Potential of Mean Force for DNA Wrapping Around a Cationic Nanoparticle

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 coarsegrained 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 sequencedependent 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.

Two decades of Martini: Better beads, broader scope

“…165 In this section, we focused on lipids and protein applications, which make up the bulk of the Martini studies in the literature. There have also been interesting recent applications using the nucleic acid parameters, for example, for modeling aspects of drug delivery 196,271 (Figure 5d), nucleosome formation, 272 DNA-scaffolded nanodiscs, 273,274 and 271 DNA-based nanopores, 275,276 and carbohydrates, in modeling cellulose 277 and glycosylated proteins, 60,278 and development of important biopolymers including peptidoglycans 279 for more realistic simulations of Gram-negative bacterial membranes. We expect such applications to become more prevalent as Martini 3 continues to be developed.…”

Structure and dynamics of double-stranded DNA rotaxanes

“…The sequences of repeating AT/AT dinucleotides are recognized for their high flexibility without any inherent structure bias. 23,24,49 Hence, these sequences are likely to be more stable in DNA minicircles where sharp bending is required. It is noted that in previous experiments on DNA rotaxanes 9,10,12 DNA minicircles contain short segments of AA/TT repeats, known as A-tracts, at several positions.…”