Case Study #1: Arginineamide-DNA Aptamer

The 33-mer oligodeoxynucleotide has a high affinity (K_d = 0.76 nM) for the amide of L-arginine.

Compare structures of arginine and arginineamide.

Toggle surface model arginineamide-aptamer complex.

Toggle between backbone trace and base stacking.

Sixty-three atoms of the DNA are in van der Waals contact with the ligand. Charge-charge interactions between the guanidino group of argininamide and two phosphate groups are obviously important; there are also cation-pi interactions involving thymine and the two positive charges on argininamide.

Toggle stoichiometric animation.

Case Study #1

Two phosphate groups are hydrogen-bonded to the guanidino group. Toggle ball-and-stick.

The charge-charge interactions undoubtedly make a significant contribution to the binding energy. The hydrogen bonds are important because they allow a closer approach between the unlike charges than would otherwise be possible.

Case Study #1

Both the α-amino and guanidino groups of argininamide interact with thymine. Toggle spacefill. Note that one of the keto groups of thymine forms a hydrogen bond with the guanidino group.

Finally, the amide group of argininamide is hydrogen bonded to a phosphate group.

As we have seen before, the NMR provides multiple sets of atom coordinates. This allows us to animate between models to give an impression of the dynamic interactions.

Case Study #2: L-arginine-RNA Aptamer

Surface model of arginine·RNA aptamer. Several research groups have used SELEX to isolate a series of RNA molecules which bind L-arginine tightly and with high specificity. None of the aptamers share primary sequence relationships to each other. This demonstrates that the tight and specific molecular recognition of arginine can be achieved by many different RNA sequences. The RNA aptamer showing the highest selectivity for L-arginine is displayed below. The binding energies for L- and D-arginine binding differ by 30 kJ/mol, corresponding to a 12,000-fold difference in the K_d values.

Toggle base stacking.

Case Study #2

Three bases interact strongly with the positively charged guanidino group of arginine via cation-pi interactions.

The α-amino group is hydrogen-bonded to the ring oxygen atom (O4′) of ribose (location of the amino hydrogens could not be resolved by the NMR).

In all, 10 atoms of the RNA are in van der Waals contact with the ligand.

Case Study #3: AMP·RNA Aptamer

This 36-mer oligoribonucleotide was selected from 10¹⁴ random sequences.

Base stacking in the host molecule.

The adenine base of the guest molecule is sandwiched between several bases of the host.

Thirty-four atoms of the host are within van der Waals distance of the guest. There are only two hydrogen bonds between the host and guest. Aside from the two hydrogen bonds, van der Waals interactions and the hydrophobic effect of base stacking account for the stability of the complex.

Summary

Write a brief essay on the structure of aptamers, based on what you have learned from this tutorial.