Abstract: The disclosure provides methods and kits involving site-specific endonuclease guided rolling circle amplification (RCA). Nucleic acid substrates, optionally generated by hybridizing a guidance primer to a single stranded nucleic acid, are cleaved with a site-specific endonuclease. In the presence of the target site, endonuclease cleavage of the substrate generates a nucleic acid having a free 3?-hydroxyl end, which is allowed to hybridize to covalently closed circular DNA probe (“take-off probe”), and initiate a rolling circle amplification (RCA) reaction. The methods and kits may be used to detect the presence of a target nucleic acid sequence, including detection of single nucleotide polymorphisms, and may be used to assess methylation status of a desired sequence, assess zygosity and/or ploidy status. The methods and kits may also be used to detect nucleic acids associated or indicative of medical conditions or pathogenic organisms.