2. Academic Validation
  3. Newly characterized interaction stabilizes DNA structure: oligoethylene glycols stabilize G-quadruplexes CH-π interactions

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

  • Nucleic Acids Res. 2017 Jul 7;45(12):7021-7030. doi: 10.1093/nar/gkx299.
Hisae Tateishi-Karimata 1,  Tatsuya Ohyama 1,  Takahiro Muraoka 2,  Peter Podbevsek 3,  Adam M Wawro 2,  Shigenori Tanaka 4,  Shu-Ichi Nakano 5,  Kazushi Kinbara 2,  Janez Plavec 3,  Naoki Sugimoto 1 5
Affiliations

Affiliations

  • 1 Frontier Institute for Biomolecular Engineering Research (FIBER), Konan University, 7-1-20 Minatojima-minamimachi, Chuo-ku, Kobe 650-0047, Japan.
  • 2 Tokyo Institute of Technology, School of Life Science and Technology, 4259 Nagatsuta, Midori-ku, Yokohama 226-8503, Japan.
  • 3 Slovenian NMR Center, National Institute of Chemistry, Slovenia.
  • 4 Department of Computational Science, Graduate School of System Informatics, Kobe University, 1-1, Rokkodai, Nada-ku, Kobe 657-8501, Japan.
  • 5 Graduate School of Frontiers of Innovative Research in Science and Technology (FIRST), Konan University, 7-1-20 Minatojima-minamimachi, Chuo-ku, Kobe 650-0047, Japan.
PMID: 28453855 DOI: 10.1093/nar/gkx299
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.

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