Fig. 3.

Polyacrylamide gel electrophoresis analysis of reaction products of activated d(pCGTA) in the presence of varying amounts of ethidium. Ethidium concentrations are given above Lanes 1–5. With no intercalator present (Lane marked 0 μM), only small amounts of cyclic octanucleotide (C8) and cyclic dodecanucleotide (C12) are produced, and almost no linear octanucleotide (L8) or linear dodecanucleotide (L12) is produced. The presence of ethidium in the reaction dramatically promotes linear polymerization, to ca. 100mer products (Lanes marked 100 to 600 μM). The tetranucleotide starting material and cyclic tetranucleotide products observed in HPLC analyses did not stain efficiently; band intensities for ≥8 mers are ca. linear with total nucleic acid (Fig. S5). Additional reaction details are provided in Materials and Methods. The gel Lane marked M contains marker bands generated by the enzymatic ligation of a tiling decanucleotide.