Effect of Cavity Size of Mesoporous Silica on Short DNA Duplex Stability

Abstract

We studied the stabilities of short (4- and 3-bp) DNA duplexes within silica mesopores modified with a positively charged trimethyl aminopropyl (TMAP) monolayer (BJH pore diameter 1.6-7.4 nm). The DNA fragments with fluorescent dye were introduced into the pores, and their fluorescence resonance energy transfer (FRET) response was measured to estimate the structuring energies of the short DNA duplexes under cryogenic conditions (temperature 233-323 K). The results confirmed the enthalpic stability gain of the duplex within size-matched pores (1.6 and 2.3 nm). The hybridization equilibrium constants found for the size-matched pores were 2 orders of magnitude larger than those for large pores (≥3.5 nm), and this size-matching effect for the enhanced duplex stability was explained by a tight electrostatic interaction between the duplex and the surface TMAP groups. These results indicate the requirement of the precise regulation of mesopore size to ensure the stabilization of hydrogen-bonded supramolecular assemblies.

For Whom a Puddle Is the Sea? Adsorption of Organic Guests on Hydrated MCM-41 Silica

“…The observed temperature and hydration effects on adsorption are of practical importance. Adsorption of phosphate groups, , pharmaceutical substances, , and DNA − on silica, removal of impurities from polluted water, − and environmental safety of sediments , are humidity-sensitive. Another potentially important type of guests are molecules, which exhibit self-assembling ability in aqueous solutions. − Such molecules have remained outside the scope of this work.…”

Structural Characterization of Proteins Adsorbed at Nanoporous Materials

“…The thermal stabilities of simple secondary structures of DNA confined inside amine-functionalized mesoporous silica pores were examined. [115][116][117] The results indicated that short-DNA duplexes were stabilized by confinement inside aminefunctionalized cylindrical silica pore channels (BJH pore diameter, 1.6 to 7.4 nm). 115,116 Particularly, short-DNA duplexes confined inside the size-matched pores (BJH pore diameter: 1.6 and 2.3 nm) were significantly stabilized; the hybridization equilibrium constants found for the size-matched pores were 2 orders of magnitude larger than those for larger pores (≥3.5 nm).…”

“…[115][116][117] The results indicated that short-DNA duplexes were stabilized by confinement inside aminefunctionalized cylindrical silica pore channels (BJH pore diameter, 1.6 to 7.4 nm). 115,116 Particularly, short-DNA duplexes confined inside the size-matched pores (BJH pore diameter: 1.6 and 2.3 nm) were significantly stabilized; the hybridization equilibrium constants found for the size-matched pores were 2 orders of magnitude larger than those for larger pores (≥3.5 nm). Since significant stabilization was observed for not only complementary but also single-mismatched DNA duplexes, 115 spatial confinement of the DNA duplex inside the size-matched pore was suggested for the enhanced duplex stability.…”

Continuous Mesoporous Aluminum Oxide Film with Perpendicularly Oriented Mesopore Channels

“…A perpendicularly oriented cylindrical mesopore channel is favored to create an effective biocatalytic system with an enzyme, but there has been no effective method to synthesize a continuous mesoporous film with perpendicular mesochannels. Yamauchi and co-workers succeeded in forming a continuous mesoporous aluminum oxide (MAO) film composed of vertically oriented nanopillars by using aluminum tri- n -butoxide as the aluminum source. , However, it is expected that a biomacromolecule tightly confined inside a cylindrical mesopore channel exhibits more enhanced stability than that embedded between nanopillars. , Recently, Mou and co-workers reported a simple method to deposit a mesoporous silica film with perpendicular nanochannels. The perpendicular silica-nanochannel can be used for the confinement of positively charged protein molecules, but the electrostatic repulsion between GOD and the silica surface would reject the GOD confinement …”

“…17,18 However, it is expected that a biomacromolecule tightly confined inside a cylindrical mesopore channel exhibits more enhanced stability than that embedded between nanopillars. 20,21 Recently, Mou and co-workers reported a simple method to deposit a mesoporous silica film with perpendicular nanochannels. The perpendicular silica-nanochannel can be used for the confinement of positively charged protein molecules, but the electrostatic repulsion between GOD and the silica surface would reject the GOD confinement.…”