Stable Stem-Loop and Cruciform DNA Structures: Isolation of Mutants with Rearrangements of the Palindromic Sequence at the Simian Virus 40 Replication Origin

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Abstract
With the objective of generating DNA molecules that form stable stem-loop structures or cruciform structures in solution, we have altered the palindromic sequence at the Simian Virus 40 (SV40) replication origin. These alterations include: (i) deletion of 18 of the 27 base pairs (bp) in the 13-bp inverted repeat; (ii) deletion of 26 of the bp; (iii) substitution of the entire 27 bp with a totally different 26-bp sequence containing a 13-bp inverted repeat; and (iv) substitution of the 27 bp with an 8-bp sequence containing a 4-bp inverted repeat. The DNA from these mutants was purified. Mutant DNAs were hybridized to wild-type SV40 DNA or to each other, and the heteroduplexes were purified. The predicted structures were verified by S1 and restriction endonuclease digestion. The mutants.sbd.the heteroduplexes have not been tested.sbd.are capable of complementing tsA mutants and/or transforming mouse cells.