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Aptamers : A Novel DNA-RNA Approach in Biotechnological Research

BY: Sandhya Anand | Category: Biotech-Research | Submitted: 2011-03-27 04:59:38
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Article Summary: "Aptamers are oligonucleotide sequences carrying out specific functions. These novel molecules are selected from random pools of such DNA/RNA sequences based on their binding ability and are emerging fast as new method of therapy..."


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Aptamers are oligonucleotide sequences carrying out specific functions. These novel molecules are selected from random pools of such DNA/RNA sequences based on their binding ability. They are RNA or DNA molecules ranging from 30 to 100 nucleotides which can recognize specific ligands. These ligands can be nucleic acids, proteins or small organic compounds. The SELEX process is used for in vitro selection of aptamers from vast populations of random sequences.

The previous methods of antisense technology and siRNA methods carry some limitations like target access, cell uptake and specificity of interaction. The new method of SELEX (systematic evolution of ligands by exponential enrichment) is a promising approach in this field. A variety of combinatorial techniques have since been described.

The process was first developed by Turek and Gold in 1990. The term 'aptamer' was the contribution of two scientists Ellington and Szostak in the same year. There are several advantages for use of aptamers in comparison to antibodies. The shape of the aptamer is based on its sequence.

Uses of Aptamers

The aptamers are also found to have a variety of uses. They include
1. design of therapeutics
2. for cancer research
3. for study of infectious diseases
4. gene therapy
5. developing analytical tools
6. Designing oligonucleotide probes for imaging etc.
7. Study of RNA structure, binding and interaction with ligands.
8. Natural aptamers are found to be the basis of riboswitches.

Some specific examples of aptamer uses include their applications against

1. Coagulation factors - against factor IXa
2. Antibodies involved in autoimmune diseases - nicotinic AChRs (for myasthenia gravis)
3. Antidote control
4. Growth factors or hormones - VEGF (Vascular Endothelial Growth Factor)
5. Inflammation markers - Elastases
6. Neuropathological targets - Synthetic βA amyloid peptide (Alzheimers disease)
7. Membrane biomarkers - CTL-4 (Cytotoxic T-Lymphocyte)
8. Whole organisms - CMV (Cytomegalovirus)

Advantages of aptamers

They are now becoming more popular and are advantageous than the antibodies in several areas.

• Aptamers exhibit high affinity and specificity
• Results are more accurate, stable and reproducible
• They are susceptible to reversible denaturation and hence can be easily modified
• Production of antibodies requires animal hosts. Aptamers does not require immunization and animal hosts.
• Manufacturing and regulatory processes are much simpler and easier.
• Chemical modification can enhance the bioavailability of aptamers. Eg: multivalent aptamers have more half-life.
• Not immunogenic and can penetrate the tissues, hence easier to deliver the drug.
• Species cross reactive aptamers are used to establish safety and function in animal models.
• Found to be efficacious in humans in manipulating the immune system in vivo.

Aptamers are now replacing the protein based drugs and other small molecules used in medicine due to a variety of advantages such as
• Ease of production
• Low risk of inducing an immune reaction
• Can be chemically modified to enhance the drug-characteristics.
• Stable and can be modified to increase their half-life in the human body.
• Present use of aptamers is mainly aimed towards macular degeneration, cancer therapy and coronary artery bypass surgery.

Sensitivity and selectivity are the key requisites for biosensors. Aptamers are best suited for this role as electrochemical aptasensors due to the following attributes.

• They are highly specific and selective in recognizing ligands. They can therefore be precise recognition tools.
• High portability and low-cost of manufacture.
• Mechanism of binding is simple, and aptasensors can be reused.
• Aptamers are short oligonucleotide sequences and due to their nanostructure and size, they can be easily miniaturized. The process of integration, automation etc applied for biosensors is easily adaptable to aptamers and hence the application of aptamers as biosensors is highly advantageous.

Databases

The Aptamer Database provides comprehensive information on aptamers and supports in vitro selection of these molecules. This database collects, organize and distribute the relevant information on aptamers and techniques of their selection.

Classification
Aptamers are broadly classified into different types based on their nucleotide sequence
1. DNA Aptamers
• The first DNA aptamer to be discovered was the aptamer against thrombin, d(GGTTGGTGTGGTTGG) having two stacked G tetramers.
• Aptamer inhibiting the action of integrase enzyme of HIV-1 was also found to the GT rich oligo with the first and last phosphodiester bonds being replaced by phosphorothioate, d(GsTGGTGGGTGGGTGGGsT).
• Aptamers against argininamide is a hairpin loop which changes its structure upon binding and the loop traps the aminoacid.
2. RNA aptamers
• flavin mononucleotide (FMN)-binding aptamer
• Another nucleotide-binding aptamer recognizes adenosine 50-monophosphate (AMP). This contains tetraloops of consensus sequence GNRA (where N is any nucleotide and R is a purine).
• Aptamers that bind the HIV-1 regulatory protein, Rev induces non Watson-Crick base pairs.
• Aptamers against reverse transcriptase of HIV- 1 exhibit a compact pseudoknot structure. Similar structures are also found in biotin binding aptamers.

The field of aptamer research is opening up new frontiers of biological research, technological development and development of drugs.

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