Published Research - Department of Chemistry


Date of this Version

February 2006


 Copyright The Author 2006. Published by Oxford University Press. All rights reserved. Nucleic Acids Research, 2006, Vol. 34, No. 3. Permission to use.


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 Fö̈rster 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.

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