Changes in DNA bending and flexing due to tethered cations detected by fluorescence resonance energy transfer

• Published in: Nucleic acids research 2006-01, Vol.34 (3), p.1028-1035
• Main Authors: Williams, Sarah L., Parkhurst, Laura K., Parkhurst, Lawrence J.
• Format: Article
• Language: English
• Subjects: Anisotropy; Base Sequence; Cations - chemistry; Cations - metabolism; DNA - chemistry; DNA - genetics; DNA - metabolism; Fluorescence; Fluorescence Resonance Energy Transfer; Nucleic Acid Conformation; Pliability; Uracil - analogs & derivatives; Uracil - chemistry
• ISSN: 0305-1048; 1362-4962
• DOI: 10.1093/nar/gkj498

Local DNA deformation arises from an interplay among sequence-related base stacking, intrastrand phosphate repulsion, and counterion and water distribution, which is further complicated by the approach and binding of a protein. The role of electrostatics in this complex chemistry was investigated using tethered cationic groups that mimic proximate side chains. A DNA duplex was modified with one or two centrally located deoxyuracils substituted at the 5-position with either a flexible 3-aminopropyl group or a rigid 3-aminopropyn-1-yl group. End-to-end helical distances and duplex flexibility were obtained from measurements of the time-resolved Förster resonance energy transfer between 5′- and 3′-linked dye pairs. A novel analysis utilized the first and second moments of the G(t) function, which encompasses only the energy transfer process. Duplex flexibility is altered by the presence of even a single positive charge. In contrast, the mean 5′–3′ distance is significantly altered by the introduction of two adjacently tethered cations into the double helix but not by a single cation: two adjacent aminopropyl groups decrease the 5′–3′ distance while neighboring aminopropynyl groups lengthen the helix.