Abstract: Assay compositions and methods for detection of analytes that include covalent modification of assay elements, such that they are preserved, destroyed, created, or immobilized. Methods for detecting an analyte in a biological sample. The method includes providing a mixture of a biological sample potentially containing the analyte, and a molecular recognition element physically coupled to a covalent modification agent, wherein the molecular recognition element is capable of specific recognition of the analyte, and exposing the mixture to a first set of reaction conditions, wherein the analyte and molecular recognition element can associate to form a recognition complex. Upon formation of the recognition complex, the method further includes generating by use of the covalent modification agent, a template complex; and exposing the template complex to a second set of reaction conditions, wherein the template complex is amplified to generate a detectable product indicative of the presence of the analyte.