Inverted repetitious sequences in the macronuclear DNA of hypotrichous ciliates

The low-molecular-weight macronuclear DNA of the hypotrichous ciliates Oxytricha, Euplotes, and Paraurostyla contains inverted repetitious sequences. Up to 89% of the denatured macronuclear DNA molecules form single-stranded circles due to intramolecular renaturation of complementary sequences at or near the ends of the same polynucleotide chain. Other ciliated protozoans, such as Tetrahymena, with high-molecular-weight macronuclear DNA and an alternative mode of macronuclear development, appear to lack these selfcomplementary sequences. The denatured macronuclear molecules of hypotrichs are held in the circular conformation by a hydrogen-bonded duplex region, which is probably less than 50 base pairs in length, since the duplex regions are not visible by electron microscopy and since the circles in 0.12 M phosphate buffer are not retained during hydroxylapatite chromatography at 60 degrees. The existence of extremely small circles, with contour lengths shorter than the smallest pieces of native DNA, suggests that inverted repetitions containing nicks (broken phosphodiester bonds in duplex DNA) or gaps (interruptions with missing nucleotides) are present at internal positions as well as at the ends of native molecules. Estimates from length measurements of native and denatured Oxytricha macronuclear DNA indicate an average of 1.7 nicks per duplex molecule. Thus, in order to account for the high frequency of circle formation, a restriction-type enzyme(s) must exist which inserts single-strand, site-specific nicks or gaps at internal positions in the macronuclear DNA of Oxytricha.