title: Flanking A·T basepairs destabilize the B(∗) conformation of DNA A-tracts.
abstract: Capillary electrophoresis has been used to characterize the interaction of monovalent cations with 26-basepair DNA oligomers containing A-tracts embedded in flanking sequences with different basepair compositions. A 26-basepair random-sequence oligomer was used as the reference; lithium and tetrabutylammonium (TBA(+)) ions were used as the probe ions. The free solution mobilities of the A-tract and random-sequence oligomers were identical in solutions containing <∼ 100 mM cation. At higher cation concentrations, the A-tract oligomers migrated faster than the reference oligomer in TBA(+) and slower than the reference in Li(+). Hence, cations of different sizes can interact very differently with DNA A-tracts. The increased mobilities observed in TBA(+) suggest that the large hydrophobic TBA(+) ions are preferentially excluded from the vicinity of the A-tract minor groove, increasing the effective net charge of the A-tract oligomers and increasing the mobility. By contrast, Li(+) ions decrease the mobility of A-tract oligomers because of the preferential localization of Li(+) ions in the narrow A-tract minor groove. Embedding the A-tracts in AT-rich flanking sequences markedly alters preferential interactions of monovalent cations with the B(∗) conformation. Hence, A-tracts embedded in genomic DNA may or may not interact preferentially with monovalent cations, depending on the relative number of A · T basepairs in the flanking sequences.
authors.affiliation: Department of Biochemistry, University of Iowa, Iowa City, Iowa.
authors.forename: Earle
authors.initials: E
authors.lastname: Stellwagen
authors.affiliation: Department of Internal Medicine, University of Iowa, Iowa City, Iowa.
authors.forename: Qian
authors.initials: Q
authors.lastname: Dong
authors.affiliation: Department of Biochemistry, University of Iowa, Iowa City, Iowa. Electronic address: nancy-stellwagen@uiowa.edu.
authors.forename: Nancy C
authors.initials: NC
authors.lastname: Stellwagen
mesh_terms: D020029:Base Pairing; D044704:DNA, A-Form / Q000737:chemistry*; D059371:DNA, B-Form / Q000737:chemistry*; D008094:Lithium / Q000737:chemistry; D000644:Quaternary Ammonium Compounds / Q000737:chemistry
chemical_list: D044704:DNA, A-Form; D059371:DNA, B-Form; D000644:Quaternary Ammonium Compounds; D008094:Lithium; C009405:tetrabutylammonium