Understanding DNA interactions in crowded environments with a coarse-grained model

Abstract

Nucleic acid interactions under crowded environments are of great importance for biological processes and nanotechnology. However, the kinetics and thermodynamics of nucleic acid interactions in a crowded environment remain poorly understood. We use a coarse-grained model of DNA to study the kinetics and thermodynamics of DNA duplex and hairpin formation in crowded environments. We find that crowders can increase the melting temperature of both an 8-mer DNA duplex and a hairpin with a stem of 6-nt depending on the excluded volume fraction of crowders in solution and the crowder size. The crowding induced stability originates from the entropic effect caused by the crowding particles in the system. Additionally, we study the hybridization kinetics of DNA duplex formation and the formation of hairpin stems, finding that the reaction rate kon is increased by the crowding effect, while koff is changed only moderately. The increase in kon mostly comes from increasing the probability of reaching a transition state with one base pair formed. A DNA strand displacement reaction in a crowded environment is also studied with the model and we find that rate of toehold association is increased, with possible applications to speeding up strand displacement cascades in nucleic acid nanotechnology.

Aqueous Triple-Phase System in Microwell Array for Generating Uniform-Sized DNA Hydrogel Particles

“…The first hypothesis is that macromolecular crowding effects, such as a depletion force, are stronger in the Dex/PEG twophase systems than in the dextran single-phase system and favor DNA aggregation. The depletion force is a force with an entropic origin often seen in macromolecular crowding environments that manifest in polymer solutions, favoring the self-assembly of biopolymers (Marenduzzo et al, 2006), and which can stabilize the DNA duplex (Nakano et al, 2004;Hong et al, 2020). The assembly of DNA tile microtubes (Zhang et al, 2020) and compacting genomic DNA (Zhang et al, 2009) under macromolecular crowding conditions have also been reported.…”

Low bias multiple displacement amplification with confinement effect based on agarose gel

“…Furthermore, thermodynamic studies have shown that crowded systems can stabilize DNA duplexes and hairpin formation through pure entropy sources. The use of a relatively crowded environment can increase the strand replacement rate [10]. The low melting point agarose is in a dynamic process of solid-liquid change at 30°C and is capable of existing in the MDA system as a macromolecule like PEG.…”

“…It is well known that polymers such as PEG are capable of improving the efficiency of PCR amplification, and molecular crowding effect of PEG might be the main reason [9,10]. Agarose, the most commonly used experimental material in molecular biology, in its solidified state can form a porous structure.…”

Stochastic Kinetic Treatment of Protein Aggregation and the Effects of Macromolecular Crowding

“…In the treatment of the effects of macromolecular crowding, − we assume that all chemical species are homogeneously distributed or well-mixed and, thus, consider only the time evolution of the concentrations or particle numbers of reactants and products. In the presence of molecular crowders, the rate constants of reaction steps may be affected, and the degree of influence varies widely among the different types of reaction steps involved.…”

“…At the cellular level, besides the reaction being contained in a small volume, the environments of proteins are crowded with other biomolecules, such as DNA, lipids, other proteins, etc. The fraction of volume occupied by these “crowders” can be as high as 30–40%, which can affect the reaction rates of proteins as well as other biopolymers in the cell in significant ways. − …”