Potential of Mean Force for DNA Wrapping around a Cationic Nanoparticle

Sehui Bae, Jun Soo Kim

Research output: Contribution to journalArticlepeer-review

3 Scopus citations


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 ∼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.

Original languageEnglish
Pages (from-to)7952-7961
Number of pages10
JournalJournal of Chemical Theory and Computation
Issue number12
StatePublished - 14 Dec 2021

Bibliographical note

Funding Information:
This research was funded by the National Research Foundation of Korea (NRF) under grant nos. NRF-2019R1A2C1084414 and NRF-2020R1A5A2019210.

Publisher Copyright:
© 2021 American Chemical Society.


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