A NOVEL HELICAL STRUCTURE IN KINETOPLAST DNA
Abstract (summary)
We have investigated the unusual structure of a restriction fragment of kinetoplast DNA, the mitochondrial DNA of trypanosomes. A gel purified fragment comprising slightly more than half of a Leishmania tarentolae minicircle has been determined by Maxam-Gilbert sequencing to be 490 bp in length. This fragment has anomalous physical behavior: its migration on polyacrylamide gels is retarded, it appears smaller than its actual size in gel filtration. In electric dichroism studies, the kinetoplast fragment gave a rotational correlation time faster than a 309 bp restriction fragment from pBR322.
Various possible causes of anomalous behavior have been experimentally ruled out. Velocity sedimentation in sucrose gradients ruled out aggregation of the fragment. Unusual secondary structure, such as a cruciform, was not detectable by S1 or mung bean nuclease digestion or by EM. Neither phenol extraction nor extensive proteinase K digestion normalized the anomalous electrophoretic behavior, demonstrating that protein was not involved. Likewise, in vivo modification was not found to play a significant role; the anomaly persisted after the fragment was cloned and grown in both E. coli HB101 and a non-methylating mutant; the anomaly persisted after fragment denaturation and renaturation. Examination of fragment helical structure by circular dichroism yielded spectra characteristic of B-type helix; there is no evidence for hybrid B-A helix or transition to Z-helix at high salt.
We propose that this molecule consists of B-DNA in a smoothly bent configuration. This model accounts for the disparity between fragment size and behavior. Bending of the molecule may be caused by periodicities in the DNA sequence which are equal to the periodicity of the B-helix.