Potential of Mean Force for DNA Wrapping Around a Cationic Nanoparticle
- 주제(기타) Chemistry, Physical
- 주제(기타) Physics, Atomic, Molecular & Chemical
- 설명문(일반) [Bae, Sehui; Kim, Jun Soo] Ewha Womans Univ, Dept Chem & Nanosci, Seoul 03760, South Korea
- 등재 SCIE, SCOPUS
- 발행기관 AMER CHEMICAL SOC
- 발행년도 2021
- 총서유형 Journal
- URI http://www.dcollection.net/handler/ewha/000000191137
- 본문언어 영어
- Published As https://doi.org/10.1021/acs.jctc.1c00797
- PubMed https://pubmed.ncbi.nlm.nih.gov/34792353
초록/요약
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.
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