Abstract Imparting molecular recognition to carbon nanotubes (CNTs) by conjugating them with bio-molecules has been an area of great interest as the resulting highly functionalized CNT-bioconjugates find their applications in various fields like molecular level electronics, pharmaceuticals, drug delivery, novel materials and many others. In this work we demonstrate the synthesis of functionally engineered single walled carbon nanotubes (SWNTs)-peptide nucleic acid (PNA) conjugates especially for nanoelectronic applications. Here we exploited the exceptional structural and chemical advantages of PNA (an artificial analogue of DNA) to join SWNTs ropes. SWNT–PNA–SWNT conjugates were synthesized using carbodiimide coupling chemistry and characterized by host of techniques like scanning electron microscopy, atomic force microscopy and Fourier transform infrared spectroscopy. The results from different techniques confirm the formation of these conjugates. Theoretical analysis of molecular orbitals obtained by quantum mechanical simulations show that the highest occupied molecular orbital is located on the glutamate linker and that this interface state will align closely to the valence band of the extended SWNT facilitating charge transfer. The unique electrical and structural properties of these conjugates make them a potential candidate for application in CNT based nanodevices.