Case Study #1: Arginineamide-DNA Aptamer
The 33-mer oligodeoxynucleotide has a high affinity (Kd = 0.76 nM) for the amide of L-arginine.
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surface model arginineamide-aptamer complex.
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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.