Newly characterized interaction stabilizes DNA structure: oligoethylene glycols stabilize G-quadruplexes CH–π interactions

Abstract

Oligoethylene glycols are used as crowding agents in experiments that aim to understand the effects of intracellular environments on DNAs. Moreover, DNAs with covalently attached oligoethylene glycols are used as cargo carriers for drug delivery systems. To investigate how oligoethylene glycols interact with DNAs, we incorporated deoxythymidine modified with oligoethylene glycols of different lengths, such as tetraethylene glycol (TEG), into DNAs that form antiparallel G-quadruplex or hairpin structures such that the modified residues were incorporated into loop regions. Thermodynamic analysis showed that because of enthalpic differences, the modified G-quadruplexes were stable and the hairpin structures were slightly unstable relative to unmodified DNA. The stability of G-quadruplexes increased with increasing length of the ethylene oxides and the number of deoxythymidines modified with ethylene glycols in the G-quadruplex. Nuclear magnetic resonance analyses and molecular dynamics calculations suggest that TEG interacts with bases in the G-quartet and loop via CH–π and lone pair–π interactions, although it was previously assumed that oligoethylene glycols do not directly interact with DNAs. The results suggest that numerous cellular co-solutes likely affect DNA function through these CH–π and lone pair–π interactions.

New Modified Deoxythymine with Dibranched Tetraethylene Glycol Stabilizes G-Quadruplex Structures

“…Moreover, it has also been reported that the carbohydrates stack on the ends of the DNA duplexes via CH-π interactions, stabilizing the duplexes [26]. We have also shown that the presence of linear TEG in the loop of the G-quadruplex allows adoption of a conformation suitable for CH-π interactions of TEG with a G-quartet [17]. Thus, the stabilization of G-quadruplexes by dibranched TEGs may also be due to CH-π interactions.…”

“…Based on a previous NMR study of the thrombin aptamer, deoxythymines in position four (T 4 ) and 13 (T 13 ) stack on a G-quartet, while deoxythymine in position seven (T 7 ) does not [19,20]. We proved that stabilization of G-quadruplexes by linear TEG-modified deoxythymines depends on the positions of incorporation; deoxythymines stacked on a G-quartet significantly increase stability, while those not stacked show almost no effect [17]. Thus, we replaced deoxythymines in the loop regions of Q1 with (2X4) or (3X4) as shown in Table 1.…”

“…Intermolecular G-quadruplexes induced by oligonucleotides containing TEG-modified deoxythymine were significantly more stable relative to unmodified DNA and efficiently inhibited reverse transcription [16]. Moreover, we found that TEG specifically stabilized G-quadruplexes via CH-π interactions between the nucleobases and the CH bonds of TEG [17]. Oligoethylene glycols covalently linked to DNA interact with G-quadruplexes and stabilize these DNA structures more significantly than free oligoethylene glycols in solution due to enthalpic contributions.…”

“…For reference, MD calculations were also performed on the structure of the unmodified G-quadruplex of Q1 and the linear TEG-modified G-quadruplex of Q1-(X4) 4 . Our previous MD calculations using a linear TEG-modified G-quadruplex did not consider the influence of KCl [17]. Thus, the calculation performed in this study accounted for 100 mM KCl because K + and Clions likely affect the G-quadruplex structure.…”

“…Chemical structures of (a) linear (X4), (b) dibranched (2X4), and tribranched (3X4) tetraethylene glycol (TEG)-modified deoxythymines. The linear TEG-modified deoxythymine (X4) was previously described [16,17]. (c) Schematic structure of the antiparallel G-quadruplex (Q1) used in this study.…”