Abstract: Provided herein are methods for the combined amplification and detection of one or a plurality of target nucleic acid molecules. The methods encompass the use of an antisense strand of a catalytic nucleic acid in a primer for amplification such that an amplicon produced thereby includes an active catalytic nucleic acid capable of indicating the presence of the target sequences through the modification of a reporter substrate. Devices and kits are also provided. DNA molecules for practicing the methods are also provided. The DNA molecules comprise at least a first portion complementary to at least a first portion of a target nucleic acid sequence, a second portion complementary to an antisense sequence of a second portion of the target nucleic acid sequence, and a third portion comprising an antisense sequence of a catalytic nucleic acid; the third portion positioned between the first and second portions of said DNA molecule.

Abstract: There is described a method for detecting alkylated cytosine in double stranded DNA employing one or more enzymes that differentially modify alkylated cytosine and cytosine. At least one region of the DNA is converted to single stranded DNA and the enzyme is reacted with a target region in the single stranded DNA. The presence or level of alkylated cytosine in the target region is detected by determining the level of enzymatic modification of the target region by the enzyme.