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Potential of Mean Force for DNA Wrapping Around a Cationic Nanoparticle
- Title
- Potential of Mean Force for DNA Wrapping Around a Cationic Nanoparticle
- Authors
- Bae, Sehui; Kim, Jun Soo
- Ewha Authors
- 김준수
- SCOPUS Author ID
- 김준수
- Issue Date
- 2021
- Journal Title
- JOURNAL OF CHEMICAL THEORY AND COMPUTATION
- ISSN
- 1549-9618
1549-9626
- Citation
- JOURNAL OF CHEMICAL THEORY AND COMPUTATION vol. 17, no. 12, pp. 7952 - 7961
- Publisher
- AMER CHEMICAL SOC
- Indexed
- SCIE; SCOPUS
- Document Type
- Article
- Abstract
- Sharp bending and wrapping of DNA around proteins and nanoparticles (NPs) has been of extensive research interest. Here, we present the potential of mean force (PMF) for wrapping a DNA double helix around a cationic NP using coarse-grained models of a double-stranded DNA and a cationic NP. Starting from a NP wrapped around by DNA, the PMF was calculated along the distance between the center of the NP and one end of the DNA molecule. A relationship between the distance and the extent of DNA wrapping is used to calculate the PMF as a function of DNA wrapping around a NP. In particular, the PMF was compared for two DNA sequences of (AT)(25)/(AT)(25) and (AC)(25)/(GT)(25), for which the persistence lengths are different by similar to 10 nm. The simulation results provide solid evidence of the thermodynamic preference for complex formation of a cationic NP with more flexible DNA over the less flexible DNA. Furthermore, we estimated the elastic energy of DNA bending, which was in good order-of-magnitude agreement with the theoretical prediction of elastic rods. This work suggests that the variation of sequence-dependent DNA flexibility can be utilized in DNA nanotechnologies, in which the position and dynamics of NPs are regulated on large-scale DNA structures, or the structural transformation of DNA is triggered by the sequence-dependent binding of NPs.
- DOI
- 10.1021/acs.jctc.1c00797
- Appears in Collections:
- 자연과학대학 > 화학·나노과학전공 > Journal papers
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