Abstract
The properties of non-canonical DNA structures, like G-quadruplexes and triplexes, change under cell-mimicking molecular crowding conditions relative to dilute aqueous solutions. The analysis of environmental effects on their stability is crucial since they play important roles in gene expression and regulation. In this study, three intramolecular and intermolecular triplex-forming sequences of different C+*G-C triplet content (*: Hoogsteen base pair; - : Watson–Crick base pair) were designed and their stability measured in the absence and presence of a crowding agent with different K+ concentrations. In dilute solution, the stability of the triplexes was reduced by decreasing the concentration of KCl. This reduction became smaller as the number of C+*G-C triplets increased. Under molecular crowding conditions, Watson–Crick base pairs and Hoogsteen base pairs were destabilized and stabilized, respectively. Interestingly, with lower KCl concentrations (≤1 M), the destabilization of the triplexes due to reduction of KCl concentration was significantly smaller than in dilute solutions. In addition, the C+*G-C content had greater influence on triplex stability under molecular crowding conditions. Our work provides quantitative information about the effects of K+ concentration on triplex stability under molecular crowding conditions and should further our understanding of the function and regulation of triplexes in bioprocesses.
Highlights
The structure and stability of nucleic acids are important for the storage of genetic information and for the regulation of various bioprocesses such as gene transcription and translation.Non-canonical structures, including triplex, G-quadruplex, i-motif, and others, are considered to play crucial roles in gene expression and regulation [1,2,3], they are much less abundant than the typical right-handed B-form helix [1]
The results indicated that no large amounts of G-quadruplexes were observed under the condition of 50 mM 2-morpholino-ethanesulfonic acid (MES) and 0.1 M KCl in the absence and presence of 40 wt% of PEG 200
Watson–Crick in the absence of PEG 200, which were 20.5 and 65.5 ◦ C respectively, the results indicate indicate that Hoogsteen base pairs were stabilized substantially by molecular crowding while that Hoogsteen base pairs were stabilized substantially by molecular crowding while Watson-Crick
Summary
The structure and stability of nucleic acids are important for the storage of genetic information and for the regulation of various bioprocesses such as gene transcription and translation. Non-canonical structures, including triplex, G-quadruplex, i-motif, and others, are considered to play crucial roles in gene expression and regulation [1,2,3], they are much less abundant than the typical right-handed B-form helix [1]. Our group has demonstrated that the formation of non-canonical structures in the template strand caused transcription to pause, slip, and arrest [4]. Obtaining more information about the stability of non-canonical structures such as triplex is necessary in order to further our understanding of gene expression and regulation. The stability of non-canonical structures is largely dictated by the surrounding environment
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