title: Conformational junctions between left-handed DNA in (dA-dT)16 and contiguous B-DNA in a supercoiled plasmid contain chemically reactive bases.
abstract: Alternating adenine-thymine sequences in supercoiled DNA may undergo a transition to the left-handed Z-conformation in the presence of Ni2+ ions and high Na+ concentrations [(1989) FEBS Lett. 243, 313-317]. In this work we have studied the junctions between B- and Z-conformations in a supercoiled plasmid containing a (dA-dT)16 insert, by means of chemical probing. We observed enhanced reactivity of bases at both ends of the alternating tract to chloro- and bromoacetaldehyde. The degree of chemical reactivity was found to increase with the level of negative supercoiling. Only individual bases were observed to be reactive in the B-Z junctions, consistent with tightly localized interfacial regions.
authors.affiliation: Institute of Biophysics, Czechoslovak Academy of Sciences, Brno.
authors.forename: K
authors.initials: K
authors.lastname: Nejedlý
authors.forename: D M
authors.initials: DM
authors.lastname: Lilley
authors.forename: E
authors.initials: E
authors.lastname: Palecek
mesh_terms: D000079:Acetaldehyde / Q000031:analogs & derivatives / Q000737:chemistry; D001483:Base Sequence; D004278:DNA, Superhelical / Q000737:chemistry*; D004047:Diethyl Pyrocarbonate / Q000737:chemistry; D006863:Hydrogen-Ion Concentration; D007202:Indicators and Reagents; D015335:Molecular Probes; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D010957:Plasmids; D011067:Poly dA-dT / Q000737:chemistry*; D015719:Single-Strand Specific DNA and RNA Endonucleases
chemical_list: D004278:DNA, Superhelical; D007202:Indicators and Reagents; D015335:Molecular Probes; C038235:bromoacetaldehyde; D011067:Poly dA-dT; C004656:chloroacetaldehyde; D015719:Single-Strand Specific DNA and RNA Endonucleases; D000079:Acetaldehyde; D004047:Diethyl Pyrocarbonate