Development of an Interaction Assay between Single-Stranded Nucleic Acids Trapped with Silica Particles and Fluorescent Compounds
Abstract
:1. Introduction
2. Experimental Procedures
2.1. Preparation of SiO2 Particles Modified with Aminoalkyl Chains
2.2. Analysis of Surface Chemical Structure
2.3. Trapping Procedure of Single-Stranded Nucleic Acids Using Aminoalkylated SiO2 Particles
2.4. Molecular Orbital Calculations of Surface Model Structure of Aminoalkylated SiO2, Polynucleotides and Fluorescent Compound
3. Results
3.1. Chemical Structure of Aminoalkylated SiO2 Surface
3.2. Orientation of Aminoalkyl Chains on the SiO2 Surface
3.3. Evaluation for Interaction of Single-stranded Nucleic Acids and Fluorescence Compound
single-stranded nucleic acid | [AO:Poly-X:A-AM silane]/SiO2 | [AO:Poly-X] | ||||
---|---|---|---|---|---|---|
FL10 | FL1 | R(1) | FL10 | FL1 | R(1) | |
Poly-G | 177 | 45 | 14.7 | 141 | 37 | 11.6 |
Poly-A | 144 | 41 | 11.4 | 130 | 20 | 12.2 |
Poly-C | 54 | 27 | 3.0 | 40 | 27 | 1.4 |
3.4. Evaluation of the Interaction Between Nucleic-Acid Base in Nucleotides and Fluorescent Compound
Calculated MO | AO(1) | Poly-C(2) | Poly-A(3) | Poly-G(4) |
---|---|---|---|---|
HOMO [eV] | −7.695 | −9.140 | −8.840 | −8.820 |
LUMO [eV] | −0.819 | −0.345 | −0.449 | −0.482 |
ΔE | – | 7.350 | 7.246 | 7.213 |
4. Discussion
5. Conclusions
Abbreviations
A-AM silane | N-2-aminoethyl-3-aminopropyltrimethoxysilane (KBM-603, Shin-Etsu Chemical Co., Ltd., Tokyo, Japan) |
B-AM silane | N-phenyl-3-aminopropyltrimethoxysilane (KBM-573, Shin-Etsu Chemical Co., Ltd., Tokyo, Japan) |
[A-AM silane]/SiO2 | silica particles surface-modified with aminoalkyl chains |
[X-AM silane]/SiO2 | X = A: amino group and B: phenyl group |
Poly-X | polynucleotides-X, X = A (adenine), G (guanine) and C (cytosine) |
AO | derivatives of acridine orange (Cellstain-AO; Dojindo Laboratories, Kumamoto, Japan).) |
FITC | fluorescein isothiocyanate |
MO | Molecular orbital |
HOMO | highest occupied molecular orbital |
LUMO | lowest unoccupied molecular orbital |
Acknowledgements
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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. https://doi.org/10.3390/jfb3030601
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. https://doi.org/10.3390/jfb3030601
Chicago/Turabian StyleIsoda, T., and R. Maeda. 2012. "Development of an Interaction Assay between Single-Stranded Nucleic Acids Trapped with Silica Particles and Fluorescent Compounds" Journal of Functional Biomaterials 3, no. 3: 601-614. https://doi.org/10.3390/jfb3030601