In this paper we describe a label-free biosensor for coralyne, prepared by combining DNA-stabilized silver nanoclusters (Ag NCs) with an exonuclease III amplification strategy. An artificial DNA probe having a polyadenine (poly-A) sequence at both the 3′- and 5′-ends was used as a probe to detect coralyne. In the absence of coralyne, the probe existed in a hairpin conformation that left both its 3′- and 5′-ends free. In the presence of coralyne, two adjacent adenine (A) bases in the poly-A sequence of the probe formed an A 2 unit and then coordinated with coralyne through non-Watson–Crick base pairing. The DNA probe, having captured coralyne, was subsequently digested by exonuclease III, even though the distance between the A 2 units in the A 2 –coralyne–A 2 complex would be much larger than that found in common Watson–Crick base pairing. After digestion, the DNA probe became a single-stranded DNA (ssDNA) residue and released its captured coralyne. The liberated coralyne was then coordinated by another DNA probe having the hairpin conformation; as a result, many ssDNA residues formed after digestion. Two kinds of Ag NCs having different optical utilities were obtained: one corresponding to the hairpin conformational DNA probe and the other to the ssDNA residue. The difference in fluorescence intensity at 588 nm of these two kinds of Ag NCs reflected the concentration of coralyne. The linear range (on a logarithmic scale) for detecting coralyne spanned from 5 to 1000 nM, with an estimated detection limit of 1.83 nM.