detailed and reliable interaction analyses. For the DNA-relates systems, so far, the FMO calculations have been applied to double-stranded DNAs and their complexes with proteins. In this study, we investigated the complex with single-stranded DNA at the first time by FMO. Several interesting differences in nature of interactions between the double-strand and single strand cases were found. In particular, it was observed that the stacking interactions among base moieties are enhanced in the single-stranded DNA.