DNA curvature in solution measured by fluorescence resonance energy transfer.
The sequence-induced curvature of DNA fragments free in solution was characterized by measurements of the end-to-end distance using fluorescence resonance energy transfer (FRET). The 31 bp oligonucleotides were labeled at their 5' ends with fluorescein as the donor and rhodamine X as the acceptor. We compared a curved oligonucleotide with three phased A6 blocks and a control containing (AT)3 instead of the A6 blocks. The increased efficiency of energy transfer of the A6-containing DNA indicates the existence of a permanent sequence-induced curvature, the magnitude of which is in good agreement with estimates from theoretical curvature predictions. Energy transfer efficiency and correspondingly curvature increases with NaCl concentration.
Tóth
K
K
Division Biophysics of Macromolecules, German Cancer Research Center, Heidelberg.
Sauermann
V
V
Langowski
J
J
D002942:Circular Dichroism; D004270:DNA, Circular / Q000737:chemistry*; D004277:DNA, Single-Stranded / Q000737:chemistry; D004735:Energy Transfer; D005452:Fluoresceins / Q000737:chemistry; D008956:Models, Chemical; D009690:Nucleic Acid Conformation; D009841:Oligonucleotides / Q000737:chemistry; D012235:Rhodamines / Q000737:chemistry; D012965:Sodium Chloride; D012996:Solutions; D013050:Spectrometry, Fluorescence
D004270:DNA, Circular; D004277:DNA, Single-Stranded; D005452:Fluoresceins; D009841:Oligonucleotides; D012235:Rhodamines; D012996:Solutions; D012965:Sodium Chloride