Question

1. After isolating and culturing breast cancer cells from a patient sample, you were able to identify a transmembrane protein that was highly upregulated and unique to the cancer cells. Your PI wants you to produce aptamers that will bind to this transmembrane protein so that you can later conjugate the aptamer with a drug.
   1. You have to look back at your BENG168 notes on how to create and select for aptamers. Sketch a simple schematic of the SELEX process.
   2. Your labmate asks why you are using aptamers instead of antibodies. You answer her by creating a table for the comparison between aptamers and antibodies. In your table, include differences in size, manufacturing, immunogenicity, targets, degradation, and stability.

Answer 1

In the given question, breast cancer cells are isolated and cultured. It was then observed that the transmembrane protein was highly upregulated which caused the cells to become cancerous. Our aim is to produce aptamers which will bind to this transmembrane protein.

a. Aptamers are synthetically produced nucleic acids. They are single stranded DNA or single stranded RNA, and their function is to selectively bind to a particular target. This target can be anything. They can be carbohydrates, proteins and even lipids. The unique property of the aptamers to get in any shape makes it easy for them to undergo the binding process. The versatility of aptamers is a great invention in the field of technology.

Aptamers undergo a process called SELEX( Sequential Evolution of Ligands by Exponential Enrichment). In this process only the aptamers which bind strongly are selected over the ones that bind weakly.

A simple schematic diagram of the SELEX process is drawn below.

b. Aptamers are used in the experiment. Aptamers and Antibodies are both used widely in experiments, hence there should a comparision and contrast made between both.

Aptamers	Antibodies
Aptamers are produced synthetically. They are produced by SELEX process.	Antibodies are found naturally. They are formed by the B cells.
Aptamers are smaller in size.	Antibodies are bigger in size.
Aptamers have a higher affinity than antibodies.	Antibodies have a lower affinity than aptamers.
Aptamers have low immunogenicity.	Antibodies have high immunogenicity.
Degraded by Nuclease degradation.	Degraded by Intracellular antibody mediated degradation(IAMD)
Higher stability	Lower stability.

oligonucleotide pool US targel-neotee hlienung SELEX puolus wwhustuste Humovala Дbg next round of selection now Вашла Haugen realitulis amplification presentation or puuval цма evruched pool