Structural Optimization and Interaction Study of a DNA Aptamer to L1 Cell Adhesion Molecule
Abstract
:1. Introduction
2. Results and Discussion
2.1. The Optimization of Aptamer yly12
2.2. Investigation into Binding Structure and Key Nucleotides of Aptamer yly20
2.3. The Aptamer-Binding Domain of L1CAM
2.4. Structural Prediction and Molecular Docking
3. Materials and Methods
3.1. Reagents and Buffers
3.2. Cell Lines and Cell Culture
3.3. Flow Cytometry Analysis
3.4. Circular Dichroism (CD) Spectroscopy
3.5. Serum Stability of Aptamers
3.6. Dimethyl Sulfate (DMS) Footprinting Assay
3.7. Plasmids and Transfection
3.8. Peptide Competition Assay
3.9. Chemical Footprinting of L1CAM via HPG-Modification of Arginine
3.10. Molecular Modeling and Docking
4. Conclusions
Supplementary Materials
Author Contributions
Funding
Data Availability Statement
Conflicts of Interest
References
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Aptamer | 4 °C | 25 °C | 37 °C |
---|---|---|---|
yly12 | 3.5 ± 2.4 | 21.6 ± 2.0 | 110.8 ± 21.7 |
yly20 | 2.3 ± 0.4 | 1.9 ± 0.3 | 7.6 ± 1.0 |
yly21 | 1.3 ± 0.4 | 0.9 ± 0.3 | 5.1 ± 0.5 |
yly31 | 26.5 ± 6.3 | 80.6 ± 15.0 | 876 ± 380 |
yly32 | 14.6 ± 4.6 | 40.8 ± 11.5 | 151 ± 162 |
yly33 | 6.2 ± 0.4 | 12.0 ± 1.1 | 41.4 ± 7.3 |
yly34 | 3.4 ± 0.2 | 7.2 ± 1.0 | 18.7 ± 1.6 |
yly20re | 4.2 ± 0.5 | 4.4 ± 0.3 | 13.0 ± 9.0 |
yly20re2 | 3.2 ± 0.2 | 58.4 ± 9.7 | 98.6 ± 23.6 |
yly13 | 369 ± 349 | ||
yly14 | 92 ± 64 | ||
yly16 | 330 ± 298 | ||
yly20-5-T | 112 ± 20 | ||
yly21-9-T | 107 ± 28 |
Aptamer Name | Kd (4 °C) |
---|---|
yly20-G8A | 18.9 ± 2.3 |
yly20-G35A | 53.1 ± 9.1 |
yly20-C46A | 46.4 ± 26.9 |
yly20-T45C | 66.9 ± 27.8 |
yly20-G22A | 1.3 ± 0.1 |
yly20-T25A | 1.7 ± 0.2 |
yly20-C17A | 3.4 ± 0.5 |
yly20-T16C | 44.2 ± 27.8 |
yly20-T28C | 5.3 ± 0.6 |
yly20-T29C | 4.2 ± 0.6 |
yly20-T33C | 9.5 ± 0.8 |
yly20-T1629C | 155.4 ± 134.3 |
yly20-T2829C | 55.9 ± 9.5 |
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Long, Z.; Bing, T.; Zhang, X.; Sheng, J.; Zu, S.; Li, W.; Liu, X.; Zhang, N.; Shangguan, D. Structural Optimization and Interaction Study of a DNA Aptamer to L1 Cell Adhesion Molecule. Int. J. Mol. Sci. 2023, 24, 8612. https://doi.org/10.3390/ijms24108612
Long Z, Bing T, Zhang X, Sheng J, Zu S, Li W, Liu X, Zhang N, Shangguan D. Structural Optimization and Interaction Study of a DNA Aptamer to L1 Cell Adhesion Molecule. International Journal of Molecular Sciences. 2023; 24(10):8612. https://doi.org/10.3390/ijms24108612
Chicago/Turabian StyleLong, Zhenhao, Tao Bing, Xiangru Zhang, Jing Sheng, Shuang Zu, Weiwei Li, Xiangjun Liu, Nan Zhang, and Dihua Shangguan. 2023. "Structural Optimization and Interaction Study of a DNA Aptamer to L1 Cell Adhesion Molecule" International Journal of Molecular Sciences 24, no. 10: 8612. https://doi.org/10.3390/ijms24108612