FAQ-Metal Ion Nucleic Acid Aptamer

1. What is metal ion aptamer screening?

A: The aptamer is a small nucleic acid folded in a three-dimensional conformation to make the aptamer a specific binding target. The target has a variety of species, either proteins small molecules, or metal ions. In contrast to antibodies, aptamers enable in vitro selection with low immunogenicity. Among them, heavy metal, as the most toxic metal pollutant, can pollute the natural environment, and detecting heavy metal pollution has become an important task. At the same time, heavy metals are also classified as trace elements because of their low content. Therefore, developing an accurate and sensitive heavy metal detection method is very important to ensure human and environmental safety. Aptamers as biological probes show high binding affinity that can be directly converted to high detection sensitivity. On the other hand, high selectivity and stability enable it to detect various targets, especially metal ions. Since identifying aptamers for metal ions, aptamer-based sensors and detection methods have become possible and provide new methods for detecting metal ions, including electrochemical, colorimetric, and fluorometry. KMD Bioscience has been studying in the field of nucleic aptamers for a long time, which can provide customers with metal ion aptamers with excellent performance to help customers better research follow-up projects.

Figure 2 Schematic diagram of fluorescence anisotropy sensor for Cd2+ using TMR-labeled aptamers. (Reference documentation: Yu H, Zhao Q. A Sensitive Aptamer Fluorescence Anisotropy Sensor for Cd2+ Using Affinity-Enhanced Aptamers with Phosphorothioate Modification. Biosensors (Basel). 2022 Oct 17;12(10):887. )

2. What are the applications of metal ion aptamers? What are its advantages?

A: Long-term exposure to toxic heavy metals may also cause cancer in both humans and animals. Therefore, the monitoring of toxic metal ions is an important issue in environmental protection as well as in disease prevention and treatment. However, the high selectivity and sensitivity detection of trace heavy metals remains a challenging area of research. Capapping of target ions from the complex matrix is a key step in detecting heavy metals. So far, researchers have designed several DNA aptamers to identify and detect heavy metal ions, mainly lead, mercury, silver, and so on. These ions can specifically interact with DNA bases to form strong and stable complexes, and some aptamer-based sensors can be used to monitor the concentration of heavy metal ions in water, providing strong support for the early warning and treatment of environmental pollution. In addition, metal ion aptamers can also be used in analytical chemistry, food science, and other fields. In analytical chemistry, aptamers can be used as efficient isolation and enrichment materials for the extraction and purification of metal ions in complex samples. In food science, aptamers can be used to detect heavy metal ion residues in food, which can ensure food safety. As novel recognition elements in biosensors, aptamers outperformed antibodies in terms of low cost, good thermal stability, simple production, ease of modification with functional groups, and conformational changes induced by binding.

3. What are the common methods used in metal ion aptamer screening? What problems do you have? How to solve it?

A: The Capture-SELEX method is often used to screen metal-ion nucleic aptamers. The Capture-SELEX method uses the strong binding force between biotin and avidin, labels the DNA chain in the library using biotin, and then uses the library with avidin, where the ssDNA library is fixed on the magnetic beads. Then, using the fixed library bound to the target, we eluted the magnetic bead library bound to the target and performed PCR amplification to obtain a certain number of secondary libraries. After the whole screening process is completed, we may find that the aptamer affinity does not meet the expected requirements, or the aptamer is not specific enough. In the above situation, we can reduce the non-specificity and improve the affinity by changing the library buffer conditions during the screening process. At the same time, using Capture-SELEX can have higher affinity than using other methods to cure the target, and ePCR can be amplified to avoid the lack of library diversity. KMD Bioscience can improve the efficiency of aptamer screening through the above techniques, but also by optimizing the experimental conditions, to better obtain aptamers. In addition to providing cell nucleic aptamer screening services, it can also provide protein customization and phage display services.

4. What are the common metal aptamers? What is the solution?

A: In the synthesis of metal ion aptamers, we will encounter errors in library design and synthesis or insufficient library diversity. The nucleic aptamer library is up to 10^10-10^14, and the number of random sequences in the library is enough to cover all possible aptamer sequences. Meanwhile, strict quality control, including sequencing verification, was performed to ensure the accuracy of the library. Too low target concentration may lead to the screening of high-affinity aptamers, while too high concentrations may increase non-specific binding. At the same time, KMD Bioscience also optimized the experiment according to the properties of the target to determine the appropriate target concentration, pH value of buffer, and ionic strength and these parameters will affect the binding of the aptamer and the target. The researchers determined the appropriate screening temperature based on the thermal stability of the target and the melting temperature of the aptamer. Negative screening through blank magnetic beads, removal, and nonspecific binding of magnetic beads. Primer dimers and non-specific amplification may occur during PCR amplification. We optimized the PCR amplification conditions, adjusted the primer concentration, and annealing temperature, and used high-quality primers and enzymes for amplification. Finally, KMD Bioscience can provide professional technicians to molecularly perform the sequencing data to ensure the accuracy of the final results.

5. What is the mechanism of the binding of the various metal ions and the aptamers?

A: The recognition of copper ions and aptamers is a process that requires highly regulated aspects, and this recognition process requires the ability of DNA to assist. There are now two possible accounts for the mechanism by which copper ions bind to aptamers, a sandwich where copper ions and 2 adjacent G form a sandwich structure and G and T binding on copper ions and different nucleotide chains. Some researchers have also found that platinum can bind to nucleotides on G and T, which can improve the stability of nucleotide DNA and prevent DNA from continuing replication, transcription, and cell division. Regarding mercury and silver ions, researchers have proposed that they interact with aptamers and lead to structural degeneration. However, the mechanism of metal ions potassium, sodium, and aptamer is related to the four-chain structure. The G-teplex is stable in the presence of monovalent cations (K +, Na +, NH4 +, etc.) because these positive ions coordinate with the negative oxygen atoms in the base to stabilize the G-teplex (G-quadraplex). The binding mechanism of metal ions to aptamers is a complex process involving a variety of interacting forces and factors. This combination has broad applications in biomedicine, materials science, and other fields.