Insights into the molecular-level effects of atmospheric and room-temperature plasma on mononucleotides and single-stranded homo- and hetero-oligonucleotides

Abstract

Atmospheric and room-temperature plasma (ARTP) has been successfully developed as a useful mutation tool for mutation breeding of various microbes and plants as well animals by genetic alterations. However, understanding of the molecular mechanisms underlying the biological responses to ARTP irradiation is still limited. Therefore, to gain a molecular understanding of how irradiation with ARTP damages DNA, we irradiated the artificially synthesized mononucleotides of dATP, dTTP, dGTP, and dCTP, and the oligonucleotides of dA 8 , dT 8 , dG 8 , dC 8 , and dA 2 dt 2 dG 2 dc 2 as chemical building blocks of DNA with ARTP for 1-4 min, identified the mononucleotide products using 31 p-and 1 H-nuclear magnetic resonance spectroscopy (NMR), and identified the oligonucleotide products using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) during ARTP treatment. The observed 31 p-and 1 H-NMR spectrum signals for the plasmatreated and untreated mononucleotides indicated that dATP was less stable to plasma irradiation than the other mononucleotides. The oligonucleotides after treatment with ARTP were found to have been broken into small fragments as shown by mass spectrometry, with the cleaved bonds and produced fragments identified according to their expected spectral m/z values or molecular weights derived from their m/z values. The stabilities of the oligonucleotides differed to ARTP irradiation, with dT 8 being the most stable and was more beneficial to stabilizing single-stranded oligonucleotide structures compared to the other base groups (A, G, and C). This was consistent with the average potential energy level obtained by the molecular dynamic simulation of the oligonucleotides, i.e., dt 8 > dc 8 > dA 8 > dG 8 > dA 2 dt 2 dG 2 dc 2. In summary, we found that ARTP treatment caused various structural changes to the oligonucleotides that may account for the wide and successful applications reported for ARTP-induced mutation breeding of various organisms.

Multi-omics Comparative Analysis of Streptomyces Mutants Obtained by Iterative Atmosphere and Room-Temperature Plasma Mutagenesis

“…As of 2018, at least 14 fungi, and 24 bacteria, plants, and other microbial communities were successfully altered to improve the tolerance of their microorganisms to certain growth conditions, increasing biomass and optimizing relevant parameters or enhancing the production of enzyme activity or medicinal chemicals ( Ottenheim et al, 2018 ). The ARTP system causes greater damage to DNA that results in various structural changes to the oligonucleotides, which accounts for the higher mutation rate compared to other methods, such as UV radiation or chemical mutagens ( Wang et al, 2020 ).…”

Understanding Antioxidant Abilities of Dihydroxybenzenes: Local and Global Electron Transfer Properties

“…The energy and electron density distributions of HOMO and LUMO for the studied phenolic compounds are given in Figure 2. The HOMO energy is an important aspect when evaluating the electron-donating ability in antioxidant studies [34]. Lower ionization potential means more capacity of donating electrons by disassociating bonds, thus ultimately leading to the higher antioxidant potential of compounds.…”

Breeding of a thermostable xylanase-producing strain of Myceliophthora thermophila by atmospheric room temperature plasma (ARTP) mutagenesis

“…The operation parameters, including RF power input, helium flow rate, plasma range and processing time, are controlled by programmable controller to make the mutagenesis of microorganisms more efficient and faster. Studies have shown that ARTP can react with biological macromolecules such as DNA ( Wang et al, 2020 ) and protein in biological cells ( Zhang et al, 2014b ), resulting in lethal or sublethal effects. There are a large number of active oxides, active nitrides and neutral active particles in ARTP, including superoxide anion (O 2- ), hydroxyl radical (-OH), ozone (O 3 ), hydroperoxide anion (HO 2- ), singlet oxygen ( 1 O 2 ), alkoxy (RO − ), peroxynitroso anion (ONOO − ) and so on.…”