Advantages and Disadvantages of Nucleic Acid Aptamers

Nucleic acid aptamers are single-stranded oligonucleotides with the ability to specifically bind to target molecules. Currently, nucleic acid aptamers are screened from large random nucleic acid libraries using SELEX technology. It can identify different types of target molecules such as proteins, viruses, bacteria, cells, etc. Nucleic acid aptamers not only have the specificity of antibodies, but also have many advantages over antibodies, such as a wider range of target molecules, better thermal stability, smaller molecular weight, chemical synthesis, small batch differences and easy modification. Therefore, nucleic acid aptamers have broad application prospects in biomedicine, diagnostic testing, drug development and other fields, but they also face challenges such as patent restrictions and lack of binding site research.

Nucleic Acid Aptamer Screening Principles

The nucleic acid aptamer screening technology is called SELEX (Systematic Evolution of Ligands by Exponential Enrichment). The SELEX technology is a process that simulates natural selection and evolution. It enriches nucleic acid aptamers that bind to specific targets from a nucleic acid library containing a large number of random sequences through repeated screening and amplification.

Aptamers Structure

Nucleic acid aptamers can form a specific three-dimensional conformation by folding themselves, and bind to target molecules with high affinity and specificity through multiple interaction forces.

Existing studies have shown that the unique structure of nucleic acid aptamers gives aptamers the following characteristics:

• Diversity

Nucleic acid aptamers can be DNA or RNA, or nucleic acid analogs (XNA), such as modifications to the structure or composition of sugars, phosphates or bases to increase diversity and stability. The length of nucleic acid aptamers is generally between 20-100 bases. The initial library capacity is 10¹⁴-10¹⁶, so it has extremely high diversity and can identify various types of target molecules.

• Flexibility

Nucleic acid aptamers are linear oligonucleotides that can form various secondary and tertiary structures such as hairpins, stem-loops and quadruplexes through complementary pairing, hydrogen bonding and van der Waals forces between bases, pseudo-nodes, etc. These structures can provide a variety of interaction sites with target molecules, such as bases, phosphate backbones, sugar rings, etc. The flexibility of nucleic acid aptamers allows them to adapt to different environmental conditions such as temperature, pH, salinity, etc. and to adjust their conformation according to changes in the target molecules.

• Stability

Nucleic acid aptamers are chemically synthesised oligonucleotides that have high thermal and chemical stability, can be stored for long periods at room temperature and are resistant to various organic solvents, proteases and other treatments. In addition, the stability of nucleic acid aptamers can also be improved by introducing chemical modifications or non-natural bases, such as increasing anti-nuclease or antiserum clearance.

• Modifiability

Nucleic acid aptamers are chemically synthesised oligonucleotides with high modifiability. Various functional groups or markers can be introduced into their fixed or random sequences to enhance their functions or detection effects. For example, fluorescein, biotin, magnetic beads, gold nanoparticles, etc. can be modified on nucleic acid aptamers for signal amplification or signal transduction; polyethylene glycol (PEG), cholesterol, etc. can be modified on nucleic acid aptamers to increase their solubility or circulation life; drugs, drug-loaded nanoparticles, etc. can be modified on nucleic acid aptamers to achieve targeted therapy or controlled release, etc.

Advantages of Nucleic Acid Aptamers

• Broad Range of Target Molecules

Nucleic acid aptamers can recognise various types of target molecules such as proteins, viruses, bacteria, cells, heavy metal ions, etc. without being limited by immunogenicity, toxicity, stability, etc. Nucleic acid aptamers can also recognise some target molecules that are difficult for antibodies to recognise, such as small molecules, non-natural molecules, allosteric antigens, etc.

• Short Screening Cycle

Nucleic acid aptamers are obtained from random nucleic acid libraries using the SELEX in vitro screening technology, which does not require animal immunisation or cell culture steps, so the screening cycle is short and can typically be completed within a few weeks. In addition, the SELEX technology can be used for high-throughput and automated screening, improving screening efficiency and quality.

• Low Cost of Preparation

Nucleic acid aptamers are produced by chemical synthesis, which does not require complex bioengineering or purification processes, so the cost of production is low and it is easy to scale up production. In addition, nucleic acid aptamers can be amplified indefinitely by methods such as PCR or RT-PCR to increase production and reduce costs.

• Small Batch Differences

Nucleic acid aptamers are produced by chemical synthesis with high structural consistency and purity, so batch-to-batch differences are small and quality is easy to control. In contrast, antibodies are produced by bioengineering or animal immunisation methods that are affected by many factors such as cell lines, culture conditions, purification methods, etc., so batch-to-batch differences are large and quality is difficult to control.

• Good Stability

Nucleic acid aptamers have high thermal and chemical stability, can be stored for a long time at room temperature, and can withstand various organic solvents, proteases and other treatments. In addition, nucleic acid aptamers can be made more stable by introducing chemical modifications or non-natural bases, such as increasing anti-nuclease or anti-serum clearance.

• Easy to Modify

Nucleic acid aptamers have high modifiability, and various functional groups or markers can be introduced on their fixed or random sequences to increase their functions or detection effects. For example, fluorescein, biotin, magnetic beads, gold nanoparticles, etc. can be modified on nucleic acid aptamers for signal amplification or signal transduction; polyethylene glycol (PEG), cholesterol, etc. can be modified on nucleic acid aptamers to increase their solubility or circulation life; drugs, drug-loaded nanoparticles, etc. can be modified on nucleic acid aptamers for targeted therapy or controlled release, etc.

• Low Immunogenicity

Nucleic acid aptamers are chemically synthesized oligonucleotides with low immunogenicity and are not easy to cause immune or allergic reactions in the body. In contrast, antibodies are natural proteins with high immunogenicity and are prone to cause immune or allergic reactions in the body, especially heterologous antibodies.

• High Reversibility

The binding of nucleic acid aptamers to target molecules is achieved through non-covalent interaction forces, so they have high reversibility and can dissociate or rebind according to changes in environmental conditions. This feature enables nucleic acid aptamers to be used in reusable detection systems or controllable drug release systems.

Disadvantages of Nucleic Acid Aptamers

• Lack of Binding Site Research

The binding site of nucleic acid aptamers and target molecules is a key factor in determining their affinity and specificity, but there is still a lack of research on the binding site of nucleic acid aptamers. The main reason is the lack of effective methods and technologies for structural analysis and functional verification. Therefore, the study of the binding site of nucleic acid aptamers is an important direction to improve their performance and application value.

• Patent Restriction Issues

As a new type of molecular probe, the screening technology and application fields of nucleic acid aptamers are protected and restricted by several patents, which has created certain obstacles to the development and innovation of this field.

• Serum Clearance Problem

As a chemically synthesized oligonucleotide, aptamers are degraded by various nucleic acid degrading enzymes (such as endonucleases, exonucleases, etc.) in the serum after entering the blood circulation, thereby reducing their stability and activity. In addition, aptamers are also rapidly cleared by the liver and kidneys, thereby reducing their circulation life and bioavailability. Therefore, it is necessary to chemically modify aptamers or combine them with carriers to improve their anti-serum clearance ability and circulation life.

In general, the main problems faced by aptamer drugs are poor serum stability, difficulty in cell entry, rapid excretion through the kidneys, unstable structure, poor repeatability, etc. In order to solve these problems, it is necessary to improve and innovate the SELEX technology, as well as conduct more in-depth research on the structure and function of aptamers.