Changes in DNA bending and flexing due to tethered cations detected by fluorescence resonance energy transfer.
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.
Williams
Sarah L
SL
Department of Chemistry, University of Nebraska-Lincoln, Lincoln, NE 68588-0304, USA.
Parkhurst
Laura K
LK
Parkhurst
Lawrence J
LJ
D016880:Anisotropy; D001483:Base Sequence; D002412:Cations / Q000737:chemistry / Q000378:metabolism; D004247:DNA / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism*; D005453:Fluorescence; D031541:Fluorescence Resonance Energy Transfer; D009690:Nucleic Acid Conformation; D018583:Pliability; D014498:Uracil / Q000031:analogs & derivatives / Q000737:chemistry
D002412:Cations; D014498:Uracil; D004247:DNA