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

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 ∼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
Volume17
Issue number12
DOIs
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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