title: Flanking AT-rich sequences may lower the activation energy of cruciform extrusion in supercoiled DNA.
abstract: In the absence of flanking AT-rich segments, cruciform transition energies of DNA palindromic sequences of random base composition are high and mainly dependent upon the base-stacking and -pairing parameters of the palindromic segment. When AT-rich sequences adjoin palindromes, the transition energy of cruciform extrusion is significantly lowered. An inverse relationship exists between the length of the AT-rich stretch and the cruciform transition energy. Long stretches lower the transition energies more than short stretches. At physiological salt and temperature conditions, equilibrium between cruciform extrusion and absorption for the inverted repeat sequences IRS-B and IRS-C of pBR322 derived plasmids is reached in less than five minutes.
authors.affiliation: Institute of Human Genetics, University of Minnesota, Minneapolis/St. Paul, 55108.
authors.forename: Y
authors.initials: Y
authors.lastname: Wang
authors.forename: W
authors.initials: W
authors.lastname: Sauerbier
mesh_terms: D001483:Base Sequence; D004252:DNA Mutational Analysis; D004278:DNA, Superhelical / Q000648:ultrastructure*; D004720:Endonucleases / Q000378:metabolism; D009690:Nucleic Acid Conformation; D010957:Plasmids; D015719:Single-Strand Specific DNA and RNA Endonucleases; D013329:Structure-Activity Relationship; D013696:Temperature; D013997:Time Factors
chemical_list: D004278:DNA, Superhelical; D004720:Endonucleases; D015719:Single-Strand Specific DNA and RNA Endonucleases