DNA bending by charged peptides: electrophoretic and spectroscopic analyses.
We are testing the idea that placement of fixed charges near one face of the DNA double helix can induce DNA bending by a purely electrostatic mechanism. If stretching forces between DNA phosphates are significant, fixed charges should induce DNA bending by asymmetrically modulating these forces. We have previously tested this hypothesis by adding charged residues to small bZIP DNA binding peptides and monitoring DNA bending using electrophoretic phasing assays. Our results were consistent with an electrostatic model of DNA bending in predicted directions. We now confirm these observations with fluorescence resonance energy transfer (FRET). Using a "U"-shaped DNA probe, we report that DNA bending by charged bZIP peptides is readily detected by FRET. We further show that charged bZIP peptides cause DNA bending rather than DNA twisting.
McDonald
Robert J
RJ
Medical Scientist Training Program, Mayo Clinic College of Medicine, Rochester, Minnesota 55905, USA.
Dragan
Anatoly I
AI
Kirk
William R
WR
Neff
Kevin L
KL
Privalov
Peter L
PL
Maher
L James
LJ
D000595:Amino Acid Sequence; D001483:Base Sequence; D050976:Basic-Leucine Zipper Transcription Factors / Q000737:chemistry / Q000378:metabolism; D002942:Circular Dichroism; D004247:DNA / Q000737:chemistry* / Q000378:metabolism; D004268:DNA-Binding Proteins / Q000737:chemistry; D004591:Electrophoresis, Polyacrylamide Gel / Q000379:methods*; D031541:Fluorescence Resonance Energy Transfer; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D029701:Saccharomyces cerevisiae Proteins / Q000737:chemistry; D013056:Spectrophotometry, Ultraviolet / Q000379:methods*; D014157:Transcription Factors / Q000737:chemistry
D050976:Basic-Leucine Zipper Transcription Factors; D004268:DNA-Binding Proteins; C501391:GCN4 protein, S cerevisiae; D029701:Saccharomyces cerevisiae Proteins; D014157:Transcription Factors; D004247:DNA