Both cellular environmental factors and chemical modifications critically affect the properties of nucleic acids. However, the structure and stability of DNA containing abasic sites under cell-mimicking molecular crowding conditions remain unclear. Here, we investigated the molecular crowding effects on the structure and stability of the G-quadruplexes including a single abasic site. Structural analysis by circular dichroism showed that molecular crowding by PEG200 did not affect the topology of the G-quadruplex structure with or without an abasic site. Thermodynamic analysis further demonstrated that the degree of stabilization of the G-quadruplex by molecular crowding decreased with substitution of an abasic site for a single guanine. Notably, we found that the molecular crowding effects on the enthalpy change for G-quadruplex formation had a linear relationship with the abasic site effects depending on its position. These results are useful for predicting the structure and stability of G-quadruplexes with abasic sites in the cell-mimicking conditions. 1. Introduction Biomolecules have evolved to function within living cells, which contain a variety of macromolecules including nucleic acids, proteins, polysaccharides, and metabolites. These molecules make the intracellular environment extremely crowded; 20–40% of the total volume is physically occupied by biomolecules [1–5]. It has been reported that molecular crowding is a critical factor determining the structure, stability and function of proteins and nucleic acids [6–18]. Because of this importance, molecular crowding effects on the structure and stability of DNA duplexes, triplexes, G-quadruplexes, and other structures have been studied [9–18]. These studies have demonstrated that the molecular crowding effects depend on the patterns of base-base hydrogen bonding in the nucleic acid structure. The stability of DNA duplexes and triplexes comprised of Watson-Crick base pairs decreases by molecular crowding [11–13]. In contrast, molecular crowding stabilizes DNA triplexes and quadruplexes formed by Hoogsteen base pairs [13, 14, 17]. These results suggest that the formation of noncanonical DNA structures such as triplexes and quadruplexes is induced under the molecular crowding conditions. In addition, a recent study has shown that the RNA cleavage activity of a ribozyme composed of noncanonical base-pairs and tertiary interactions was enhanced by molecular crowding [18]. These results indicate that noncanonical structures of nucleic acids can be stabilized by molecular crowding, leading to a
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