Figure 1. A Basic, Directional Cloning Experiment. (A) The experimental insert is designed to include restriction sites found in the (multiple cloning site) MCS of the vector, in this case for the enzymes HindIII and KpnI (red). Additional nonspecific base pairs (4-6) outside of the restriction enzyme recognition sites are included to provide for efficient restriction enzyme binding [1]. The blue lines indicate the cut sites. (B) HindIII and KpnI restriction digestion of both vector and insert produce complementary overhangs allowing the DNA insert to base pair with the linear plasmid. Hydrogen bonds stabilize this binding, making this method highly efficient. A subsequent ligation reaction covalently links the insert to plasmid.