Abstract: The present disclosure provides compositions and methods for labeling a single stranded target nucleic acid. Subject compositions include a Cas9 protein, a Cas9 guide RNA, and a quenched PAMmer. A subject quenched PAMmer is a single stranded oligonucleotide having (i) a protospacer adjacent motif (PAM) sequence; (ii) a detectable label; (iii) a quencher moiety that quenches the detectable label; and (iv) at least one of: a specificity segment positioned 5? of the PAM sequence, and an orientation segment positioned 3? of the PAM sequence. In the subject methods, the Cas9 protein cleaves the quenched PAMmer at a cleavage site positioned between the detectable label and the quencher moiety to produce: (a) a first cleavage product that is hybridized with the target nucleic acid and comprises the detectable label; and (b) a second cleavage product that is not hybridized with the target nucleic acid and comprises the quencher moiety.

Abstract: The present disclosure provides compositions and methods for labeling a single stranded target nucleic acid. Subject compositions include a Cas9 protein, a Cas9 guide RNA, and a quenched PAMmer. A subject quenched PAMmer is a single stranded oligonucleotide having (i) a protospacer adjacent motif (PAM) sequence; (ii) a detectable label; (iii) a quencher moiety that quenches the detectable label; and (iv) at least one of: a specificity segment positioned 5 of the PAM sequence, and an orientation segment positioned 3 of the PAM sequence. In the subject methods, the Cas9 protein cleaves the quenched PAMmer at a cleavage site positioned between the detectable label and the quencher moiety to produce: (a) a first cleavage product that is hybridized with the target nucleic acid and comprises the detectable label; and (b) a second cleavage product that is not hybridized with the target nucleic acid and comprises the quencher moiety.