Methods are provided for post incorporation labeling of a nucleic acid, including for example cRNA, labeled with nucleotide analogs having a formula selected from the group consisting of wherein A is H or a functional group that permits the attachment of the nucleic acid labeling compound to a nucleic acid; Y and Z are independently H or OH; L is linker group; and P is a connecting group. After incorporation of the nucleic acid (including cRNA) with the above nucleotide analogs, the nucleic acid is labeled with a detectable group reagent wherein said detetable group reagent comprises a chemical moiety which is capable of specifically reacting with said P group to allow coupling of the detectable group to said primed cRNA. Compounds comprising nucleotide analogs are also presented in accordance with the present invention. Methods are also presented for incorporating these compounds into nucleic acids and subsequently labeling the incorporated nucleotide analog with detectable moiety reagent.