The invention is to supply a novel way for the isolation and identification of proteins bound to any kind of interesting nucleic acid sequence (Sequence-of-Interest: SoI), advantageously to any kind of interesting DNA sequence, particularly in the context of chromosomal DNA or RNA or episomal DNA in living cells or in test tubes.In the context of the present invention, living cells include any organism that contains nucleic acid material as for example viruses, bacteria, cells, the bound protein of which have to be analyzed.The invention is based upon the use of a specific nucleic acid sequence tag, advantageously a specific double-stranded DNA able to form triplex helix, referred to as the Triplex-Forming Tag sequence, (TFT sequence), that will be located nearby the SoI.