BackgroundMembranous tunneling tubes (TTs) are a recently discovered new form of communication between remote cells allowing their electrical synchronization, migration, and transfer of cellular materials. TTs have been identified in the brain and share similarities with neuronal processes. TTs can be open-ended, close-ended or contain functional gap junctions at the membrane interface. Gap junctions are formed of two unapposed hemichannels composed of six connexin (Cx) subunits. There are evidences that Cxs also play channel-independent role in cell adhesion, migration, division, differentiation, formation of neuronal networks and tumorigenicity. These properties of Cxs and TTs may synergetically determine the cellular and intercellular processes. Therefore, we examined the impact of Cxs expressed in the nervous system (Cx36, Cx40, Cx43, Cx45, and Cx47) on: 1) cell mobility; 2) formation and properties of TTs; and 3) transfer of siRNA between remote cells through TTs.ResultsWe have identified two types of TTs between HeLa cells: F-actin rich only and containing F-actin and α-tubulin. The morphology of TTs was not influenced by expression of examined connexins; however, Cx36-EGFP-expressing cells formed more TTs while cells expressing Cx43-EGFP, Cx45, and Cx47 formed fewer TTs between each other compared with wt and Cx40-CFP-expressing cells. Also, Cx36-EGFP and Cx40-CFP-expressing HeLa cells were more mobile compared with wt and other Cxs-expressing cells. TTs containing Cx40-CFP, Cx43-EGFP, or Cx47 gap junctions were capable of transmitting double-stranded small interfering RNA; however, Cx36-EGFP and Cx45 were not permeable to it. In addition, we show that Cx43-EGFP-expressing HeLa cells and laryngeal squamous cell carcinoma cells can couple to the mesenchymal stem cells through TTs.ConclusionsDifferent Cxs may modulate the mobility of cells and formation of TTs in an opposite manner; siRNA transfer through the GJ-containing TTs is Cx isoform-dependent.Electronic supplementary materialThe online version of this article (doi:10.1186/s12860-016-0080-1) contains supplementary material, which is available to authorized users.