Aptamers

Question 1

What are aptamers?

Answer 1

They are RNA or DNA oligonucleotides that bind to varying targets (can be protein, DNA, RNA, peptides, cells, etc.) similar to antibodies because they can recognize targets with high affinity and specificity.

Question 2

What are the differences between aptamers and anitbodies?

Answer 2

Aptamers:
- DNA/RNA
- Light (small)
- Stable
- Synthesised chemically
- Easily modified
- Poor immunogens
- High affinity with desirable Kd.

Antibodies:
- Proteins
- Bulky
- Unstable
- Impossible to synthesise
- Need animals to modify
- Immunogenic
- High affinity with defined Kd.

Question 3

What does SELEX stand for?

Answer 3

Systematic Evolution of Ligands by Exponential Enrichment

Question 4

What are the steps in the SELEX process?

Answer 4

1. SsDNA library is synthesised with a random in the middle with a constant seuqence on either side.
2. SsRNA library is made from the ssDNA library.
3. RNA library is incubated with a target that is bound to the surface.
4. The ligand-target remain binded to the surface of the assay and the free ligands are washed out.
5. Bound ligands are desorbed and collected
6. Bound ligands are amplified using PCR
7. Cloning and sequencing of the aptamer.

Question 5

What are some areas that can go wrong in the SELEX process?

Answer 5

• There can be non-specific binding of a ligand to the surface that will end up being amplified and contaminate the true ligands.
• PCR is always error prone too, simply just not working.

Question 6

What are spiegelmers?

Answer 6

D-confirmation is an aptamer and a spiegelmer is a mirror image L-configuration.