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How to Tell If an Aptamer Has Found Its Target

Aptamers are relatively short chains of nucleotides created to bind to a specific target. The nucleotides are the same components that make up DNA or RNA molecules, and when they̵7;re put into the right configuration they are highly specific and have high affinity for their targets. The high specificity means the aptamer binds only to the target it̵7;s designed for, and high affinity means the aptamer binds very easily to its target.
But these are just tiny molecules, and you can̵7;t just take a peek and see that they matched up with their targets. Luckily, there are ways to get that aptamer to report back. There are two different general configurations, one in which the aptamer binds its target internally or at only one external binding site, and the other in which the target binds at two sites.

Things You'll Need

Aptamer synthesis equipment
Gold electrodes and nanoparticles
Target molecules in appropriate buffer solutions
Ammeter

Instructions

Single Site Binding
- 1
  Attach a ferrocene complex to one end of the aptamer. Ferrocene is an organometallic compound that has good electron-transfer properties.
- 2
  Build the aptamer with a thiol group to terminate the other end. The thiol group is a sulfur-hydrogen arrangement that has a strong affinity for gold.
- 3
  Construct a gold electrode, and allow the aptamers to attach to the surface.
- 4
  Immerse the electrode in the solution of interest, and monitor the current. When the aptamer binds its target, it will change its configuration and bring its two ends close to each other. This brings the ferrocene close to the gold electrode, which increases the current, so monitoring the current can tell you how many of the aptamers have found their targets.
Double Site Binding
- 5
  
  Color change is one method of verifying aptamer binding.
  
  Immobilize one end of an aptamer to a fixed surface.
- 6
  Introduce the target molecule into the solution surrounding the aptamers on the fixed surface.
- 7
  Construct another aptamer specific to the same target molecule, and attach a gold nanoparticle to the other end.
- 8
  Wash the solution, then introduce a nanoparticle growth solution. The growth solution will deposit additional gold on the nanoparticle seeds and create a visible color change where the target molecule is present. You can just look at the surface and see the difference in color where the aptamer has found its target.

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