title: Direct comparison of A- and T-strand minor groove interactions in DNA curvature at A tracts.
abstract: To investigate the relative contributions of minor-groove electrostatic interactions in the mechanism of A-tract DNA curvature, we carried out experiments with modified DNA bases in both strands of the tract. We employed 3-deazaadenine nucleoside (D), which lacks the adenine N3 nitrogen in the minor groove and thus cannot act as an electron donor, as well as difluorotoluene (F), a nonpolar thymine mimic. The effects of these analogues in A-tract curvature were quantified using ligation ladder gel mobility methods developed by Crothers and by Maher. Through single substitutions of D in A(5) tracts, we found that this analogue results in decreased curvature only when situated toward the 3' end of the tract. This is distinct from the behavior in the T-rich strand where F substitution causes the greatest reductions in curvature toward the 5' end. To test for cooperative pairwise effects, we also studied 10 different D + F double substitutions and found evidence supporting a number of localized cooperative electrostatic interactions but not between the two most sensitive sites in the opposite strands. These results suggest that there are two discrete locations in the A-tract minor groove where electrostatic interactions are important in causing curvature: one near the 5' end of the T-rich strand, and one near the 3' end of the A-rich strand. The results are consistent with an important role of localized cations in the minor groove. Possible effects of groove solvation and stacking at the A-tract junction are also discussed.
authors.affiliation: Department of Chemistry, Stanford University, Stanford, California 94305-5080, USA.
authors.forename: Angèle S
authors.initials: AS
authors.lastname: Maki
authors.forename: TaeWoo
authors.initials: T
authors.lastname: Kim
authors.forename: Eric T
authors.initials: ET
authors.lastname: Kool
mesh_terms: D000225:Adenine / Q000031:analogs & derivatives* / Q000138:chemical synthesis / Q000737:chemistry*; D001482:Base Composition; D020029:Base Pairing; D001665:Binding Sites; D002412:Cations; D004247:DNA / Q000737:chemistry*; D006860:Hydrogen Bonding; D009690:Nucleic Acid Conformation; D009692:Nucleic Acid Heteroduplexes / Q000138:chemical synthesis; D055672:Static Electricity; D013873:Thionucleotides / Q000138:chemical synthesis; D013941:Thymine / Q000737:chemistry*
chemical_list: D002412:Cations; D009692:Nucleic Acid Heteroduplexes; D013873:Thionucleotides; C055133:3-deazaadenine; D004247:DNA; D000225:Adenine; D013941:Thymine