Restriction enzymes

One of the first restriction enzymes, dubbed EcoR1, was discovered in E. coli and found to cut only within the nucleotide sequence GAATTC (or its mirror image CTTAAG), and specifically between the G and A. The enzyme cuts both DNA strands of the double helix creating small single-stranded fragments at the cut sites that stick out:

Double-stranded DNA before cutting:

XXXXXXXGAATTCXXXXXXX

XXXXXXXCTTAAGXXXXXXX

Double-stranded DNA after cutting with EcoR1:

XXXXXXXG     AATTCXXXXXXX

XXXXXXXCTTAA GXXXXXXX

Note that the Xs in this example can be A, T, C, or G, corresponding to the basic alphabet of the genetic code. The dangling TTAA and AATT ends are termed sticky ends because they can come back together, as in the top illustration, by complimentary base pairing (A with T and C with G) and, thus, create an intact DNA molecule. These dangling ends can also facilitate the joining of two distinct DNA molecules that have been cut with the same restriction enzyme.¹