Trinucleotide duplex formation inside a confined nanospace under supercooled conditions

Hiroyuki Arafune, Akira Yamaguchi, Manato Namekawa, Yusuke Sato, Tetsuji Itoh, Ryoko Yoshida, Norio Teramae

Research output: Contribution to journalArticlepeer-review

9 Citations (Scopus)


Self-assembly of nucleotides of fewer than three base pairs is often found in protein-nucleotide conjugations, despite their energetic instability, and is regarded as the potential starting point for the creation of artificial hydrogen-bonded supramolecular complexes. Here we report duplex formation of 3-mer DNA fragments confined within silica mesopores modified with a positively charged trimethyl aminopropyl monolayer, and their further stabilization under supercooled conditions (T<273K). We load 3-mer DNA fragments with donor- or acceptor-dye into modified silica mesopores and examine their hybridization behaviours using FRET measurements. The FRET results clearly reveal that efficient duplex formation through at least two A-T base pairs can be achieved at 233K. Enthalpy changes for duplex formation are found to be nearly equal between complementary and single-mismatched 3-mer DNA duplexes. These results confirm confined mesoscale cavities to be a novel low-temperature reaction space for hydrogen-bonded supramolecular complexes.

Original languageEnglish
Article number5151
JournalNature Communications
Publication statusPublished - 2014 Oct 13


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