Direct Comparison of A- and T-Strand Minor Groove Interactions in DNA Curvature at A Tracts

• Published in: Biochemistry (Easton) Vol. 43; no. 4; pp. 1102 - 1110
• Main Authors: Maki, Angèle S, Kim, TaeWoo, Kool, Eric T
• Format: Journal Article
• Language: English
• Published: United States American Chemical Society 03.02.2004
• Subjects: Adenine - analogs & derivatives; Adenine - chemical synthesis; Adenine - chemistry; Base Composition; Base Pairing; Binding Sites; Cations; DNA - chemistry; Hydrogen Bonding; Nucleic Acid Conformation; Nucleic Acid Heteroduplexes - chemical synthesis; Static Electricity; Thionucleotides - chemical synthesis; Thymine - chemistry
• ISSN: 0006-2960; 1520-4995
• DOI: 10.1021/bi035340m

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 A5 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.