This Article Full Text (PDF) Alert me when this article is cited Alert me if a correction is posted Services Similar articles in this journal Similar articles in PubMed Alert me to new issues of the journal Download to citation manager Reprints and Permissions Copyright Information Books from ASM Press MicrobeWorld Citing Articles Citing Articles via Google Scholar Google Scholar Articles by Woodworth-Gutai, M Articles by Lebowitz, J Search for Related Content PubMed PubMed Citation Articles by Woodworth-Gutai, M Articles by Lebowitz, J

Introduction of interrupted secondary structure in supercoiled DNA as a function of superhelix density: consideration of hairpin structures in superhelical DNA.

ABSTRACT

PM2 DNA was prepared with different superhelical densities (sigma) in order to examine the relationship betweenn supercoiling and the occurrence of a region(s) of unpaired bases in this DNA. A previous study showed that CH3HgOH reacts with native superhelical PM2 DNA more rapidly than the nicked form II. This evaluation of binding, monitored through the change of sedimentation velocity, was repeated on PM2 DNA I with different superhelical densities. Early binding is detected by an increase in sedimentation velocity and occurs with molecules with sigma' values betwee -0.025 and -0.037. The conversion of form I to form II with the single-strand-specific endonuclease from Neurospora crassa also occurs above a sigma value of -0.025. This data strongly supports the view that supercoiling produces interrupted secondary structure. The question whether the interrupted regions remain single stranded in character or form small intrastrand hairpin regions is considered by examining which model best fits the CH3HgOH- induced sedimentation velocity changes and the standard sedimentation velocity versus the superhelical density curve for the in vitro made DNAs. The hairpin model offers the most satisfactory explanations for all the results of this and previous studies.