Investigation of ssDNA molecule using clustered atomistic method and its application to the dsDNA analysis

Cheng-Nan Han; Cadmus Yuan; Kuo-Ning Chiang

doi:10.1117/12.638568

19 January 2006 Investigation of ssDNA molecule using clustered atomistic method and its application to the dsDNA analysis

Cheng-Nan Han, Cadmus Yuan, Kuo-Ning Chiang

Author Affiliations +

Proceedings Volume 6036, BioMEMS and Nanotechnology II; 603605 (2006) https://doi.org/10.1117/12.638568
Event: Microelectronics, MEMS, and Nanotechnology, 2005, Brisbane, Australia

Abstract

A novel single-stranded DNA (ssDNA) model based on the clustered atomistic method is conducted to simulate the meso-mechanics of ssDNA molecule. Through the validation of the single molecular experiment, the proposed ssDNA model could represent the ssDNA molecule in different counter length, and the mechanical characteristic of the ssDNA molecule in external tensile loading could be elucidated. Furthermore, the characteristic of the validated ssDNA model is adapted in the double-stranded DNA (dsDNA) model. The simulation result of the dsDNA model under external loading reveals mechanical behavior of the dsDNA B-S structural transition. Good agreement is achieved between the numerical simulation and single molecular manipulation experimental result, and the mechanical behavior of stretching nicked dsDNA could be revealed.

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Cheng-Nan Han, Cadmus Yuan, and Kuo-Ning Chiang "Investigation of ssDNA molecule using clustered atomistic method and its application to the dsDNA analysis", Proc. SPIE 6036, BioMEMS and Nanotechnology II, 603605 (19 January 2006); https://doi.org/10.1117/12.638568

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