Biophysical Society Thematic Meeting| Santa Cruz 2018

Genome Biophysics: Integrating Genomics and Biophysics to Understand Structural and Functional Aspects of Genomes

Poster Abstracts

16-POS Board 16 Computational Modeling of Chromosomes and Carbon Nanotubes as a Probe of Atomic Force Microscopy Takashi Sumikama 1 ; Keisuke Miyazawa 2 ; Taku Higasayama 2 ; Kyosuke Nakayama 2 ; Masayuki Harada 2 ; Takeshi Fukuma 1,2 ; 1 Kanazawa University, Nano Life Science Institute (WPI-NanoLSI), Kanazawa, Ishikawa, Japan 2 Kanazawa University, Division of Electrical Engineering and Computer Science, Kanazawa, Ishikawa, Japan Chromosomes are central DNA molecules coding genetic information of life. Recently developed methods such as Hi-C clarified that chromosomes in the interphase take fractal globular structures in each chromosome territory; however, their fine structure at the molecular or nanometer scale is still unclear. The atomic force microscope (AFM) is capable of observing molecules at the nanometer scale even in liquid environment, thus is one of the promising tools to see the chromosomes in nucleus. Accordingly, we are planning to measure the chromosome structures by using the AFM, but the AFM measurements of soft matters such as DNA fluctuating in solution are still challenging. In prior to the AFM measurement, we are going to theoretically calculate the AFM image using computational simulations. To do so, we have to develop computational models of chromosomes and carbon nanotubes (CNT) used as the AFM probe. There already exist some literatures describing chromosome as a polymer simulation, while some other groups developed polymer simulations for CNT. Here, we combine these two simulations to simulate chromosomes and CNT simultaneously. In this presentation, a movie of CNT going in and out of chromosomes, mimicking the measurement of chromosomes by the AFM, will be shown. The AFM images are going to be calculated by our simulation. Also, we will analyze what kind of motions of chromosomes are induced by such observation to reveal their effects on the AFM images.

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