Fluorescence labelling of nucleic acids is being used for a wide range of biological applications. The performance of these techniques is dependent on fluorochrome labels with a high sensitivity and high resistance to photobleaching. Indo-cyanine dyes such as Cy3, Cy5 or Cy7 have been found to fulfil these requirements. This study describes several different RNA labelling techniques allowing for a Cy5 based detection of mRNA transcripts.