Model studies of the effects of intracellular crowding on nucleic acid interactions

Abstract

Molecular interactions and reactions in living cells occur with high concentrations of background molecules and ions. Many research studies have shown that intracellular molecules have characteristics different from those obtained using simple aqueous solutions. To better understand the behavior of biomolecules in intracellular environments, biophysical experiments were conducted under cell-mimicking conditions in a test tube. It has been shown that the molecular environments at the physiological level of macromolecular crowding, spatial confinement, water activity and dielectric constant, have significant effects on the interactions of DNA and RNA for hybridization, higher-order folding, and catalytic activity. The experimental approaches using in vitro model systems are useful to reveal the origin of the environmental effects and to bridge the gap between the behaviors of nucleic acids in vitro and in vivo. This paper highlights the model experiments used to evaluate the influences of intracellular environment on nucleic acid interactions.

Bridging the spatiotemporal scales of macromolecular transport in crowded biomimetic systems

“…4,[19][20][21] These studies have also shown evidence of macromolecular compaction, swelling, and elongation depending on type and size of tracer macromolecule and crowder. 4,5,22 These crowdinginduced conformational changes in turn impact the resulting transport properties.…”

Bulky cations greatly increase the turnover of a native hammerhead ribozyme

“…It has been reported that an addition of PEG, conventionally used as a molecular crowding agent, alters the catalytic activity of several types of ribozymes, including hammerhead ribozymes. 38,39 We observed here that PEGs with average molecular weights of 200 (PEG200) and 8000 (PEG8000) in a concentration range from 10% to 30% by weight increased the turnover rate of HH10 by 4.3-6.4-fold ( Fig. 1C and D).…”

Catalytic Nucleic Acids: Biochemistry, Chemical Biology, Biosensors, and Nanotechnology

“…Another aspect is the diluted in vitro assay conditions in contrast to the crowded intracellular environment. By adding crowding polymers, such as polyethylene glycol, the folding and activity of some ribozymes was promoted (Nakano and Sugimoto, 2017;Paudel et al, 2018). It was also reported that diphosphate can boost the activity of Mg 2+ for both ribozymes and DNAzymes (Yamagami et al, 2019).…”