The present invention provides compositions comprising oligonucleotides that have 3' end groups (e.g. lipophilic moieties) that are useful in invasive cleavage reactions such as the INVADER assay. Specifically, the present invention provides compositions containing oligonucleotides with 3' end groups configured for generating a detectable signal in invasive cleavages assays with a high signal-to-background ratio, as well as methods for generating such compositions.