한빛사
>
한빛사논문
한빛사논문
- 조회109
Nat. Commun., Jul 31 2024, 15 (1) 6446 | https://doi.org/10.1038/s41467-024-50871-3
Predicting the effect of binding molecules on the shape and mechanical properties of structured DNA assemblies
Jae Young Lee1, Yanggyun Kim2 & Do-Nyun Kim1,2,3,4
1Institute of Advanced Machines and Design, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul, Korea.
2Department of Mechanical Engineering, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul, Korea.
3Soft Foundry Institute, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul, Korea.
4Institute of Engineering Research, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul, Korea.
Corresponding author
Correspondence to Do-Nyun Kim.
Abstract
Chemo-mechanical deformation of structured DNA assemblies driven by DNA-binding ligands has offered promising avenues for biological and therapeutic applications. However, it remains elusive how to effectively model and predict their effects on the deformation and mechanical properties of DNA structures. Here, we present a computational framework for simulating chemo-mechanical change of structured DNA assemblies. We particularly quantify the effects of ethidium bromide (EtBr) intercalation on the geometry and mechanical properties of DNA base-pairs through molecular dynamics simulations and integrated them into finite-element-based structural analysis to predict the shape and properties of DNA objects. The proposed model captures various structural changes induced by EtBr-binding such as shape variation, flexibility modulation, and supercoiling instability. It enables a rational design of structured DNA assemblies with tunable shapes and mechanical properties by binding molecules.
논문정보
- Research article
- 2024년 07월 (BRIC 등록일 2024-08-08)
- 국내 연구진
- 바이오·의료융합 > 바이오센싱 및 나노바이오물질
댓글 작성 로그인
팝업 닫기관련 링크
관련분야 연구자보기
소속기관 논문보기
관련분야 논문보기
해당논문 저자보기
