J. Funct. Biomater. 2012, 3(3), 601-614; doi:10.3390/jfb3030601
Article

Development of an Interaction Assay between Single-Stranded Nucleic Acids Trapped with Silica Particles and Fluorescent Compounds

1,* email and 2email
1 Department of Life and Environment Engineering, Faculty of Environmental Engineering, University of Kitakyushu, 1-1, Hibikino, Wakamatsu, Kitakyushu 808-0135, Japan 2 Department of Life and Environment Engineering, Graduate School of Environmental Engineering, University of Kitakyushu, 1-1, Hibikino, Wakamatsu, Kitakyushu 808-0135, Japan
* Author to whom correspondence should be addressed.
Received: 13 July 2012; in revised form: 7 August 2012 / Accepted: 21 August 2012 / Published: 5 September 2012
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Abstract: Biopolymers are easily denatured by heating, a change in pH or chemical substances when they are immobilized on a substrate. To prevent denaturation of biopolymers, we developed a method to trap a polynucleotide on a substrate by hydrogen bonding using silica particles with surfaces modified by aminoalkyl chains ([A-AM silane]/SiO2). [A-AM silane]/SiO2 was synthesized by silane coupling reaction of N-2-(aminoethyl)-3-aminopropyltrimethoxysilane (A-AM silane) with SiO2 particles with a diameter of 5 μm at 100 °C for 20 min. The surface chemical structure of [A-AM silane]/SiO2 was characterized by Fourier transform infrared spectroscopy and molecular orbital calculations. The surface of the silica particles was modified with A-AM silane and primary amine groups were formed. [A-AM silane]/SiO2 was trapped with single-stranded nucleic acids [(Poly-X; X = A (adenine), G (guanine) and C (cytosine)] in PBS solution at 37 °C for 1 h. The single-stranded nucleic acids were trapped on the surface of the [A-AM silane]/SiO2 by hydrogen bonding to form conjugated materials. The resulting complexes were further conjugated by derivatives of acridine orange (AO) as fluorescent labels under the same conditions to form [AO:Poly-X:A-AM silane]/SiO2 complexes. Changes in the fluorescence intensity of these complexes originating from interactions between the single-stranded nucleic acid and aromatic compounds were also evaluated. The change in intensity displayed the order [AO: Poly-G: A-AM silane]/SiO2 > [AO:Poly-A:A-AM silane]/SiO2 >> [AO:Poly-C:A-AM silane]/SiO2. This suggests that the single-stranded nucleic acids conjugated with aminoalkyl chains on the surfaces of SiO2 particles and the change in fluorescence intensity reflected the molecular interaction between AO and the nucleic-acid base in a polynucleotide.
Keywords: nucleic acid; polynucleotide; assay; fluorescence; cellstain-AO

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MDPI and ACS Style

Isoda, T.; Maeda, R. Development of an Interaction Assay between Single-Stranded Nucleic Acids Trapped with Silica Particles and Fluorescent Compounds. J. Funct. Biomater. 2012, 3, 601-614.

AMA Style

Isoda T, Maeda R. Development of an Interaction Assay between Single-Stranded Nucleic Acids Trapped with Silica Particles and Fluorescent Compounds. Journal of Functional Biomaterials. 2012; 3(3):601-614.

Chicago/Turabian Style

Isoda, T.; Maeda, R. 2012. "Development of an Interaction Assay between Single-Stranded Nucleic Acids Trapped with Silica Particles and Fluorescent Compounds." J. Funct. Biomater. 3, no. 3: 601-614.

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