Nucleic Acids Research, 1980, Vol. 8, No. 22 5519-5532
© 1980
MOLECULAR BIOLOGY |
Counterion dependent variation of DNA secondary structure in (A•T) clusters: evidence by use of netropsin as a structural probe
aDepartment of Biophysical Chemistry, Academy of Sciences of the GDR, Central Institute of Microbiology and Experimental Therapy DDR-69 Jena, Beutenbergstr. II, GDR bDepartment of Chemistry of Antibiotics, Academy of Sciences of the GDR, Central Institute of Microbiology and Experimental Therapy DDR-69 Jena, Beutenbergstr. II, GDR cDepartment of Molecular Biochemistry, Academy of Sciences of the GDR, Central Institute of Microbiology and Experimental Therapy DDR-69 Jena, Beutenbergstr. II, GDR
To whom correspondence should be addressed
Received July 24, 1980. The interaction of the oligopeptide antibiotic netropsin(Nt) with (A•T) regions of DNA is characterized by a spectrum of discrete modes. This has been revealed by viscometric analysis, at 20°C and 0.2 M ‘counterions’, for NaDNA in a preceding and for NE4DNA in this paper. The increase of DNA contour length as induced by one Nt molecule was found to depend on the special mode only, while the respective stiffening is generally higher for NH4DNA. The latter property is interpreted in terms of an enhanced flexibility, relative to that of NaDNA, of the (A•T) cluster segments before complex formation.
For some of the interaction modes of the DNA-Nt systems a difference in the number of corresponding binding sites has been observed. This phenomenon is understood by assuming an influence of the counterion species upon existing equilibria between different forms of the (A•T) cluster secondary structure. Not less than 5 to 10% of the total DNA are effected in this manner. Upper limits for the local differences in the axial rise per base pair are 0.04nm and 0.02nm.