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Computational determination of radiation damage effects on DNA structure

コンピュータシミュレーションを用いた放射線によってDNA分子構造に生じた障害の解明

Pinak, M.

Pinak, M.

修復酵素によるDNA損傷の認識過程について調べるために、放射線により生じる数種類のDNA損傷に関して分子動力学シミュレーションを用いた研究を行った。シミュレーションにはプログラムAMBER 5.0を用い、損傷毎に分子力場を変更して数百ピコ秒の計算を行った。全てのケースにおいて、DNA2重らせん構造に重大な変化が観察されたが、この構造変化が修復酵素のDNAへの結合と複合体形成を助けていると考えられる。これに加え、損傷部位における静電エネルギーの変化も観察されており、これも損傷認識に重要な要因であることが明らかになってきている。

The molecular dynamics (MD) studies of several radiation originated lesions on the DNA molecules are presented with the respect to the proper recognition of the lesion by the respective repair enzyme. Several pyrimidine and purine lesions were subjected to the MD simulations for several hundreds picoseconds using MD simulation code AMBER 5.0 and respective force field modified for the lesion. In all cases the significant structural changes in the DNA double helical structure were observed. These changes were related to the overall collapsing double helical structure around the lesion and are supposed to facilitate the docking of the repair enzyme into the DNA in formation of DNA-enzyme complex. In addition to the structural changes, the specific values of electrostatic interaction energy were found at several lesion sites.

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