title: Trinucleotide duplex formation inside a confined nanospace under supercooled conditions.
abstract: 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<273 K). 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 233 K. 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.
authors.affiliation: Department of Chemistry, Graduate School of Science, Tohoku University, Aoba-ku, Sendai 980-8578, Japan.
authors.forename: Hiroyuki
authors.initials: H
authors.lastname: Arafune
authors.affiliation: College of Science, Ibaraki University, 2-1-1 Bunkyo, Mito, Ibaraki 310-8512, Japan.
authors.forename: Akira
authors.initials: A
authors.lastname: Yamaguchi
authors.affiliation: Department of Chemistry, Graduate School of Science, Tohoku University, Aoba-ku, Sendai 980-8578, Japan.
authors.forename: Manato
authors.initials: M
authors.lastname: Namekawa
authors.affiliation: Department of Chemistry, Graduate School of Science, Tohoku University, Aoba-ku, Sendai 980-8578, Japan.
authors.forename: Yusuke
authors.initials: Y
authors.lastname: Sato
authors.affiliation: Research Center for Compact Chemical System, National Institute of Advanced Industrial Science and Technology (AIST), 4-2-1 Nigatake, Miyagino, Sendai 983-8551, Japan.
authors.forename: Tetsuji
authors.initials: T
authors.lastname: Itoh
authors.affiliation: College of Science, Ibaraki University, 2-1-1 Bunkyo, Mito, Ibaraki 310-8512, Japan.
authors.forename: Ryoko
authors.initials: R
authors.lastname: Yoshida
authors.affiliation: Department of Chemistry, Graduate School of Science, Tohoku University, Aoba-ku, Sendai 980-8578, Japan.
authors.forename: Norio
authors.initials: N
authors.lastname: Teramae
mesh_terms: D020029:Base Pairing; D006860:Hydrogen Bonding; D009690:Nucleic Acid Conformation; D009711:Nucleotides / Q000737:chemistry*; D013816:Thermodynamics
chemical_list: D009711:Nucleotides