The current disclosure provides a method that can specifically label and directly amplify 5hmC site on genomic DNA without pull-down or bisulfite treatment, which enables one to map the 5hmC site from a single DNA molecule. Aspects of the disclosure relate to a method for detecting 5-hydroxymethylcytosine (5hmC) nucleic acid bases in a nucleic acid molecule or a plurality of nucleic acid molecules, the method comprising: a. modifying the 5hmC nucleic acid base with a first functional group; b. covalently attaching a modified nucleic acid probe comprising a second functional group to the first functional group; wherein the nucleic acid probe and nucleic acid molecule are covalently linked through the first and second functional groups; c. annealing a primer to the nucleic acid probe; d. performing primer extension of the annealed primer to make a new strand; and e. detecting the new strand.