The present invention provides systems and methods for determining the presence or absence of one or more target nucleic acid sequences in a sample. Also provided are kits comprising these systems, and uses of these systems in such applications as determining the presence or absence of at least one target nucleic acid sequence in a sample, detecting microorganism transcripts and host transcripts, differentiating microorganism transcripts from host transcripts, screening blood products, assaying a food product for contamination, assaying a sample for environmental contamination, detecting genetically-modified organisms, biodefense, forensics, and genetic-comparability studies. The present invention further provides a complex that includes a target nucleic acid sequence, a capture nucleic acid, and a reporter nucleic acid.