Provided herein are methods, compositions and kits for detecting a target nucleic acid. A target nucleic acid can be produced, for example, by a cleavage reaction in an assay for detection of biological samples. In one aspect, a described method comprises the following steps: hybridizing the target nucleic acid having a 5′ end and a 3′ end to a probe to form a circular hybridization complex; forming a covalent circular target nucleic acid using the probe as a template for nucleic acid synthesis; and detecting the covalent circular target nucleic acid.