Trinucleotide duplex formation inside a confined nanospace under supercooled conditions.

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.

Microviscosity of supercooled water confined within aminopropyl-modified mesoporous silica as studied by time-resolved fluorescence spectroscopy.

The fluorescence dynamics of rhodamine B (RhB) immobilized on the pore surface of aminopropyl (AP)-modified mesoporous silica (diameter of the silica framework, 3.1 nm) was examined at temperatures between 293 and 193 K to study the microviscosity of supercooled water confined inside the pores. The mesoporous silica specimen with a dense AP layer (2.1 molecules nm(-2)) was prepared, and RhB isothiocyanate was covalently bound to part of the surface AP groups. The fluorescence lifetime of the surface RhB increased with decreasing temperature from 293 to 223 K, indicating that freezing of the confined water did not occur in this temperature range. The microviscosity of the supercooled confined water was evaluated from an analysis of the lifetime data based on a frequency-dependent friction model.

Functionalization of mesoporous silica membrane with a Schiff base fluorophore for Cu(II) ion sensing.

A Schiff base (SB) immobilized hybrid mesoporous silica membrane (SB-HMM) was prepared by immobilizing a Schiff base onto the pore surface of mesoporous silica (pore size=3.1 nm) embedded in the pores of a porous anodic alumina membrane. In contrast to the non-fluorescent analogous SB molecule in homogeneous solutions, SB-HMM exhibited intense fluorescence due to emission enhancement caused by aggregation of SB groups on the pore surface. The high quantum efficiency of the surface SB groups allows SB-HMM to function as a fluorescent sensor for Cu(II) ions in an aqueous solution with good sensitivity, selectivity and reproducibility. Under the optimal conditions described, the linear ranges of fluorescence intensity for Cu(II) are 1.2-13.8(M (R(2)=0.993) and 19.4-60 (R(2)=0.992) (M. The limit of detection for Cu(II) is 0.8 µM on basis of the definition by IUPAC (C(LOD)=3.3S(b)/m).

Acid-base equilibria inside amine-functionalized mesoporous silica.

Acid-base equilibria and effective proton concentration inside a silica mesopore modified with a trimethyl ammonium (TMAP) layer were studied by steady-state fluorescence experiments. The mesoporous silica with a dense TMAP layer (1.4 molecules/nm(2)) was prepared by a post grafting of N-trimethoxysilylpropyl-N,N,N-trimethylammonium at surfactant-templated mesoporous silica (diameter of silica framework =3.1 nm). The resulting TMAP-modified mesoporous silica strongly adsorbed of anionic fluorescence indicator dyes (8-hydroxypyrene-1,3,6-trisulfonate (pyranine), 8-aminopyrene-1,3,6-trisulfonate (APTS), 5,10,15,20-tetraphenyl-21H,23H-porphinetetrasulfonic acid disulfuric acid (TPPS), 2-naphthol-3,6-disulfonate (2NT)) and fluorescence excitation spectra of these dyes within TMAP-modified mesoporous silica were measured by varying the solution pH. The fluorescence experiments revealed that the acid-base equilibrium reactions of all pH indicator dyes within the TMAP-modified silica mesopore were quite different from those in bulk water. From the analysis of the acid-base equilibrium of pyranine, the following relationships between solution pH (pH(bulk)) and the effective proton concentration inside the pore (pH(pore)) were obtained: (1) shift of pH(pore) was 1.8 (ΔpH(pore)=1.8) for the pH(bulk) change from 2.1 to 9.1 (ΔpH(bulk)=7.0); (2) pH(pore) was not simply proportional to pH(bulk); (3) the inside of the TMAP-modified silica mesopore was suggested to be in a weak acidic or neutral condition when pH(bulk) was changed from 2.0 to 9.1. Since these relationships between pH(bulk) and pH(pore) could explain the acid-base equilibria of other pH indicator dyes (APTS, TPPS, 2NT), these relationships were inferred to describe the effective proton concentration inside the TMAP-modified silica mesopore.