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Sugar cubes

Can Aptamers Bind to Sugar Molecules?

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Our answer to this poll will be short and sweet:

Sugars are molecules that have a generic formula of CnH2nOn. They can be described as polyhydroxy compounds containing one ether bond. Most sugars are optically active, and this comes from the presence of asymmetrically substituted carbons in the sugar. In an aqueous environment the rings can take two forms. During the formation of the ring if the hydroxy group is trapped above the ring it will be the Beta form, if it is trapped below the ring it will be alpha. The two forms will slowly interconvert until equilibrium is established.

We have tried to identify aptamers for monosaccharides and disaccharides but have not been able to identify aptamers that bind well to sugar molecules. This could be because of the abundance of negative charges on sugars (hydroxyl groups) and because sugars are in constant flux between shapes, both in and out of the chair form, and the hydroxyls spinning such that the distance between them is not constant.

For aptamer selection to be effective, there needs to be a fixed distance between charges. If the charges are changing in space, then all aptamer sequences are equally good at binding to them. If charges are fixed because of double bonds in the target molecule, or even better, double bonds in a ring, then the charges are not rotating and the distance between them is fixed. The more defined the solution space is physically for a target the more successful the aptamer selection will be.